Package: profileplyr 1.23.0

Tom Carroll

profileplyr: Visualization and annotation of read signal over genomic ranges with profileplyr

Quick and straightforward visualization of read signal over genomic intervals is key for generating hypotheses from sequencing data sets (e.g. ChIP-seq, ATAC-seq, bisulfite/methyl-seq). Many tools both inside and outside of R and Bioconductor are available to explore these types of data, and they typically start with a bigWig or BAM file and end with some representation of the signal (e.g. heatmap). profileplyr leverages many Bioconductor tools to allow for both flexibility and additional functionality in workflows that end with visualization of the read signal.

Authors:Tom Carroll and Doug Barrows

profileplyr_1.23.0.tar.gz
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profileplyr.pdf |profileplyr.html✨
profileplyr/json (API)
NEWS

# Install 'profileplyr' in R:
install.packages('profileplyr', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Datasets:
  • K27ac_GRlist_hind_liver_top5000 - GRangesList of the top 5000 H3K27ac peaks from hindbrain and liver downloaded from ENCODE
  • gene_list_character - Character vector of the top differentially expressed genes from hindbrain versus liver as measured by RNA-seq
  • gene_list_dataframe - Dataframe of top differentially expressed genes from hindbrain versus liver as measured by RNA-seq

On BioConductor:profileplyr-1.23.0(bioc 3.21)profileplyr-1.22.0(bioc 3.20)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

chipseqdataimportsequencingchiponchipcoverage

3.99 score 49 scripts 406 downloads 16 exports 196 dependencies

Last updated 23 days agofrom:580fe4151f. Checks:OK: 1 NOTE: 4 WARNING: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 31 2024
R-4.5-winNOTEOct 31 2024
R-4.5-linuxNOTEOct 31 2024
R-4.4-winNOTEOct 31 2024
R-4.4-macWARNINGOct 31 2024
R-4.3-winNOTEOct 31 2024
R-4.3-macWARNINGOct 31 2024

Exports:annotateRangesannotateRanges_greatas_profileplyrBamBigwig_to_chipProfileclusterRangesconvertToEnrichedHeatmapMatexport_deepToolsMatgenerateEnrichedHeatmapgenerateProfilePlotgroupByimport_deepToolsMatorderByparamssampleDatasampleData<-summarize

Dependencies:abindAnnotationDbiapeaplotaskpassbase64encBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobbootbslibcachemcaToolsChIPseekerchipseqcirclizecliclueclustercodetoolscolorspacecommonmarkComplexHeatmapcowplotcpp11crayoncrosstalkcurldata.tableDBIDelayedArraydeldirdigestdoParallelDOSEdplyrDTEnrichedHeatmapenrichplotevaluatefansifarverfastmapfastmatchfgseafontawesomeforeachformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesGetoptLongggforceggfunggnewscaleggplot2ggplotifyggrepelggtangleggtreeGlobalOptionsglueGO.dbGOSemSimgplotsgridGraphicsgtablegtoolshighrhmshtmltoolshtmlwidgetshttpuvhttrhwriterigraphinterpIRangesisobanditeratorsjpegjquerylibjsonliteKEGGRESTKernSmoothknitrlabelinglambda.rlaterlatticelatticeExtralazyevallifecyclelocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeopensslorg.Hs.eg.dborg.Mm.eg.dbpatchworkpheatmappillarpkgconfigplogrplotrixplyrpngpolyclippreprocessCoreprettyunitsprogresspromisespurrrpwalignqvalueR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRcppEigenRCurlreshape2restfulrrGREATRhtslibrjsonrlangrmarkdownRsamtoolsRSQLitertracklayerS4ArraysS4VectorssassscalesscatterpieshapeshinyShortReadsnowsoGGisourcetoolsSparseArraystringistringrSummarizedExperimentsyssystemfontstibbletidyrtidyselecttidytreetifftinytextreeiotweenrTxDb.Hsapiens.UCSC.hg19.knownGeneTxDb.Hsapiens.UCSC.hg38.knownGeneTxDb.Mmusculus.UCSC.mm10.knownGeneTxDb.Mmusculus.UCSC.mm9.knownGeneUCSC.utilsutf8vctrsviridisLitewithrxfunXMLxtableXVectoryamlyulab.utilszlibbioc

Visualization and annotation of read signal over genomic ranges with profileplyr

Doug Barrows and Tom Carroll

Rendered fromprofileplyr.Rmdusingknitr::rmarkdownon Oct 31 2024.

Last update: 2022-10-10
Started: 2019-04-10

Readme and manuals

Help Manual

Help pageTopics
Annotate profileplyr ranges to genes using ChIPseekerannotateRanges annotateRanges,profileplyr-method
Annotate profileplyr ranges to genes using rGREATannotateRanges_great annotateRanges_great,profileplyr-method
Import ChIPprofile object to profileplyras_profileplyr
BamBigwig_to_chipProfileBamBigwig_to_chipProfile
Cluster RangesclusterRanges clusterRanges,profileplyr-method
export a profileplyr object to a list of matrices that can be used as an input for EnrichedHeatmapconvertToEnrichedHeatmapMat convertToEnrichedHeatmapMat,profileplyr-method
Export and import profileplyr from/to deeptoolsexport_deepToolsMat export_deepToolsMat,profileplyr-method import_deepToolsMat
Character vector of the top differentially expressed genes from hindbrain versus liver as measured by RNA-seqgene_list_character
Dataframe of top differentially expressed genes from hindbrain versus liver as measured by RNA-seqgene_list_dataframe
generateEnrichedHeatmapgenerateEnrichedHeatmap
Import ChIPprofile object to profileplyrgenerateProfilePlot
group the rows and ranges of the profileplyr objectgroupBy groupBy,profileplyr-method
Redundant code for inheriting grouping wrapped into subsetbyRangeOverlap() or subsetbyGeneListOverlap() functionsinherit_group_function
GRangesList of the top 5000 H3K27ac peaks from hindbrain and liver downloaded from ENCODEK27ac_GRlist_hind_liver_top5000
choose the column by which to order the ranges by within each grouporderBy orderBy,profileplyr-method
Retrieve and set parameters in profileplyr objectparams
Join, subset and manipulate ChIPprofile objectsc,profileplyr-method profileplyr-class [,profileplyr,ANY,ANY,ANY-method
Retrieve and set sample data in profileplyr objectsampleData sampleData,profileplyr-method sampleData<- sampleData<-,profileplyr,DataFrame-method
Redundant code wrapped into subsetbyRangeOverlap() or subsetbyGeneListOverlap() functionssubset_GR_GL_common_top
Subset ranges based on overlap with lists of Gene setssubsetbyGeneListOverlap
Subset ranges based on overlap with a GRanges objectsubsetbyRangeOverlap
summarize the rows of a deepTools matrixsummarize summarize,profileplyr-method