refactor: rename package from reneeTools to MOSuite

.Rbuildignore

@@ -1,4 +1,4 @@
-^reneeTools\.Rproj$
+^MOSuite\.Rproj$
 ^\.Rproj\.user$
 ^LICENSE\.md$
 ^_pkgdown\.yml$

.github/CONTRIBUTING.md

@@ -1,4 +1,4 @@
-# Contributing to reneeTools
+# Contributing to MOSuite
 
 ## Proposing changes with issues
 
@@ -15,7 +15,7 @@ so others will know you're working on it.
 We use [GitHub Flow](https://docs.github.com/en/get-started/using-github/github-flow)
 as our collaboration process.
 Follow the steps below for detailed instructions on contributing changes to
-reneeTools.
+MOSuite.
 
 ![GitHub Flow diagram](./img/GitHub-Flow_bg-white.png)
 
@@ -28,10 +28,10 @@ Otherwise, you will first need to
 the repo and clone your fork. You only need to do this step once.
 
 ```sh
-git clone https://github.com/CCBR/reneeTools
+git clone https://github.com/CCBR/MOSuite
 ```
 
-> Cloning into 'reneeTools'... <br>
+> Cloning into 'MOSuite'... <br>
 > remote: Enumerating objects: 1136, done. <br>
 > remote: Counting objects: 100% (463/463), done. <br>
 > remote: Compressing objects: 100% (357/357), done. <br>
@@ -40,7 +40,7 @@ git clone https://github.com/CCBR/reneeTools
 > Resolving deltas: 100% (530/530), done. <br>
 
 ```sh
-cd reneeTools
+cd MOSuite
 ```
 
 ### If this is your first time cloning the repo, install dependencies
@@ -204,22 +204,22 @@ git push --set-upstream origin iss-10
 > remote: Resolving deltas: 100% (3/3), completed with 3 local objects. <br>
 > remote: <br>
 > remote: Create a pull request for 'iss-10' on GitHub by visiting: <br>
-> remote: https://github.com/CCBR/reneeTools/pull/new/iss-10 <br>
+> remote: https://github.com/CCBR/MOSuite/pull/new/iss-10 <br>
 > remote: <br>
-> To https://github.com/CCBR/reneeTools <br>
+> To https://github.com/CCBR/MOSuite <br>
 > <br>
 >   [new branch] iss-10 -> iss-10 <br>
 >   branch 'iss-10' set up to track 'origin/iss-10'. <br>
 
 We recommend pushing your commits often so they will be backed up on GitHub.
 You can view the files in your branch on GitHub at
-`https://github.com/CCBR/reneeTools/tree/<your-branch-name>`
+`https://github.com/CCBR/MOSuite/tree/<your-branch-name>`
 (replace `<your-branch-name>` with the actual name of your branch).
 
 ### Create the PR
 
 Once your branch is ready, create a PR on GitHub:
-<https://github.com/CCBR/reneeTools/pull/new/>
+<https://github.com/CCBR/MOSuite/pull/new/>
 
 Select the branch you just pushed:
 

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -5,7 +5,7 @@ body:
   - type: markdown
     attributes:
       value: |
-        Before you submit this issue, please check the documentation: <https://ccbr.github.io/reneeTools/>
+        Before you submit this issue, please check the documentation: <https://ccbr.github.io/MOSuite/>
 
   - type: textarea
     id: description
@@ -22,7 +22,7 @@ body:
       description: Please include a minimal reproducible example (AKA a reprex). If you've never heard of a [reprex](http://reprex.tidyverse.org/) before, start by reading <https://www.tidyverse.org/help/#reprex>.
       render: console
       placeholder: |
-        library(reneeTools)
+        library(MOSuite)
         ... insert_your_code_here() ...
 
         Paste some output where something broke
@@ -40,6 +40,6 @@ body:
       label: System information
       description: |
         * Version of R
-        * Version of CCBR/reneeTools
+        * Version of CCBR/MOSuite
         * OS _(eg. Ubuntu Linux, macOS)_
         * Hardware _(eg. HPC, Desktop)_

.github/ISSUE_TEMPLATE/config.yml

@@ -1,4 +1,4 @@
 contact_links:
   - name: Discussions
-    url: https://github.com/CCBR/reneeTools/discussions
+    url: https://github.com/CCBR/MOSuite/discussions
     about: Please ask and answer questions here.

.github/workflows/docker.yml

@@ -6,7 +6,7 @@ on:
     types: [published]
 
 env:
-  IMAGE_NAME: "reneeTools"
+  IMAGE_NAME: "MOSuite"
   CONTEXT: "./"
   NAMESPACE: "nciccbr"
 

CITATION.cff

@@ -4,32 +4,35 @@
 # --------------------------------------------
 
 cff-version: 1.2.0
-message: 'To cite package "reneeTools" in publications use:'
+message: 'To cite package "MOSuite" in publications use:'
 type: software
 license: MIT
-title: 'reneeTools: Helper functions for RENEE'
+title: 'MOSuite: R package for downstream multi-omics analysis'
 version: 0.0.0.9000
 abstract: TODO What the package does (one paragraph).
 authors:
-- family-names: Koparde
-  given-names: Vishal
-  email: [email protected]
-  orcid: https://orcid.org/0000-0001-8978-8495
 - family-names: Sovacool
   given-names: Kelly
   email: [email protected]
   orcid: https://orcid.org/0000-0003-3283-829X
+- family-names: Homan
+  given-names: Philip
+  email: [email protected]
+- family-names: Koparde
+  given-names: Vishal
+  email: [email protected]
+  orcid: https://orcid.org/0000-0001-8978-8495
 - family-names: Chill
   given-names: Samantha
   email: [email protected]
   orcid: https://orcid.org/0000-0002-8734-9875
-repository-code: https://github.com/CCBR/reneeTools
-url: https://ccbr.github.io/reneeTools/
+repository-code: https://github.com/CCBR/MOSuite
+url: https://ccbr.github.io/MOSuite/
 contact:
-- family-names: Koparde
-  given-names: Vishal
-  email: vishal.koparde@nih.gov
-  orcid: https://orcid.org/0000-0001-8978-8495
+- family-names: Sovacool
+  given-names: Kelly
+  email: kelly.sovacool@nih.gov
+  orcid: https://orcid.org/0000-0003-3283-829X
 references:
 - type: software
   title: 'R: A Language and Environment for Statistical Computing'
@@ -320,7 +323,7 @@ references:
   title: S7
   abstract: 'S7: An Object Oriented System Meant to Become a Successor to S3 and S4'
   notes: Imports
-  url: https://github.com/rconsortium/S7/
+  url: https://rconsortium.github.io/S7/
   repository: https://CRAN.R-project.org/package=S7
   authors:
   - family-names: Vaughan

DESCRIPTION

@@ -1,20 +1,20 @@
-Package: reneeTools
-Title: Helper functions for RENEE
+Package: MOSuite
+Title: R package for downstream multi-omics analysis
 Version: 0.0.0.9000
 Authors@R: c(
-    person("Vishal", "Koparde", , "[email protected]", role = c("aut", "cre"),
-           comment = c(ORCID = "0000-0001-8978-8495")),
-    person("Kelly", "Sovacool", , "[email protected]", role = "aut",
+    person("Kelly", "Sovacool", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0003-3283-829X")),
+    person("Philip", "Homan", , "[email protected]", role = "aut"),
+    person("Vishal", "Koparde", , "[email protected]", role = "aut",
+           comment = c(ORCID = "0000-0001-8978-8495")),
     person("Samantha", "Chill", , "[email protected]", role = "aut",
            comment = c(ORCID = "0000-0002-8734-9875")),
     person("CCR Collaborative Bioinformatics Resource", role = "cph")
   )
 Description: TODO What the package does (one paragraph).
 License: MIT + file LICENSE
-URL: https://github.com/CCBR/reneeTools,
-    https://ccbr.github.io/reneeTools/
-BugReports: https://github.com/CCBR/reneeTools/issues
+URL: https://github.com/CCBR/MOSuite, https://ccbr.github.io/MOSuite/
+BugReports: https://github.com/CCBR/MOSuite/issues
 Depends:
     R (>= 2.10)
 Imports:

Dockerfile

@@ -91,8 +91,8 @@ RUN mamba install -c conda-forge \
   r-devtools
 
 # install R package
-COPY . /opt2/reneeTools
-RUN R -e "devtools::install_local('/opt2/reneeTools', dependencies = TRUE)"
+COPY . /opt2/MOSuite
+RUN R -e "devtools::install_local('/opt2/MOSuite', dependencies = TRUE)"
 
 # Save Dockerfile in the docker
 COPY Dockerfile /opt2/Dockerfile_${REPONAME}.${BUILD_TAG}

NAMESPACE

@@ -2,8 +2,8 @@
 
 export("%>%")
 export(calc_cpm)
-export(create_reneeDataSet_from_dataframes)
-export(create_reneeDataSet_from_files)
+export(create_multiOmicDataSet_from_dataframes)
+export(create_multiOmicDataSet_from_files)
 export(filter_counts)
 export(meta_tbl_to_dat)
 export(run_deseq2)

NEWS.md

@@ -1,14 +1,15 @@
-# reneeTools development version 0.0.0.9000
+# MOSuite development version 0.0.0.9000
 
-This is the first release of reneeTools 🎉
+This is the first release of MOSuite 🎉
 
-- Create a `NEWS.md` file to track changes to the package.
+- Note: at the start of development, this package was called reneeTools.
+  Later it was renamed to MOSuite. (#76, @kelly-sovacool)
 
 ## Main functions & classes
 
-- `reneeDataSet` (#16, #28, @kelly-sovacool)
-  - `create_reneeDataSet_from_files()`
-  - `create_reneeDataSet_from_dataframes()`
+- `multiOmicDataSet` (#16, #28, @kelly-sovacool)
+  - `create_multiOmicDataSet_from_files()`
+  - `create_multiOmicDataSet_from_dataframes()`
 - `run_deseq2()`
 - `calc_cpm()` (#38, @kelly-sovacool)
 - `filter_counts()` (#38, @kelly-sovacool)

R/0_renee-class.R → R/0_mo-class.R

@@ -1,11 +1,11 @@
-#' reneeDataSet class
+#' multiOmicDataSet class
 #'
 #' @param sample_meta_dat sample metadata as a data frame or tibble.
 #'   Must contain a `sample_id` column.
 #' @param counts_lst named list of dataframes containing counts, e.g. expected gene counts from RSEM. Each data frame is expected to contain a `gene_id` column and a column for each sample ID in the metadata.
 #'
 #'
-reneeDataSet <- S7::new_class("renee",
+multiOmicDataSet <- S7::new_class("multiOmicDataSet",
   properties = list(
     sample_meta = S7::class_data.frame,
     counts = S7::class_list, # list of data frames
@@ -29,49 +29,49 @@ reneeDataSet <- S7::new_class("renee",
   }
 )
 
-#' Construct a reneeDataSet object from tsv files.
+#' Construct a multiOmicDataSet object from tsv files.
 #'
 #' @param sample_meta_filepath path to tsv file with sample IDs and metadata for differential analysis.
 #' @param gene_counts_filepath path to tsv file of expected gene counts from RSEM.
 #' @param count_type type to assign the values of `gene_counts_filepath` to in the `counts` slot
 #' @param sample_id_colname name of the column in `sample_meta_filepath` that contains the sample IDs
 #'
-#' @return reneeDataSet object
+#' @return multiOmicDataSet object
 #' @export
 #'
 #' @examples
-#' renee_ds <- create_reneeDataSet_from_files(
+#' moo <- create_multiOmicDataSet_from_files(
 #'   sample_meta_filepath = system.file("extdata",
 #'     "sample_metadata.tsv.gz",
-#'     package = "reneeTools"
+#'     package = "MOSuite"
 #'   ),
 #'   gene_counts_filepath = system.file("extdata",
 #'     "RSEM.genes.expected_count.all_samples.txt.gz",
-#'     package = "reneeTools"
+#'     package = "MOSuite"
 #'   )
 #' )
-#' renee_ds@counts$raw %>% head()
-#' renee_ds@sample_meta
-create_reneeDataSet_from_files <- function(sample_meta_filepath, gene_counts_filepath,
-                                           count_type = "raw",
-                                           sample_id_colname = "sample_id") {
+#' moo@counts$raw %>% head()
+#' moo@sample_meta
+create_multiOmicDataSet_from_files <- function(sample_meta_filepath, gene_counts_filepath,
+                                               count_type = "raw",
+                                               sample_id_colname = "sample_id") {
   count_dat <- readr::read_tsv(gene_counts_filepath)
   sample_meta_dat <- readr::read_tsv(sample_meta_filepath)
-  return(create_reneeDataSet_from_dataframes(
+  return(create_multiOmicDataSet_from_dataframes(
     sample_meta_dat = sample_meta_dat,
     count_dat = count_dat,
     count_type = "raw",
     sample_id_colname = sample_id_colname
   ))
 }
 
-#' Construct a reneeDataSet object from data frames
+#' Construct a multiOmicDataSet object from data frames
 #'
-#' @inheritParams reneeDataSet
-#' @inheritParams create_reneeDataSet_from_files
+#' @inheritParams multiOmicDataSet
+#' @inheritParams create_multiOmicDataSet_from_files
 #' @param count_dat data frame of feature counts (e.g. expected gene counts from RSEM)
 #'
-#' @return reneeDataSet object
+#' @return multiOmicDataSet object
 #' @export
 #'
 #' @examples
@@ -82,11 +82,11 @@ create_reneeDataSet_from_files <- function(sample_meta_filepath, gene_counts_fil
 #'     levels = c("wildtype", "knockout")
 #'   )
 #' )
-#' create_reneeDataSet_from_dataframes(sample_meta, gene_counts)
-create_reneeDataSet_from_dataframes <- function(sample_meta_dat,
-                                                count_dat,
-                                                sample_id_colname = "sample_id",
-                                                count_type = "raw") {
+#' create_multiOmicDataSet_from_dataframes(sample_meta, gene_counts)
+create_multiOmicDataSet_from_dataframes <- function(sample_meta_dat,
+                                                    count_dat,
+                                                    sample_id_colname = "sample_id",
+                                                    count_type = "raw") {
   gene_columns <- c("gene_id", "GeneName", "Gene")
   # sample IDs must be in the same order
   gene_sample_colnames <- count_dat %>%
@@ -109,5 +109,5 @@ create_reneeDataSet_from_dataframes <- function(sample_meta_dat,
   counts <- list()
   counts[[count_type]] <- count_dat
 
-  return(reneeDataSet(sample_meta_dat, counts))
+  return(multiOmicDataSet(sample_meta_dat, counts))
 }

R/reneeTools-package.R → R/MOSuite-package.R

@@ -1,6 +1,6 @@
-#' reneeTools: R helper functions for RENEE
+#' MOSuite: R helper functions for RENEE
 #'
-#' `reneeTools` implements helper functions for RENEE, a comprehensive
+#' `MOSuite` implements helper functions for RENEE, a comprehensive
 #' quality-control and quantification RNA-seq pipeline
 #'
 #' @keywords internal

R/counts.R

@@ -1,9 +1,9 @@
-#' Calculate counts-per-million (CPM) on raw counts in a reneeDataSet
+#' Calculate counts-per-million (CPM) on raw counts in a multiOmicDataSet
 #'
-#' @param renee_ds reneeDataSet object
+#' @param moo multiOmicDataSet object
 #' @param ... additional arguments to pass to edgeR::cpm()
 #'
-#' @return reneeDataSet with cpm-transformed counts
+#' @return multiOmicDataSet with cpm-transformed counts
 #' @export
 #'
 #' @examples
@@ -14,17 +14,17 @@
 #'     levels = c("wildtype", "knockout")
 #'   )
 #' )
-#' renee_ds <- create_reneeDataSet_from_dataframes(sample_meta, gene_counts) %>%
+#' moo <- create_multiOmicDataSet_from_dataframes(sample_meta, gene_counts) %>%
 #'   calc_cpm()
-#' head(renee_ds@counts$cpm)
-calc_cpm <- S7::new_generic("calc_cpm", "renee_ds", function(renee_ds, ...) {
+#' head(moo@counts$cpm)
+calc_cpm <- S7::new_generic("calc_cpm", "moo", function(moo, ...) {
   S7::S7_dispatch()
 })
 
-S7::method(calc_cpm, reneeDataSet) <- function(renee_ds, gene_colname = "gene_id", ...) {
-  renee_ds@counts$cpm <- renee_ds@counts$raw %>%
+S7::method(calc_cpm, multiOmicDataSet) <- function(moo, gene_colname = "gene_id", ...) {
+  moo@counts$cpm <- moo@counts$raw %>%
     calc_cpm_df(gene_colname = gene_colname)
-  return(renee_ds)
+  return(moo)
 }
 
 #' Calculate CPM on a data frame