Merge pull request #261 from databio/dev

v0.10.6 Release

.gitignore

@@ -46,4 +46,5 @@ examples/test_project/test_fseq.yaml
 examples/test_project/test_genrich.yaml
 examples/test_project/test_hmmratac.yaml
 examples/test_project/test_homer.yaml
-examples/test_project/test_macs.yaml
+examples/test_project/test_macs.yaml
+.Rproj.user

PEPATACr/DESCRIPTION

@@ -1,11 +1,13 @@
 Package: PEPATACr
 Title: Functions and libraries to analyze ATAC-seq data
-Version: 0.0.1.0000
+Version: 0.0.2.0000
 Authors@R: person("Jason", "Smith", email = "[email protected]", role = c("aut", "cre"))
 Maintainer: Jason Smith <[email protected]>
 Description: Installs required libraries to calculate the fraction of reads in features, TSS enrichments, and fragment length distributions. 
-Depends: R (>= 3.5.1), data.table, pepr, gplots, grid, ggplot2, optigrab, scales, GenomicDistributions
+BiocViews:
+Depends: R (>= 4.0), GenomicRanges
+Imports: data.table, pepr, gplots, grid, ggplot2, optigrab, scales, yaml, GenomicDistributions, GenomicDistributionsData
 License: BSD 2-Clause "Simplified" License
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.1.1
+RoxygenNote: 7.2.3

PEPATACr/NAMESPACE

@@ -23,3 +23,6 @@ export(sampleName)
 export(setPanelSize)
 export(splitDataTable)
 export(summarizer)
+import(data.table)
+import(ggplot2)
+import(optigrab)

PEPATACr/NAMESPACE.bak

@@ -0,0 +1,25 @@
+# Generated by roxygen2: do not edit by hand
+
+export(consensusPeaks)
+export(createAssetsSummary)
+export(createStatsSummary)
+export(fileIcon)
+export(getPrealignments)
+export(narrowPeakToBigBed)
+export(peakCounts)
+export(plotAlignedPct)
+export(plotAlignedRaw)
+export(plotAnno)
+export(plotComplexityCurves)
+export(plotFLD)
+export(plotFRiF)
+export(plotLibSizes)
+export(plotTSS)
+export(plotTSSscores)
+export(readPepatacPeakCounts)
+export(reducePeaks)
+export(roundUpNice)
+export(sampleName)
+export(setPanelSize)
+export(splitDataTable)
+export(summarizer)

PEPATACr/PEPATACr.Rproj

@@ -1,21 +1,21 @@
-Version: 1.0
-
-RestoreWorkspace: No
-SaveWorkspace: No
-AlwaysSaveHistory: Default
-
-EnableCodeIndexing: Yes
-UseSpacesForTab: Yes
-NumSpacesForTab: 4
-Encoding: UTF-8
-
-RnwWeave: Sweave
-LaTeX: pdfLaTeX
-
-AutoAppendNewline: Yes
-StripTrailingWhitespace: Yes
-
-BuildType: Package
-PackageUseDevtools: Yes
-PackageInstallArgs: --no-multiarch --with-keep.source
-PackageRoxygenize: rd,collate,namespace
+Version: 1.0
+
+RestoreWorkspace: No
+SaveWorkspace: No
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 4
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX
+
+AutoAppendNewline: Yes
+StripTrailingWhitespace: Yes
+
+BuildType: Package
+PackageUseDevtools: Yes
+PackageInstallArgs: --no-multiarch --with-keep.source
+PackageRoxygenize: rd,collate,namespace