Package: EpiCompare 1.11.0

Hiranyamaya Dash

EpiCompare: Comparison, Benchmarking & QC of Epigenomic Datasets

EpiCompare is used to compare and analyse epigenetic datasets for quality control and benchmarking purposes. The package outputs an HTML report consisting of three sections: (1. General metrics) Metrics on peaks (percentage of blacklisted and non-standard peaks, and peak widths) and fragments (duplication rate) of samples, (2. Peak overlap) Percentage and statistical significance of overlapping and non-overlapping peaks. Also includes upset plot and (3. Functional annotation) functional annotation (ChromHMM, ChIPseeker and enrichment analysis) of peaks. Also includes peak enrichment around TSS.

Authors:Sera Choi [aut], Brian Schilder [aut], Leyla Abbasova [aut], Alan Murphy [aut], Nathan Skene [aut], Thomas Roberts [ctb], Hiranyamaya Dash [cre]

EpiCompare_1.11.0.tar.gz
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EpiCompare.pdf |EpiCompare.html✨
EpiCompare/json (API)
NEWS

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

Peer review:

Bug tracker:https://github.com/neurogenomics/epicompare/issues

Datasets:

On BioConductor:EpiCompare-1.9.10(bioc 3.20)EpiCompare-1.8.1(bioc 3.19)

epigeneticsgeneticsqualitycontrolchipseqmultiplecomparisonfunctionalgenomicsatacseqdnaseseqbenchmarkbenchmarkingbioconductorbioconductor-packagecomparisonhtmlinteractive-reporting

7.55 score 12 stars 47 scripts 76 downloads 31 exports 183 dependencies

Last updated 23 days agofrom:5b7c54eb1c. Checks:OK: 3 NOTE: 4. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 30 2024
R-4.5-winNOTEOct 31 2024
R-4.5-linuxNOTEOct 30 2024
R-4.4-winNOTEOct 31 2024
R-4.4-macNOTEOct 31 2024
R-4.3-winOKOct 31 2024
R-4.3-macOKOct 31 2024

Exports:bpplapplycheck_workerscompute_consensus_peakscompute_corrdownload_buttonEpiComparefragment_infogather_filesgroup_filesliftover_grlistoverlap_heatmapoverlap_percentoverlap_stat_plotoverlap_upset_plotpeak_infoplot_ChIPseeker_annotationplot_chromHMMplot_corrplot_enrichmentplot_precision_recallprecision_recallpredict_precision_recallrebin_peaksreport_commandreport_headertidy_chromosomestidy_peakfiletranslate_genometss_plotwidth_boxplotwrite_example_peaks

Dependencies:abindAnnotationDbiAnnotationHubapeaplotaskpassb64base64encBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocManagerBiocParallelBiocVersionBiostringsbitbit64bitopsblobbootBSgenomebslibbspluscachemcaToolsChIPseekerclicliprcodetoolscolorspacecowplotcpp11crayoncrosstalkcurldata.tableDBIdbplyrDelayedArraydigestDOSEdownloadthisdplyrenrichplotevaluatefansifarverfastmapfastmatchfgseafilelockfontawesomeformatRfsfutile.loggerfutile.optionsgenericsgenomationGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesggforceggfunggnewscaleggplot2ggplotifyggrepelggtangleggtreeglueGO.dbGOSemSimgplotsgridBasegridGraphicsgtablegtoolshighrhmshtmltoolshtmlwidgetshttrigraphimputeIRangesisobandjquerylibjsonliteKEGGRESTKernSmoothknitrlabelinglambda.rlaterlatticelazyevallifecyclelubridatemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeopensslpatchworkpillarpkgconfigplogrplotlyplotrixplyrpngpolyclipprettyunitsprogresspromisespurrrqvalueR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRcppEigenRCurlreadrreshape2restfulrRhtslibrjsonrlangrmarkdownRsamtoolsRSQLitertracklayerS4ArraysS4VectorssassscalesscatterpieseqPatternsnowSparseArraystringistringrSummarizedExperimentsyssystemfontstibbletidyrtidyselecttidytreetimechangetinytextreeiotweenrTxDb.Hsapiens.UCSC.hg19.knownGenetzdbUCSC.utilsutf8vctrsviridisLitevroomwithrwritexlxfunXMLXVectoryamlyulab.utilszipzlibbioc

Docker/Singularity Containers

Authors: `r auths <- eval(parse(text = gsub('person','c',read.dcf('../DESCRIPTION', fields = 'Authors@R'))));paste(auths[names(auths)=='given'],auths[names(auths)=='family'], collapse = ', ')`

Rendered fromdocker.Rmdusingknitr::rmarkdownon Oct 30 2024.

Last update: 2022-06-14
Started: 2022-06-14

EpiCompare: Getting started

Authors: `r auths <- eval(parse(text = gsub('person','c',read.dcf('../DESCRIPTION', fields = 'Authors@R'))));paste(auths[names(auths)=='given'],auths[names(auths)=='family'], collapse = ', ')`

Rendered fromEpiCompare.Rmdusingknitr::rmarkdownon Oct 30 2024.

Last update: 2023-03-09
Started: 2022-03-21

Example report

Authors: `r auths <- eval(parse(text = gsub('person','c',read.dcf('../DESCRIPTION', fields = 'Authors@R'))));paste(auths[names(auths)=='given'],auths[names(auths)=='family'], collapse = ', ')`

Rendered fromexample_report.Rmdusingknitr::rmarkdownon Oct 30 2024.

Last update: 2023-03-09
Started: 2022-12-16

Readme and manuals

Help Manual

Help pageTopics
Wrapper for bplapplybpplapply
Check workerscheck_workers
Example CUT&Run peak fileCnR_H3K27ac
Example Picard duplication metrics file 2CnR_H3K27ac_picard
Example CUT&Tag peak fileCnT_H3K27ac
Example Picard duplication metrics file 1CnT_H3K27ac_picard
Compute consensus peakscompute_consensus_peaks
Compute correlation matrixcompute_corr
Download local filedownload_button
Example ChIP-seq peak fileencode_H3K27ac
Compare epigenomic datasetsEpiCompare
Summary on fragmentsfragment_info
Gather filesgather_files
Group filesgroup_files
Human genome hg19 blacklisted regionshg19_blacklist
Human genome hg38 blacklisted regionshg38_blacklist
Liftover peak listliftover_grlist
Mouse genome mm10 blacklisted regionsmm10_blacklist
Mouse genome mm9 blacklisted regionsmm9_blacklist
Generate heatmap of percentage overlapoverlap_heatmap
Calculate percentage of overlapping peaksoverlap_percent
Statistical significance of overlapping peaksoverlap_stat_plot
Generate Upset plot for overlapping peaksoverlap_upset_plot
Summary of Peak Informationpeak_info
Create ChIPseeker annotation plotplot_ChIPseeker_annotation
Plot ChromHMM heatmapplot_chromHMM
Plot correlation of peak filesplot_corr
Generate enrichment analysis plotsplot_enrichment
Plot precision-recall curvesplot_precision_recall
Compute precision-recallprecision_recall
Predict precision-recallpredict_precision_recall
Rebin peaksrebin_peaks
Report commandreport_command
Report headerreport_header
Tidy peakfiles in GRangestidy_peakfile
Translate genometranslate_genome
Read count frequency around TSStss_plot
Peak width boxplotwidth_boxplot
Write example peakswrite_example_peaks