Package: ATACseqTFEA 1.7.0

Jianhong Ou

ATACseqTFEA: Transcription Factor Enrichment Analysis for ATAC-seq

Assay for Transpose-Accessible Chromatin using sequencing (ATAC-seq) is a technique to assess genome-wide chromatin accessibility by probing open chromatin with hyperactive mutant Tn5 Transposase that inserts sequencing adapters into open regions of the genome. ATACseqTFEA is an improvement of the current computational method that detects differential activity of transcription factors (TFs). ATACseqTFEA not only uses the difference of open region information, but also (or emphasizes) the difference of TFs footprints (cutting sites or insertion sites). ATACseqTFEA provides an easy, rigorous way to broadly assess TF activity changes between two conditions.

Authors:Jianhong Ou [aut, cre]

ATACseqTFEA_1.7.0.tar.gz
ATACseqTFEA_1.7.0.zip(r-4.5)ATACseqTFEA_1.7.0.zip(r-4.4)ATACseqTFEA_1.7.0.zip(r-4.3)
ATACseqTFEA_1.7.0.tgz(r-4.4-any)ATACseqTFEA_1.7.0.tgz(r-4.3-any)
ATACseqTFEA_1.7.0.tar.gz(r-4.5-noble)ATACseqTFEA_1.7.0.tar.gz(r-4.4-noble)
ATACseqTFEA_1.7.0.tgz(r-4.4-emscripten)ATACseqTFEA_1.7.0.tgz(r-4.3-emscripten)
ATACseqTFEA.pdf |ATACseqTFEA.html✨
ATACseqTFEA/json (API)
NEWS

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

Peer review:

Bug tracker:https://github.com/jianhong/atacseqtfea/issues

On BioConductor:ATACseqTFEA-1.7.0(bioc 3.20)ATACseqTFEA-1.6.0(bioc 3.19)

bioconductor-package

20 exports 0.49 score 123 dependencies

Last updated 2 months agofrom:f88ce035df

Exports:calWeightscoercecount5endscountsNormalizationDBscoredoTFEAESvolcanoploteventsFilterexpandBindingSitesgetBindingSitesgetEnrichmentScoregetMotifIDgetWeightedBindingScoreimportFimoBindingSitesplotESprepareBindingSitesreduceByPercentageshowTFEATFEAresults

Dependencies:abindannotateAnnotationDbiaskpassBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobBSgenomecachemcaToolsclicliprCNErcodetoolscolorspacecpp11crayoncurlDBIDelayedArrayDirichletMultinomialdplyrfansifarverfastmapformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesggplot2ggrepelglueGO.dbgtablegtoolshmshttrIRangesisobandjsonliteKEGGRESTlabelinglambda.rlatticelifecyclelimmamagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemotifmatchrmunsellnlmeopensslpillarpkgconfigplogrplyrpngpoweRlawpracmaprettyunitsprogresspwalignR.methodsS3R.ooR.utilsR6RColorBrewerRcppRcppArmadilloRCurlreadrreshape2restfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsscalesseqLogosnowSparseArraystatmodstringistringrSummarizedExperimentsysTFBSToolsTFMPvaluetibbletidyselecttzdbUCSC.utilsutf8vctrsviridisLitevroomwithrXMLxtableXVectoryamlzlibbioc

ATACseqTFEA Guide

Jianhong Ou

Rendered fromATACseqTFEA.Rmdusingknitr::rmarkdownon Jul 05 2024.

Last update: 2022-06-21
Started: 2020-05-12

Readme and manuals

Help Manual

Help pageTopics
Transcription Factor Enrichment Analysis for ATAC-seqATACseqTFEA-package ATACseqTFEA
Calculate the weights for binding scorecalWeights
Prepare counts matrix for enrichment analysiscount5ends
Normalize counts by width of count regioncountsNormalization
Differential binding analysisDBscore
Transcription factor enrichment analysisdoTFEA
Plot enrichment score for one transcription factorESvolcanoplot
Filter the RangedSummarizedExperiment objectseventsFilter
Prepare the genomic ranges for proximal and distal regions for countingexpandBindingSites
Data in extdatacluster_PWMs extdata PWMatrixList
The methods for TFEAresults-class$,TFEAresults-method $<-,TFEAresults-method as,TFEAresults,data.frame-method coerce,TFEAresults,data.frame-method getBindingSites getBindingSites,TFEAresults-method getEnrichmentScore getEnrichmentScore,TFEAresults-method getMotifID getMotifID,TFEAresults-method show,TFEAresults-method TFEAresults-methods [[,TFEAresults,ANY,ANY-method [[<-,TFEAresults,ANY,ANY-method
Calculate the weighted binding scoregetWeightedBindingScore
Prepare binding site by fimo resultsimportFimoBindingSites
Plot enrichment score for one transcription factorplotES
Prepare binding site for TFEAprepareBindingSites
Reduce by percentage of overlaps of GRanges objectreduceByPercentage
Transcription factor enrichment analysisTFEA
Class '"TFEAresults"'TFEAresults TFEAresults-class