diff --git a/DESCRIPTION b/DESCRIPTION
index 0dc38a9..6542ceb 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: pepr
 Type: Package
 Title: Reading Portable Encapsulated Projects
-Version: 0.5.0
-Date: 2023-11-16
+Version: 0.6.0
+Date: 2024-08-10
 Authors@R: c(person("Nathan", "Sheffield", email = "nathan@code.databio.org",
     role = c("aut", "cph","cre")),person("Michal","Stolarczyk",email="michal@virginia.edu",role=c("aut")))
 Maintainer: Nathan Sheffield <nathan@code.databio.org>
@@ -18,7 +18,9 @@ Imports:
     pryr,
     data.table,
     methods,
-    RCurl
+    RCurl,
+    tidyr,
+    httr
 Suggests:
     knitr,
     testthat,
@@ -27,5 +29,5 @@ Suggests:
 VignetteBuilder: knitr
 License: BSD_2_clause + file LICENSE
 BugReports: https://github.com/pepkit/pepr
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.2
 Encoding: UTF-8
diff --git a/NAMESPACE b/NAMESPACE
index 4074ce8..729942c 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -18,16 +18,21 @@ export(getSample)
 export(getSubsample)
 export(listAmendments)
 export(makeSectionsAbsolute)
+export(pullProject)
 export(sampleTable)
+export(saveJWT)
+export(saveProject)
 exportClasses(Config)
 exportClasses(Project)
 exportMethods("$")
 exportMethods("[")
 exportMethods("[[")
 import(RCurl)
+import(httr)
 import(pryr)
 import(stringr)
 import(yaml)
 importFrom(methods,as)
 importFrom(methods,callNextMethod)
 importFrom(methods,is)
+importFrom(tidyr,unnest)
diff --git a/R/config.R b/R/config.R
index bc26438..947ee7a 100644
--- a/R/config.R
+++ b/R/config.R
@@ -26,6 +26,11 @@ setMethod("initialize", "Config", function(.Object, data) {
 #' @export
 #' @rdname Config-class
 Config = function(file, amendments = NULL) {
+  ### if the config from the Project constructor is a list and not a filepath, it is from a PEP fetched from PEPhub
+  if (typeof(file) == 'list') {
+    config = methods::new("Config", data = file)
+    return(config)
+  }
   message("Loading config file: ", file)
   cfg_data = .loadConfig(filename = file, amendments = amendments)
   config = methods::new("Config", data = cfg_data)
@@ -58,7 +63,7 @@ setMethod(
 #' .expandList(x)
 #' @export
 #' @keywords internal
-.expandList <- function(x) {
+.expandList = function(x) {
   if (is.list(x))
     return(lapply(x, .expandList))
   if (length(x) > 1)
@@ -81,7 +86,7 @@ setMethod(
 #' .getSubscript(l, 1) == .getSubscript(l, "a")
 #' @export
 #' @keywords internal
-.getSubscript <- function(lst, i) {
+.getSubscript = function(lst, i) {
   if (is.character(i))
     return(grep(paste0("^", i, "$"), names(lst)))
   return(i)
@@ -135,7 +140,7 @@ setMethod("[[", "Config", function(x, i) {
 })
 
 
-.DollarNames.Config <- function(x, pattern = "")
+.DollarNames.Config = function(x, pattern = "")
   grep(paste0("^", pattern), grep(names(x), value = TRUE))
 
 #' @rdname select-config
diff --git a/R/constants.R b/R/constants.R
index 367578e..4fc750a 100644
--- a/R/constants.R
+++ b/R/constants.R
@@ -20,4 +20,5 @@ CFG_DUPLICATE_KEY = "duplicate"
 CFG_REMOVE_KEY = "remove"
 CFG_LOOPER_KEY = "looper"
 SAMPLE_NAME_ATTR = "sample_name"
-SUBSAMPLE_NAME_ATTR = "subsample_name"
\ No newline at end of file
+SUBSAMPLE_NAME_ATTR = "subsample_name"
+BASE_URL = "https://pephub-api.databio.org/api/v1/"
\ No newline at end of file
diff --git a/R/pepr.R b/R/pepr.R
index 6d02440..bd09605 100644
--- a/R/pepr.R
+++ b/R/pepr.R
@@ -8,6 +8,8 @@
 #' @import yaml
 #' @import stringr
 #' @import pryr
+#' @import httr
+#' @importFrom tidyr unnest
 #'
 #' @references 
 #' GitHub: \url{https://github.com/pepkit/pepr}, Documentation: \url{https://code.databio.org/pepr/}
diff --git a/R/project.R b/R/project.R
index 61e7807..ef70cd0 100644
--- a/R/project.R
+++ b/R/project.R
@@ -21,49 +21,65 @@
 #'
 #' @export
 setClass(
-    "Project",
-    slots = c(
-        file = "character",
-        samples = "data.frame",
-        config = "list",
-        sampleNameAttr = "character",
-        subSampleNameAttr = "character"
-    )
+  "Project",
+  slots = c(
+    file = "character",
+    samples = "data.frame",
+    config = "list",
+    sampleNameAttr = "character",
+    subSampleNameAttr = "character"
+  )
 )
 
 
 # Project class methods ---------------------------------------------------
 
-
 setMethod("initialize", "Project", function(.Object, ...) {
-    .Object = methods::callNextMethod(.Object)  # calls generic initialize
-    ellipsis <- list(...)
-    stIndex = ellipsis$sampleTableIndex
-    sstIndex = ellipsis$subSampleTableIndex
-    if (!is.null(ellipsis$file)) {
-        # check if 'file' path provided
-        if (.isCfg(ellipsis$file)) {
-            # provided 'file' seems to be a config
-            .Object@file = .makeAbsPath(ellipsis$file, parent = path.expand(getwd()))
-            # instantiate config object and stick it in the config slot
-            .Object@config = Config(.Object@file, ellipsis$amendments)
-            # determine the effective (sub)sample table indexes
-            .Object = .getTableIndexes(.Object, stIndex, sstIndex)
-            sampleTablePath = .getSampleTablePathFromConfig(config = config(.Object))
-            .Object@samples = .loadSampleAnnotation(sampleTablePath = sampleTablePath)
-            .Object = .modifySamples(.Object)
-        } else {
-            # provided 'file' seems to be a sample table
-            # determine the effective (sub)sample table indexes
-            .Object = .getTableIndexes(.Object, stIndex, sstIndex)
-            .Object@samples = .loadSampleAnnotation(sampleTablePath = ellipsis$file)
-            .Object = .autoMergeDuplicatedNames(.Object)
-        }
+  .Object = methods::callNextMethod(.Object)  # calls generic initialize
+  ellipsis = list(...)
+  stIndex = ellipsis$sampleTableIndex
+  sstIndex = ellipsis$subSampleTableIndex
+  if (ellipsis$api) {
+    # called with pullProject
+    rawPEP = fetchPEP(ellipsis$file, raw = TRUE)
+    if (length(rawPEP) < 3) {
+      # peps contain 3 elements, failed pep lookup will result in 1 element
+      stop('PEP does not exist in database. Did you spell it correctly?')
     }
-    # no 'file' provided, creating an empty object
-    # determine the effective (sub)sample table indexes
+    .Object@file = ellipsis$file
+    .Object@config = Config(rawPEP$config)
+    
     .Object = .getTableIndexes(.Object, stIndex, sstIndex)
-    return(.Object)
+    sampleTablePath = rawPEP$sample_table
+    
+    .Object@samples = data.table::setDT(as.data.frame(do.call(rbind, rawPEP$sample_list)))
+    subsamples = lapply(rawPEP$subsample_list, .listOfListToListOfDT)
+    
+    .Object = .modifySamplesFetched(.Object, subsamples)
+    
+  } else if (!is.null(ellipsis$file)) {
+    if (.isCfg(ellipsis$file)) {
+      # provided 'file' seems to be a config
+      .Object@file = .makeAbsPath(ellipsis$file, parent = path.expand(getwd()))
+      # instantiate config object and stick it in the config slot
+      .Object@config = Config(.Object@file, ellipsis$amendments)
+      # determine the effective (sub)sample table indexes
+      .Object = .getTableIndexes(.Object, stIndex, sstIndex)
+      sampleTablePath = .getSampleTablePathFromConfig(config = config(.Object))
+      .Object@samples = .loadSampleAnnotation(sampleTablePath = sampleTablePath)
+      .Object = .modifySamples(.Object)
+    } else {
+      # provided 'file' seems to be a sample table
+      # determine the effective (sub)sample table indexes
+      .Object = .getTableIndexes(.Object, stIndex, sstIndex)
+      .Object@samples = .loadSampleAnnotation(sampleTablePath = ellipsis$file)
+      .Object = .autoMergeDuplicatedNames(.Object)
+    }
+  }
+  # no 'file' provided, creating an empty object
+  # determine the effective (sub)sample table indexes
+  .Object = .getTableIndexes(.Object, stIndex, sstIndex)
+  return(.Object)
 })
 
 
@@ -87,31 +103,55 @@ Project = function(file = NULL,
                    amendments = NULL,
                    sampleTableIndex = NULL,
                    subSampleTableIndex = NULL) {
-    methods::new(
-        "Project",
-        file = file,
-        amendments = amendments,
-        sampleTableIndex = sampleTableIndex,
-        subSampleTableIndex = subSampleTableIndex
-    )
+  methods::new(
+    "Project",
+    file = file,
+    api = FALSE,
+    amendments = amendments,
+    sampleTableIndex = sampleTableIndex,
+    subSampleTableIndex = subSampleTableIndex
+  )
+}
+
+
+#' Pull a PEP from PEPhub API
+#'
+#' This is a helper that creates the project with empty samples and config slots
+#'
+#' @param registryPath a string specifying a registry path from PEPhub
+#' @return an object of \code{"\linkS4class{Project}"}
+#' @examples
+#' registryPath = 'databio/example:default'
+#' p=pullProject(registryPath)
+#' @export
+pullProject = function(registryPath = NULL) {
+  methods::new(
+    "Project",
+    file = registryPath,
+    api = TRUE,
+    amendments = NULL,
+    sampleTableIndex = NULL,
+    subSampleTableIndex = NULL
+  )
 }
 
 
 setMethod(
-    "show",
-    signature = "Project",
-    definition = function(object) {
-        cat("PEP project object. Class: ", class(object), fill = T)
-        cat("  file: ", object@file, fill = T)
-        cat("  samples: ", NROW(object@samples), fill = T)
-        if (length(object@config) != 0) {
-            .listAmendments(object@config, style = "cat")
-        }
-        invisible(NULL)
+  "show",
+  signature = "Project",
+  definition = function(object) {
+    cat("PEP project object. Class: ", class(object), fill = T)
+    cat("  file: ", object@file, fill = T)
+    cat("  samples: ", NROW(object@samples), fill = T)
+    if (length(object@config) != 0) {
+      .listAmendments(object@config, style = "cat")
     }
+    invisible(NULL)
+  }
 )
 
 
+
 #' Extract \code{"\linkS4class{Project}"}
 #'
 #' This method can be used to view the config slot of
@@ -129,15 +169,15 @@ setMethod(
 #'
 #' @export
 setGeneric("config", function(object)
-    standardGeneric("config"))
+  standardGeneric("config"))
 
 #' @describeIn config Extract \code{"\linkS4class{Project}"} of the object of \code{"\linkS4class{Project}"}
 setMethod(
-    "config",
-    signature = "Project",
-    definition = function(object) {
-        object@config
-    }
+  "config",
+  signature = "Project",
+  definition = function(object) {
+    object@config
+  }
 )
 
 
@@ -148,22 +188,47 @@ setMethod(
 #' @return modified Project object
 #' @keywords internal
 setGeneric(".modifySamples", function(object)
-    standardGeneric(".modifySamples"))
+  standardGeneric(".modifySamples"))
 
 setMethod(
-    ".modifySamples",
-    signature = "Project",
-    definition = function(object) {
-        object = .removeAttrs(object)
-        object = .appendAttrs(object)
-        object = .duplicateAttrs(object)
-        object = .implyAttrs(object)
-        object = .autoMergeDuplicatedNames(object)
-        object = .mergeAttrs(object,
-                             .getSubSampleTablePathFromConfig(config(object)))
-        object = .deriveAttrs(object)
-        return(object)
-    }
+  ".modifySamples",
+  signature = "Project",
+  definition = function(object) {
+    object = .removeAttrs(object)
+    object = .appendAttrs(object)
+    object = .duplicateAttrs(object)
+    object = .implyAttrs(object)
+    object = .autoMergeDuplicatedNames(object)
+    object = .mergeAttrs(object,
+                         .getSubSampleTablePathFromConfig(config(object)))
+    object = .deriveAttrs(object)
+    return(object)
+  }
+)
+
+
+#' Perform all the sample attribute modifications for fetched PEPs
+#'
+#' @param object an object of \code{"\linkS4class{Project}"}
+#'
+#' @return modified Project object
+#' @keywords internal
+setGeneric(".modifySamplesFetched", function(object, subsamples)
+  standardGeneric(".modifySamplesFetched"))
+
+setMethod(
+  ".modifySamplesFetched",
+  signature = "Project",
+  definition = function(object, subsamples) {
+    # object = .removeAttrs(object)
+    # object = .appendAttrs(object)
+    # object = .duplicateAttrs(object)
+    # object = .implyAttrs(object)
+    # object = .autoMergeDuplicatedNames(object)
+    object = .mergeAttrs(object, subsampleAannotationPaths = NULL, subsamplesTables = subsamples)
+    # object = .deriveAttrs(object)
+    return(object)
+  }
 )
 
 
@@ -188,21 +253,21 @@ setMethod(
 #' getSample(p, sampleName)
 #' @export
 setGeneric(name = "getSample", function(.Object, sampleName)
-    standardGeneric("getSample"))
+  standardGeneric("getSample"))
 
 #' @describeIn getSample extracts the sample from the \code{"\linkS4class{Project}"} object
 setMethod(
-    f = "getSample",
-    signature(.Object = "Project",
-              sampleName = "character"),
-    definition = function(.Object, sampleName) {
-        sampleNames = unlist(.Object@samples[[.Object@sampleNameAttr]])
-        rowNumber = which(sampleNames == sampleName)
-        if (length(rowNumber) == 0)
-            stop("Such sample name does not exist.")
-        result = sampleTable(.Object)[rowNumber,]
-        return(result)
-    }
+  f = "getSample",
+  signature(.Object = "Project",
+            sampleName = "character"),
+  definition = function(.Object, sampleName) {
+    sampleNames = unlist(.Object@samples[[.Object@sampleNameAttr]])
+    rowNumber = which(sampleNames == sampleName)
+    if (length(rowNumber) == 0)
+      stop("Such sample name does not exist.")
+    result = sampleTable(.Object)[rowNumber,]
+    return(result)
+  }
 )
 
 
@@ -230,41 +295,41 @@ setMethod(
 #' getSubsample(p, sampleName, subsampleName)
 #' @export
 setGeneric(name = "getSubsample", function(.Object, sampleName, subsampleName)
-    standardGeneric("getSubsample"))
+  standardGeneric("getSubsample"))
 
 #' @describeIn getSubsample extracts the subsamples from the \code{"\linkS4class{Project}"} object
 setMethod(
-    f = "getSubsample",
-    signature(
-        .Object = "Project",
-        sampleName = "character",
-        subsampleName = "character"
-    ),
-    definition = function(.Object, sampleName, subsampleName) {
-        if (is.null(.Object@samples[[.Object@subSampleNameAttr]]))
-            stop(
-                "There is no subsample_name attribute in the subsample table, ",
-                " therefore this method cannot be called."
-            )
-        sampleNames = unlist(.Object@samples[[.Object@sampleNameAttr]])
-        rowNumber = which(sampleNames == sampleName)
-        if (length(rowNumber) == 0)
-            stop("Such sample name does not exist.")
-        subsampleNames = .Object@samples[[.Object@subSampleNameAttr]][[rowNumber]]
-        sampleNumber = which(subsampleNames == subsampleName)
-        if (length(sampleNumber) == 0)
-            stop("Such sample and sub sample name combination does not exist.")
-        result = .Object@samples[1, ]
-        for (iColumn in names(result)) {
-            if (length(.Object@samples[[iColumn]][[rowNumber]]) > 1) {
-                result[[iColumn]] =
-                    .Object@samples[[iColumn]][[rowNumber]][[sampleNumber]]
-            } else{
-                result[[iColumn]] = .Object@samples[[iColumn]][[rowNumber]][[1]]
-            }
-        }
-        return(result)
+  f = "getSubsample",
+  signature(
+    .Object = "Project",
+    sampleName = "character",
+    subsampleName = "character"
+  ),
+  definition = function(.Object, sampleName, subsampleName) {
+    if (is.null(.Object@samples[[.Object@subSampleNameAttr]]))
+      stop(
+        "There is no subsample_name attribute in the subsample table, ",
+        " therefore this method cannot be called."
+      )
+    sampleNames = unlist(.Object@samples[[.Object@sampleNameAttr]])
+    rowNumber = which(sampleNames == sampleName)
+    if (length(rowNumber) == 0)
+      stop("Such sample name does not exist.")
+    subsampleNames = .Object@samples[[.Object@subSampleNameAttr]][[rowNumber]]
+    sampleNumber = which(subsampleNames == subsampleName)
+    if (length(sampleNumber) == 0)
+      stop("Such sample and sub sample name combination does not exist.")
+    result = .Object@samples[1, ]
+    for (iColumn in names(result)) {
+      if (length(.Object@samples[[iColumn]][[rowNumber]]) > 1) {
+        result[[iColumn]] =
+          .Object@samples[[iColumn]][[rowNumber]][[sampleNumber]]
+      } else{
+        result[[iColumn]] = .Object@samples[[iColumn]][[rowNumber]][[1]]
+      }
     }
+    return(result)
+  }
 )
 
 
@@ -286,16 +351,16 @@ setMethod(
 #' availAmendemtns = listAmendments(p)
 #' @export
 setGeneric("listAmendments", function(.Object)
-    standardGeneric("listAmendments"))
+  standardGeneric("listAmendments"))
 
 #' @describeIn listAmendments list amendments in a \code{"\linkS4class{Project}"} object
 setMethod(
-    f = "listAmendments",
-    signature = signature(.Object = "Project"),
-    definition = function(.Object) {
-        config = config(.Object)
-        .listAmendments(cfg = config, style = "message")
-    }
+  f = "listAmendments",
+  signature = signature(.Object = "Project"),
+  definition = function(.Object) {
+    config = config(.Object)
+    .listAmendments(cfg = config, style = "message")
+  }
 )
 
 
@@ -322,24 +387,24 @@ setMethod(
 #' activateAmendments(p, availAmendments[1])
 #' @export
 setGeneric("activateAmendments", function(.Object, amendments)
-    standardGeneric("activateAmendments"))
+  standardGeneric("activateAmendments"))
 
 #' @describeIn activateAmendments activate amendments in a \code{"\linkS4class{Project}"} object
 setMethod(
-    f = "activateAmendments",
-    signature = signature(.Object = "Project", amendments = "character"),
-    definition = function(.Object, amendments) {
-        .Object@config = .applyAmendments(.Object@config, amendments)
-        .Object@config = makeSectionsAbsolute(
-            .Object@config,
-            c(CFG_SAMPLE_TABLE_KEY, CFG_SUBSAMPLE_TABLE_KEY),
-            .Object@file
-        )
-        sampleTablePath = .getSampleTablePathFromConfig(config = config(.Object))
-        .Object@samples = .loadSampleAnnotation(sampleTablePath = sampleTablePath)
-        .Object = .modifySamples(.Object)
-        return(.Object)
-    }
+  f = "activateAmendments",
+  signature = signature(.Object = "Project", amendments = "character"),
+  definition = function(.Object, amendments) {
+    .Object@config = .applyAmendments(.Object@config, amendments)
+    .Object@config = makeSectionsAbsolute(
+      .Object@config,
+      c(CFG_SAMPLE_TABLE_KEY, CFG_SUBSAMPLE_TABLE_KEY),
+      .Object@file
+    )
+    sampleTablePath = .getSampleTablePathFromConfig(config = config(.Object))
+    .Object@samples = .loadSampleAnnotation(sampleTablePath = sampleTablePath)
+    .Object = .modifySamples(.Object)
+    return(.Object)
+  }
 )
 
 
@@ -359,15 +424,15 @@ setMethod(
 #'
 #' @export
 setGeneric("sampleTable", function(object)
-    standardGeneric("sampleTable"))
+  standardGeneric("sampleTable"))
 
 #' @describeIn sampleTable extract sample table from a \code{"\linkS4class{Project}"}
 setMethod(
-    "sampleTable",
-    signature = "Project",
-    definition = function(object) {
-        object@samples
-    }
+  "sampleTable",
+  signature = "Project",
+  definition = function(object) {
+    object@samples
+  }
 )
 
 # Sample modifiers --------------------------------------------------------
@@ -378,22 +443,22 @@ setMethod(
 #'
 #' @return an object of \code{"\linkS4class{Project}"}
 #' @keywords internal
-.removeAttrs <- function(.Object) {
-    if (!CFG_S_MODIFIERS_KEY %in% names(config(.Object)))
-        return(.Object)
-    modifiers = config(.Object)[[CFG_S_MODIFIERS_KEY]]
-    if (!CFG_REMOVE_KEY %in% names(modifiers))
-        return(.Object)
-    toRemove = modifiers[[CFG_REMOVE_KEY]]
-    if (!is.null(toRemove)) {
-        # get a copy of samples to get the dimensions
-        for (rem in toRemove) {
-            if (rem %in% colnames(sampleTable(.Object))) {
-                .Object@samples[, rem] = NULL
-            }
-        }
-    }
+.removeAttrs = function(.Object) {
+  if (!CFG_S_MODIFIERS_KEY %in% names(config(.Object)))
+    return(.Object)
+  modifiers = config(.Object)[[CFG_S_MODIFIERS_KEY]]
+  if (!CFG_REMOVE_KEY %in% names(modifiers))
     return(.Object)
+  toRemove = modifiers[[CFG_REMOVE_KEY]]
+  if (!is.null(toRemove)) {
+    # get a copy of samples to get the dimensions
+    for (rem in toRemove) {
+      if (rem %in% colnames(sampleTable(.Object))) {
+        .Object@samples[, rem] = NULL
+      }
+    }
+  }
+  return(.Object)
 }
 
 
@@ -403,32 +468,32 @@ setMethod(
 #'
 #' @return an object of \code{\link{Project-class}}
 #' @keywords internal
-.appendAttrs <- function(.Object) {
-    if (!CFG_S_MODIFIERS_KEY %in% names(config(.Object)))
-        return(.Object)
-    modifiers = config(.Object)[[CFG_S_MODIFIERS_KEY]]
-    if (!CFG_APPEND_KEY %in% names(modifiers))
-        return(.Object)
-    constants = modifiers[[CFG_APPEND_KEY]]
-    if (is.list(constants)) {
-        # get names
-        constantsNames = names(constants)
-        # get a copy of samples to get the dimensions
-        colLen = dim(sampleTable(.Object))[1]
-        for (iConst in seq_along(constants)) {
-            # create a one column data.table and append it to the current one
-            if (!constantsNames[iConst] %in% colnames(sampleTable(.Object))) {
-                tempDT = data.table::data.table(matrix(matrix(
-                    list(constants[[iConst]]),
-                    ncol = 1,
-                    nrow = colLen
-                )))
-                names(tempDT) = constantsNames[iConst]
-                .Object@samples = cbind(.Object@samples, tempDT)
-            }
-        }
-    }
+.appendAttrs = function(.Object) {
+  if (!CFG_S_MODIFIERS_KEY %in% names(config(.Object)))
     return(.Object)
+  modifiers = config(.Object)[[CFG_S_MODIFIERS_KEY]]
+  if (!CFG_APPEND_KEY %in% names(modifiers))
+    return(.Object)
+  constants = modifiers[[CFG_APPEND_KEY]]
+  if (is.list(constants)) {
+    # get names
+    constantsNames = names(constants)
+    # get a copy of samples to get the dimensions
+    colLen = dim(sampleTable(.Object))[1]
+    for (iConst in seq_along(constants)) {
+      # create a one column data.table and append it to the current one
+      if (!constantsNames[iConst] %in% colnames(sampleTable(.Object))) {
+        tempDT = data.table::data.table(matrix(matrix(
+          list(constants[[iConst]]),
+          ncol = 1,
+          nrow = colLen
+        )))
+        names(tempDT) = constantsNames[iConst]
+        .Object@samples = cbind(.Object@samples, tempDT)
+      }
+    }
+  }
+  return(.Object)
 }
 
 #' Duplicate a selected attribute across all the samples
@@ -437,17 +502,17 @@ setMethod(
 #'
 #' @return an object of \code{"\linkS4class{Project}"}
 #' @keywords internal
-.duplicateAttrs <- function(.Object) {
-    if (!CFG_S_MODIFIERS_KEY %in% names(config(.Object)))
-        return(.Object)
-    modifiers = config(.Object)[[CFG_S_MODIFIERS_KEY]]
-    if (!CFG_DUPLICATE_KEY %in% names(modifiers))
-        return(.Object)
-    duplicated = modifiers[[CFG_DUPLICATE_KEY]]
-    for (oriAttrName in names(duplicated)) {
-        .Object@samples[, duplicated[[oriAttrName]]] = .Object@samples[, oriAttrName]
-    }
+.duplicateAttrs = function(.Object) {
+  if (!CFG_S_MODIFIERS_KEY %in% names(config(.Object)))
+    return(.Object)
+  modifiers = config(.Object)[[CFG_S_MODIFIERS_KEY]]
+  if (!CFG_DUPLICATE_KEY %in% names(modifiers))
     return(.Object)
+  duplicated = modifiers[[CFG_DUPLICATE_KEY]]
+  for (oriAttrName in names(duplicated)) {
+    .Object@samples[, duplicated[[oriAttrName]]] = .Object@samples[, oriAttrName]
+  }
+  return(.Object)
 }
 
 #' Imply attributes
@@ -457,46 +522,46 @@ setMethod(
 #' @return an object of \code{"\linkS4class{Project}"}
 #' @keywords internal
 .implyAttrs = function(.Object) {
-    if (!CFG_S_MODIFIERS_KEY %in% names(config(.Object)))
-        return(.Object)
-    modifiers = config(.Object)[[CFG_S_MODIFIERS_KEY]]
-    if (!CFG_IMPLY_KEY %in% names(modifiers))
-        return(.Object)
-    implications = modifiers[[CFG_IMPLY_KEY]]
-    for (implication in implications) {
-        if (!(
-            CFG_IMPLY_IF_KEY %in% names(implication) &&
-            CFG_IMPLY_THEN_KEY %in% names(implication)
-        ))
-            stop(CFG_IMPLY_KEY, " section is not formatted properly")
-        implierAttrs = names(implication[[CFG_IMPLY_IF_KEY]])
-        implierVals = implication[[CFG_IMPLY_IF_KEY]]
-        impliedAttrs = names(implication[[CFG_IMPLY_THEN_KEY]])
-        impliedVals = as.character(implication[[CFG_IMPLY_THEN_KEY]])
-        attrs = colnames(.Object@samples)
-        if (!all(implierAttrs %in% attrs))
-            next
-        allHitIds = list()
-        for (i in seq_along(implierAttrs)) {
-            hitIds = list()
-            implierStrings = as.character(unlist(implierVals[i]))
-            for (j in seq_along(implierStrings)) {
-                hitIds[[j]] = which(.Object@samples[, implierAttrs[i]] == implierStrings[j])
-            }
-            allHitIds[[i]] = Reduce(union, hitIds)
-            if (length(allHitIds[[i]]) < 1)
-                break
-        }
-        qualIds = Reduce(intersect, allHitIds)
-        if (length(qualIds) < 1)
-            next
-        for (i in seq_along(impliedAttrs)) {
-            if (!impliedAttrs[i] %in% attrs)
-                .Object@samples[, impliedAttrs[i]] = ""
-            .Object@samples[qualIds, impliedAttrs[i]] = impliedVals[i]
-        }
-    }
+  if (!CFG_S_MODIFIERS_KEY %in% names(config(.Object)))
+    return(.Object)
+  modifiers = config(.Object)[[CFG_S_MODIFIERS_KEY]]
+  if (!CFG_IMPLY_KEY %in% names(modifiers))
     return(.Object)
+  implications = modifiers[[CFG_IMPLY_KEY]]
+  for (implication in implications) {
+    if (!(
+      CFG_IMPLY_IF_KEY %in% names(implication) &&
+      CFG_IMPLY_THEN_KEY %in% names(implication)
+    ))
+      stop(CFG_IMPLY_KEY, " section is not formatted properly")
+    implierAttrs = names(implication[[CFG_IMPLY_IF_KEY]])
+    implierVals = implication[[CFG_IMPLY_IF_KEY]]
+    impliedAttrs = names(implication[[CFG_IMPLY_THEN_KEY]])
+    impliedVals = as.character(implication[[CFG_IMPLY_THEN_KEY]])
+    attrs = colnames(.Object@samples)
+    if (!all(implierAttrs %in% attrs))
+      next
+    allHitIds = list()
+    for (i in seq_along(implierAttrs)) {
+      hitIds = list()
+      implierStrings = as.character(unlist(implierVals[i]))
+      for (j in seq_along(implierStrings)) {
+        hitIds[[j]] = which(.Object@samples[, implierAttrs[i]] == implierStrings[j])
+      }
+      allHitIds[[i]] = Reduce(union, hitIds)
+      if (length(allHitIds[[i]]) < 1)
+        break
+    }
+    qualIds = Reduce(intersect, allHitIds)
+    if (length(qualIds) < 1)
+      next
+    for (i in seq_along(impliedAttrs)) {
+      if (!impliedAttrs[i] %in% attrs)
+        .Object@samples[, impliedAttrs[i]] = ""
+      .Object@samples[qualIds, impliedAttrs[i]] = impliedVals[i]
+    }
+  }
+  return(.Object)
 }
 
 
@@ -507,37 +572,37 @@ setMethod(
 #' @return an object of \code{"\linkS4class{Project}"}
 #' @keywords internal
 .deriveAttrs = function(.Object) {
-    if (!CFG_S_MODIFIERS_KEY %in% names(config(.Object)))
-        return(.Object)
-    parentDir = dirname(.Object@file)
-    modifiers = config(.Object)[[CFG_S_MODIFIERS_KEY]]
-    if (!CFG_DERIVE_KEY %in% names(modifiers))
-        return(.Object)
-    derivations = modifiers[[CFG_DERIVE_KEY]]
-    if (!all(c(CFG_DERIVE_ATTRS_KEY, CFG_DERIVE_SOURCES_KEY)
-             %in% names(derivations)))
-        stop(CFG_DERIVE_KEY, " section is not formatted properly")
-    for (derivedAttr in derivations[[CFG_DERIVE_ATTRS_KEY]]) {
-        if (!derivedAttr %in% colnames(.Object@samples))
-            stop(paste(
-                "Failed to derive. Sample attribute not found:",
-                derivedAttr
-            ))
-        derivedSamplesVals = .Object@samples[, derivedAttr]
-        for (derivedSource in names(derivations[[CFG_DERIVE_SOURCES_KEY]])) {
-            hitIds = which(derivedSamplesVals == derivedSource)
-            if (length(hitIds) < 1)
-                next
-            for (hitId in hitIds) {
-                rgx = derivations[[CFG_DERIVE_SOURCES_KEY]][[derivedSource]]
-                res = .matchesAndRegexes(.strformat(rgx, as.list(sampleTable(
-                    .Object
-                )[hitId, ]), parentDir))
-                .Object@samples[hitId, derivedAttr] = list(unique(unlist(res)))
-            }
-        }
-    }
+  if (!CFG_S_MODIFIERS_KEY %in% names(config(.Object)))
+    return(.Object)
+  parentDir = dirname(.Object@file)
+  modifiers = config(.Object)[[CFG_S_MODIFIERS_KEY]]
+  if (!CFG_DERIVE_KEY %in% names(modifiers))
     return(.Object)
+  derivations = modifiers[[CFG_DERIVE_KEY]]
+  if (!all(c(CFG_DERIVE_ATTRS_KEY, CFG_DERIVE_SOURCES_KEY)
+           %in% names(derivations)))
+    stop(CFG_DERIVE_KEY, " section is not formatted properly")
+  for (derivedAttr in derivations[[CFG_DERIVE_ATTRS_KEY]]) {
+    if (!derivedAttr %in% colnames(.Object@samples))
+      stop(paste(
+        "Failed to derive. Sample attribute not found:",
+        derivedAttr
+      ))
+    derivedSamplesVals = .Object@samples[, derivedAttr]
+    for (derivedSource in names(derivations[[CFG_DERIVE_SOURCES_KEY]])) {
+      hitIds = which(derivedSamplesVals == derivedSource)
+      if (length(hitIds) < 1)
+        next
+      for (hitId in hitIds) {
+        rgx = derivations[[CFG_DERIVE_SOURCES_KEY]][[derivedSource]]
+        res = .matchesAndRegexes(.strformat(rgx, as.list(sampleTable(
+          .Object
+        )[hitId, ]), parentDir))
+        .Object@samples[hitId, derivedAttr] = list(unique(unlist(res)))
+      }
+    }
+  }
+  return(.Object)
 }
 
 
@@ -548,12 +613,12 @@ setMethod(
 #' @return an data.frame with samples; one sample per row
 #' @keywords internal
 .loadSampleAnnotation = function(sampleTablePath) {
-    if (.safeFileExists(sampleTablePath)) {
-        samples = data.table::fread(sampleTablePath)
-    } else{
-        warning("The sample table does not exist: ", sampleTablePath)
-        samples = data.frame()
-    }
+  if (.safeFileExists(sampleTablePath)) {
+    samples = data.table::fread(sampleTablePath)
+  } else{
+    warning("The sample table does not exist: ", sampleTablePath)
+    samples = data.frame()
+  }
 }
 
 
@@ -561,52 +626,56 @@ setMethod(
 #'
 #' @param .Object an object of \code{"\linkS4class{Project}"}
 #' @param path string, a path to the subsample table to read and incorporate
+#' @param subsamplesTable data.table, provided from constructor if PEP is fetched from API
 #'
 #' @return an object of \code{"\linkS4class{Project}"}
 #' @keywords internal
-.loadSubsampleAnnotation = function(.Object, path) {
+.loadSubsampleAnnotation = function(.Object, path = NULL, subsamplesTable = NULL) {
+  if (is.null(subsamplesTable) & !is.null(path)) {
     if (.safeFileExists(path)) {
-        subsamplesTable = data.table::fread(path)
+      subsamplesTable = data.table::fread(path)
     } else{
-        subsamplesTable = data.table::data.table()
+      subsamplesTable = data.table::data.table()
     }
-    subNames = unique(subsamplesTable[[.Object@sampleNameAttr]])
-    samples = sampleTable(.Object)
-    samples = .listifyDF(samples)
-    rowNum = nrow(samples)
-    # Creating a list to be populated in the loop and inserted
-    # into the samples data.table as a column. This way the "cells"
-    # in the samples table can consist of multiple elements
-    for (iName in subNames) {
-        whichNames = which(subsamplesTable[[.Object@sampleNameAttr]] == iName)
-        subTable = subsamplesTable[whichNames, ]
-        dropCol = which(names(subsamplesTable[whichNames, ]) == .Object@sampleNameAttr)
-        subTable = subset(subTable, select = -dropCol)
-        colList = vector("list", rowNum)
-        for (iColumn in seq_len(ncol(subTable))) {
-            colName = names(subset(subTable, select = iColumn))
-            if (!any(names(samples) == colName)) {
-                # The column doesn't exist, creating
-                samples[, colName] = NULL
-            } else{
-                colList = samples[[colName]]
-            }
-            # The column exists
-            whichColSamples = which(names(samples) == colName)
-            whichRowSamples = which(samples[[.Object@sampleNameAttr]] == iName)
-            if (length(whichRowSamples) < 1) {
-                warning("No samples named '", iName, "'")
-            } else {
-                # Inserting element(s) into the list
-                colList[[whichRowSamples]] = subTable[[colName]]
-                # Inserting the list as a column in the data.table
-                samples[[colName]] = colList
-            }
-        }
+  }
+  
+  subNames = unique(subsamplesTable[[.Object@sampleNameAttr]])
+  samples = sampleTable(.Object)
+  samples = .listifyDF(samples)
+  rowNum = nrow(samples)
+  # Creating a list to be populated in the loop and inserted
+  # into the samples data.table as a column. This way the "cells"
+  # in the samples table can consist of multiple elements
+  for (iName in subNames) {
+    whichNames = which(subsamplesTable[[.Object@sampleNameAttr]] == iName)
+    subTable = subsamplesTable[whichNames, ]
+    dropCol = which(names(subsamplesTable[whichNames, ]) == .Object@sampleNameAttr)
+    subTable = subset(subTable, select = -dropCol)
+    colList = vector("list", rowNum)
+    for (iColumn in seq_len(ncol(subTable))) {
+      colName = names(subset(subTable, select = iColumn))
+      if (!any(names(samples) == colName)) {
+        # The column doesn't exist, creating
+        samples[, colName] = NULL
+      } else{
+        colList = samples[[colName]]
+      }
+      # The column exists
+      whichColSamples = which(names(samples) == colName)
+      whichRowSamples = which(samples[[.Object@sampleNameAttr]] == iName)
+      if (length(whichRowSamples) < 1) {
+        warning("No samples named '", iName, "'")
+      } else {
+        # Inserting element(s) into the list
+        colList[[whichRowSamples]] = subTable[[colName]]
+        # Inserting the list as a column in the data.table
+        samples[[colName]] = colList
+      }
     }
-    samples[is.na(samples)] = ""
-    .Object@samples = samples
-    return(.Object)
+  }
+  samples[is.na(samples)] = ""
+  .Object@samples = samples
+  return(.Object)
 }
 
 
@@ -618,13 +687,19 @@ setMethod(
 #'
 #' @return an object of \code{"\linkS4class{Project}"}
 #' @keywords internal
-.mergeAttrs = function(.Object, subsampleAannotationPaths) {
-    if (is.null(subsampleAannotationPaths))
-        return(.Object)
-    for (p in subsampleAannotationPaths) {
-        .Object = .loadSubsampleAnnotation(.Object, p)
+.mergeAttrs = function(.Object, subsampleAannotationPaths, subsamplesTables = NULL) {
+  if (!is.null(subsamplesTables)) {
+    for (sst in subsamplesTables) {
+      .Object = .loadSubsampleAnnotation(.Object, subsamplesTable = sst)
     }
     return(.Object)
+  }
+  if (is.null(subsampleAannotationPaths))
+    return(.Object)
+  for (p in subsampleAannotationPaths) {
+    .Object = .loadSubsampleAnnotation(.Object, path = p)
+  }
+  return(.Object)
 }
 
 
@@ -637,39 +712,39 @@ setMethod(
 #' @return an object of \code{"\linkS4class{Project}"}
 #' @keywords internal
 .autoMergeDuplicatedNames = function(.Object) {
-    s = sampleTable(.Object)
-    sampleNames = s[[.Object@sampleNameAttr]]
-    dups = duplicated(sampleNames)
-    if (!any(dups))
-        return(.Object)
-    duplicatedSampleNames = sampleNames[which(dups)]
-    if (!is.null(.getSubSampleTablePathFromConfig(config(.Object))))
-        stop(
-            paste0(
-                "Duplicated sample names were found (",
-                duplicatedSampleNames,
-                ") and subsample_table is specified in the config. ",
-                "You may use either auto-merging or subsample_table-based merging."
-            )
-        )
-    rowsWithDuplicates = which(s[[.Object@sampleNameAttr]] %in% duplicatedSampleNames)
-    dupRows = s[rowsWithDuplicates,]
-    combinedList = list()
-    # create a list of list that combined rows with duplicated sample names
-    for (duplicatedSampleName in duplicatedSampleNames) {
-        toCombine = s[which(sampleNames == duplicatedSampleName),]
-        combinedList[[duplicatedSampleName]] = apply(toCombine, 2, function(x) {
-            return(list(unique(x)))
-        })
-    }
-    # remove rows that include duplicates
-    s = s[-rowsWithDuplicates,]
-    # insert the combined rows
-    for (combinedRow in combinedList) {
-        s = rbind(s, combinedRow)
-    }
-    .Object@samples = s
+  s = sampleTable(.Object)
+  sampleNames = s[[.Object@sampleNameAttr]]
+  dups = duplicated(sampleNames)
+  if (!any(dups))
     return(.Object)
+  duplicatedSampleNames = sampleNames[which(dups)]
+  if (!is.null(.getSubSampleTablePathFromConfig(config(.Object))))
+    stop(
+      paste0(
+        "Duplicated sample names were found (",
+        duplicatedSampleNames,
+        ") and subsample_table is specified in the config. ",
+        "You may use either auto-merging or subsample_table-based merging."
+      )
+    )
+  rowsWithDuplicates = which(s[[.Object@sampleNameAttr]] %in% duplicatedSampleNames)
+  dupRows = s[rowsWithDuplicates,]
+  combinedList = list()
+  # create a list of list that combined rows with duplicated sample names
+  for (duplicatedSampleName in duplicatedSampleNames) {
+    toCombine = s[which(sampleNames == duplicatedSampleName),]
+    combinedList[[duplicatedSampleName]] = apply(toCombine, 2, function(x) {
+      return(list(unique(x)))
+    })
+  }
+  # remove rows that include duplicates
+  s = s[-rowsWithDuplicates,]
+  # insert the combined rows
+  for (combinedRow in combinedList) {
+    s = rbind(s, combinedRow)
+  }
+  .Object@samples = s
+  return(.Object)
 }
 
 #' Set table indexes
@@ -687,23 +762,23 @@ setMethod(
 #' @param stIndex character string indicating a constructor-specified sample table index
 #' @param sstIndex character string indicating a constructor-specified subsample table index
 #' @keywords internal
-.getTableIndexes <- function(.Object, stIndex, sstIndex) {
-    .getIndexVal <- function(spec, config, default, key) {
-        if (!is.null(spec))
-            return(spec)
-        if (length(config))
-            return(ifelse(is.null(config[[key]]), default, config[[key]]))
-        return(default)
-    }
-    
-    .Object@sampleNameAttr = .getIndexVal(stIndex,
-                                          config(.Object),
-                                          SAMPLE_NAME_ATTR,
-                                          CFG_SAMPLE_TABLE_INDEX_KEY)
-    .Object@subSampleNameAttr = .getIndexVal(sstIndex,
-                                             config(.Object),
-                                             SUBSAMPLE_NAME_ATTR,
-                                             CFG_SUBSAMPLE_TABLE_INDEX_KEY)
-    
-    return(.Object)
+.getTableIndexes = function(.Object, stIndex, sstIndex) {
+  .getIndexVal = function(spec, config, default, key) {
+    if (!is.null(spec))
+      return(spec)
+    if (length(config))
+      return(ifelse(is.null(config[[key]]), default, config[[key]]))
+    return(default)
+  }
+  
+  .Object@sampleNameAttr = .getIndexVal(stIndex,
+                                        config(.Object),
+                                        SAMPLE_NAME_ATTR,
+                                        CFG_SAMPLE_TABLE_INDEX_KEY)
+  .Object@subSampleNameAttr = .getIndexVal(sstIndex,
+                                           config(.Object),
+                                           SUBSAMPLE_NAME_ATTR,
+                                           CFG_SUBSAMPLE_TABLE_INDEX_KEY)
+  
+  return(.Object)
 }
diff --git a/R/utils.R b/R/utils.R
index 1c7d0eb..fa725e3 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -358,6 +358,7 @@ fetchSamples = function(samples,
   }
 }
 
+
 #' Check for a section existence in a nested list
 #'
 #' @param object list to inspect
@@ -433,3 +434,156 @@ fetchSamples = function(samples,
     return(FALSE)
   stop("File path does not point to an annotation or a config: ", filePath)
 }
+
+
+#' Fetch a PEP from PEPhub using a registry path (namespace/project:tag)
+#'
+#' Calls the PEPhub API to fetch PEPs.
+#'
+#' @param registryPath a string for the PEP registry path (namespace/project:tag)
+#' @param raw a boolean for whether to return a raw PEP
+#'
+#' @return a list, with sublists for config, sample_list, and subsample_list for the fetched PEP
+#' @keywords internal
+fetchPEP = function(registryPath, raw = TRUE) {
+  pathSplit = strsplit(registryPath, '/|:')[[1]]
+  if (length(pathSplit) < 3) {
+    stop('Invalid registry path.')
+  }
+  queryURL = paste0(BASE_URL, 'projects/', pathSplit[[1]], '/', pathSplit[[2]], '?tag=', pathSplit[[3]], '&raw=', raw)
+  
+  jwtPath = file.path(path.expand('~'), '.pephubclient', 'jwt.txt')
+  jwtToken = ''
+  
+  if (file.exists(jwtPath)) {
+    if (difftime(Sys.time(), file.info(jwtPath)$mtime, units = 'days') <= 2) {
+      jwtToken = readLines(jwtPath, warn = FALSE)
+      res = httr::GET(queryURL, httr::add_headers(authorization = jwtToken))
+    } else {
+      warning('Authentication token is more than 2 days old. Generate a new one with PEPhub Client.')
+      res = httr::GET(queryURL)
+    }
+  } else {
+    warning('No authentication token found. Generate one with PEPhub Client to access private PEPs.')
+    res = httr::GET(queryURL)
+  }
+  
+  pep = httr::content(res, as = 'parsed')
+  
+  return(pep)
+}
+
+
+#' Save a modified PEP Project to a local directory
+#'
+#' This is a helper that saves a PEP Project to a local output directory
+#'
+#' @param project a PEP Project
+#' @param outputDir a string for the output directory, defaults to current working directory
+#' @param overwrite a boolean for whether to overwrite an existing project at the output directory
+#' 
+#' @return a boolean, TRUE if the save was successful and FALSE if otherwise
+#' @export
+saveProject = function(project = NULL,
+                       outputDir = getwd(),
+                       overwrite = FALSE) {
+  saved = FALSE
+  
+  if (!file.exists(outputDir)) {
+    stop('Specified Project directory does not exist.')
+  }
+  
+  pattern = "^[a-zA-Z0-9_-]+/[a-zA-Z0-9_-]+:[a-zA-Z0-9_-]+$"
+  
+  if (grepl(pattern, project@file, perl = TRUE)) {
+    # if file is a registry path
+    projectName = gsub('/|:', '-', project@file)
+    projectPath = file.path(outputDir, projectName)
+  } else {
+    projectPath = file.path(outputDir, basename(dirname(project@file)))
+  }
+  
+  if ((!dir.exists(projectPath) | overwrite)) {
+    dir.create(projectPath, showWarnings = FALSE)
+    
+    samplesTable = as.data.frame(project@samples)
+    
+    subsampleColsIdx = unname(which(sapply(samplesTable, function(x) any(sapply(x, is.list)))))
+    subsampleColsNames = names(which(sapply(samplesTable, function(x) any(sapply(x, is.list)))))
+    sampleNameColIdx = which(names(samplesTable) == project@sampleNameAttr)
+    
+    samplesTableRaw = samplesTable
+    subsamplesTableRaw = NULL
+    if (length(subsampleColsIdx) > 0) {
+      samplesTableRaw = samplesTable[, -subsampleColsIdx]
+      subsamplesTable = samplesTable[, c(sampleNameColIdx, subsampleColsIdx)]
+      subsamplesTableRaw = tidyr::unnest(subsamplesTable, cols = subsampleColsNames)
+    }
+    
+    sampleTableName = ifelse(CFG_SAMPLE_TABLE_KEY %in% names(project@config), 
+                                basename(project@config[[CFG_SAMPLE_TABLE_KEY]]),
+                                paste0(CFG_SAMPLE_TABLE_KEY, '.csv'))
+    
+    subsampleTableName = ifelse(CFG_SUBSAMPLE_TABLE_KEY %in% names(project@config),
+                                   basename(project@config[[CFG_SUBSAMPLE_TABLE_KEY]]), 
+                                   paste0(CFG_SUBSAMPLE_TABLE_KEY, '.csv'))
+    
+    project@config[[CFG_SAMPLE_TABLE_KEY]] = sampleTableName
+    project@config[[CFG_SUBSAMPLE_TABLE_KEY]] = subsampleTableName
+    
+    yaml::write_yaml(project@config, file = file.path(projectPath, 'project_config.yaml'))
+    if (!is.null(samplesTableRaw)) {
+      data.table::fwrite(samplesTableRaw, file = file.path(projectPath, sampleTableName))
+    }
+    if (!is.null(subsamplesTableRaw)) {
+      data.table::fwrite(subsamplesTableRaw, file = file.path(projectPath, subsampleTableName))
+    }
+    saved = TRUE
+  } else {
+    stop('Project directory already exists. Use overwrite = TRUE if you would like to overwrite the existing local PEP.')
+  }
+  
+  return(saved)
+}
+
+
+#' Dataframify list sublists
+#'
+#' This function turns each list sublist into a data frame
+#'
+#' @param list an object of class list
+#' @return an object of class data.frame
+#' @keywords internal
+.listOfListToListOfDT = function(list) {
+  data.table::setDT(as.data.frame(do.call(rbind, list)))
+}
+
+
+
+#' Save or update JWT
+#'
+#' Save or update local authentication token to fetch private PEPs
+#'
+#' @param jwt a string for the new jwt to save
+#'
+#' @return a boolean for whether the authentication token was saved
+#' @export
+saveJWT = function(jwt) {
+  if (typeof(jwt) == 'character') {
+    jwtPath = file.path(path.expand('~'), '.pephubclient', 'jwt.txt')
+    
+    if (file.exists(jwtPath)) {
+      warning('Overwriting existing authentication token...')
+    }
+    
+    cat(jwt, file = jwtPath)
+    print(paste0('JWT saved to ', jwtPath))
+    
+    return(TRUE)
+  } else {
+    warning('Invalid authentication token provided.')
+    return(FALSE)
+  }
+}
+
+
diff --git a/man/dot-listOfListToListOfDT.Rd b/man/dot-listOfListToListOfDT.Rd
new file mode 100644
index 0000000..5e81e54
--- /dev/null
+++ b/man/dot-listOfListToListOfDT.Rd
@@ -0,0 +1,18 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/utils.R
+\name{.listOfListToListOfDT}
+\alias{.listOfListToListOfDT}
+\title{Dataframify list sublists}
+\usage{
+.listOfListToListOfDT(list)
+}
+\arguments{
+\item{list}{an object of class list}
+}
+\value{
+an object of class data.frame
+}
+\description{
+This function turns each list sublist into a data frame
+}
+\keyword{internal}
diff --git a/man/dot-loadSubsampleAnnotation.Rd b/man/dot-loadSubsampleAnnotation.Rd
index 47f80da..23bef76 100644
--- a/man/dot-loadSubsampleAnnotation.Rd
+++ b/man/dot-loadSubsampleAnnotation.Rd
@@ -4,12 +4,14 @@
 \alias{.loadSubsampleAnnotation}
 \title{Load single subsample annotation}
 \usage{
-.loadSubsampleAnnotation(.Object, path)
+.loadSubsampleAnnotation(.Object, path = NULL, subsamplesTable = NULL)
 }
 \arguments{
 \item{.Object}{an object of \code{"\linkS4class{Project}"}}
 
 \item{path}{string, a path to the subsample table to read and incorporate}
+
+\item{subsamplesTable}{data.table, provided from constructor if PEP is fetched from API}
 }
 \value{
 an object of \code{"\linkS4class{Project}"}
diff --git a/man/dot-mergeAttrs.Rd b/man/dot-mergeAttrs.Rd
index 3410abf..457b1dc 100644
--- a/man/dot-mergeAttrs.Rd
+++ b/man/dot-mergeAttrs.Rd
@@ -4,7 +4,7 @@
 \alias{.mergeAttrs}
 \title{Merge samples defined in sample table with ones in subsample table(s)}
 \usage{
-.mergeAttrs(.Object, subsampleAannotationPaths)
+.mergeAttrs(.Object, subsampleAannotationPaths, subsamplesTables = NULL)
 }
 \arguments{
 \item{.Object}{an object of \code{"\linkS4class{Project}"}}
diff --git a/man/dot-modifySamplesFetched.Rd b/man/dot-modifySamplesFetched.Rd
new file mode 100644
index 0000000..231d785
--- /dev/null
+++ b/man/dot-modifySamplesFetched.Rd
@@ -0,0 +1,18 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/project.R
+\name{.modifySamplesFetched}
+\alias{.modifySamplesFetched}
+\title{Perform all the sample attribute modifications for fetched PEPs}
+\usage{
+.modifySamplesFetched(object, subsamples)
+}
+\arguments{
+\item{object}{an object of \code{"\linkS4class{Project}"}}
+}
+\value{
+modified Project object
+}
+\description{
+Perform all the sample attribute modifications for fetched PEPs
+}
+\keyword{internal}
diff --git a/man/fetchPEP.Rd b/man/fetchPEP.Rd
new file mode 100644
index 0000000..b409584
--- /dev/null
+++ b/man/fetchPEP.Rd
@@ -0,0 +1,20 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/utils.R
+\name{fetchPEP}
+\alias{fetchPEP}
+\title{Fetch a PEP from PEPhub using a registry path (namespace/project:tag)}
+\usage{
+fetchPEP(registryPath, raw = TRUE)
+}
+\arguments{
+\item{registryPath}{a string for the PEP registry path (namespace/project:tag)}
+
+\item{raw}{a boolean for whether to return a raw PEP}
+}
+\value{
+a list, with sublists for config, sample_list, and subsample_list for the fetched PEP
+}
+\description{
+Calls the PEPhub API to fetch PEPs.
+}
+\keyword{internal}
diff --git a/man/pepr.Rd b/man/pepr.Rd
index 0f7739b..223e7ed 100644
--- a/man/pepr.Rd
+++ b/man/pepr.Rd
@@ -2,6 +2,7 @@
 % Please edit documentation in R/pepr.R
 \docType{package}
 \name{pepr}
+\alias{pepr-package}
 \alias{pepr}
 \title{pepr}
 \description{
@@ -9,6 +10,13 @@ Package documentation
 }
 \references{
 GitHub: \url{https://github.com/pepkit/pepr}, Documentation: \url{https://code.databio.org/pepr/}
+}
+\seealso{
+Useful links:
+\itemize{
+  \item Report bugs at \url{https://github.com/pepkit/pepr}
+}
+
 }
 \author{
 Michal Stolarczyk, Nathan Sheffield
diff --git a/man/pullProject.Rd b/man/pullProject.Rd
new file mode 100644
index 0000000..4bcab77
--- /dev/null
+++ b/man/pullProject.Rd
@@ -0,0 +1,21 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/project.R
+\name{pullProject}
+\alias{pullProject}
+\title{Pull a PEP from PEPhub API}
+\usage{
+pullProject(registryPath = NULL)
+}
+\arguments{
+\item{registryPath}{a string specifying a registry path from PEPhub}
+}
+\value{
+an object of \code{"\linkS4class{Project}"}
+}
+\description{
+This is a helper that creates the project with empty samples and config slots
+}
+\examples{
+registryPath = 'databio/example:default'
+p=pullProject(registryPath)
+}
diff --git a/man/saveJWT.Rd b/man/saveJWT.Rd
new file mode 100644
index 0000000..b92e3dd
--- /dev/null
+++ b/man/saveJWT.Rd
@@ -0,0 +1,17 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/utils.R
+\name{saveJWT}
+\alias{saveJWT}
+\title{Save or update JWT}
+\usage{
+saveJWT(jwt)
+}
+\arguments{
+\item{jwt}{a string for the new jwt to save}
+}
+\value{
+a boolean for whether the authentication token was saved
+}
+\description{
+Save or update local authentication token to fetch private PEPs
+}
diff --git a/man/saveProject.Rd b/man/saveProject.Rd
new file mode 100644
index 0000000..fa04237
--- /dev/null
+++ b/man/saveProject.Rd
@@ -0,0 +1,21 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/utils.R
+\name{saveProject}
+\alias{saveProject}
+\title{Save a modified PEP Project to a local directory}
+\usage{
+saveProject(project = NULL, outputDir = getwd(), overwrite = FALSE)
+}
+\arguments{
+\item{project}{a PEP Project}
+
+\item{outputDir}{a string for the output directory, defaults to current working directory}
+
+\item{overwrite}{a boolean for whether to overwrite an existing project at the output directory}
+}
+\value{
+a boolean, TRUE if the save was successful and FALSE if otherwise
+}
+\description{
+This is a helper that saves a PEP Project to a local output directory
+}
diff --git a/tests/testthat/test_project.R b/tests/testthat/test_project.R
index 7834bbb..fe7bc7c 100644
--- a/tests/testthat/test_project.R
+++ b/tests/testthat/test_project.R
@@ -157,6 +157,17 @@ test_that("Project constructor throws errors if nonexistant init files are provi
   expect_error(Project(file = "test.yaml"))
 })
 
+context("Pull test PEP from PEPhub")
+
+test_that("Pulling public PEP from PEPhub creates Project object", {
+  expect_is(pullProject(registryPath = "databio/example:default"), "Project")
+})
+
+context("Attempt to pull invalid registry path")
+
+test_that("pullProject throws error if invalid registry path is provided", {
+  expect_error(pullProject(registryPath = "invalid path"))
+})
 
 context("Sample automerging")
 
diff --git a/vignettes/gettingStarted.Rmd b/vignettes/gettingStarted.Rmd
index 0f75385..f5fd9ee 100644
--- a/vignettes/gettingStarted.Rmd
+++ b/vignettes/gettingStarted.Rmd
@@ -43,7 +43,19 @@ Loading your project metadata into R is a single line of code:
 p = pepr::Project(file=projectConfigFile)
 ```
 
-That's it! You've now have a `Project` object, *p*, to interact with in `R`.
+That's it! You now have a `Project` object, *p*, to interact with in `R`. You can also use PEPhub registry paths to fetch them online:
+
+```{r}
+p2 = pepr::pullProject(registryPath='databio/example:default')
+```
+
+To fetch private PEPs, use PEPhub Client to login and generate an authentication token. Or, login to PEPhub and generate a new key to save it locally:
+
+```{r, eval=FALSE}
+pepr::saveJWT('*your authetication token goes here*')
+```
+
+You should then be able to fetch your private PEPs by registry path.
 
 ## Interfacing with your `pepr::Project` object in R
 
@@ -65,4 +77,10 @@ And you can also access the project configuration metadata with the `config()` f
 config(p)
 ```
 
+If you would like to save your project to a new directory, use the `saveProject()` function:
+
+```{r}
+saveProject(p2, outputDir=tempdir())
+```
+
 Follow the other vignettes for more advanced capabilities of `pepr`.