Package: TFEA.ChIP 1.25.0

Laura Puente Santamaría

TFEA.ChIP: Analyze Transcription Factor Enrichment

Package to analize transcription factor enrichment in a gene set using data from ChIP-Seq experiments.

Authors:Laura Puente Santamaría, Luis del Peso

TFEA.ChIP_1.25.0.tar.gz
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TFEA.ChIP.pdf |TFEA.ChIP.html✨
TFEA.ChIP/json (API)
NEWS

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

Peer review:

Datasets:

On BioConductor:TFEA.ChIP-1.25.0(bioc 3.20)TFEA.ChIP-1.24.0(bioc 3.19)

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

bioconductor-package

16 exports 0.71 score 96 dependencies 8 mentions

Last updated 2 months agofrom:17c9186337

Exports:contingency_matrixGeneID2entrezget_chip_indexgetCMstatsGSEA_EnrichmentScoreGSEA_runmakeChIPGeneDBmatrixDB_to_listDBplot_CMplot_ESplot_RESpreprocessInputDatarankTFsSelect_genesset_user_datatxt2GR

Dependencies:abindAnnotationDbiaskpassBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocParallelbiomaRtBiostringsbitbit64bitopsblobcachemclicodetoolscpp11crayoncurlDBIdbplyrDelayedArraydigestdplyrfansifastmapfilelockformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesgluehmshttrhttr2IRangesjsonliteKEGGRESTlambda.rlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeopensslorg.Hs.eg.dbpillarpkgconfigplogrpngprettyunitsprogresspurrrR.methodsS3R.ooR.utilsR6rappdirsRCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorssnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselectUCSC.utilsutf8vctrswithrXMLxml2XVectoryamlzlibbioc

TFEA.ChIP: a tool kit for transcription factor enrichment analysis capitalizing on ChIP-seq datasets

Laura Puente-Santamaria, Luis del Peso

Rendered fromTFEA.ChIP.Rmdusingknitr::rmarkdownon Jun 30 2024.

Last update: 2022-02-03
Started: 2017-10-09

Readme and manuals

Help Manual

Help pageTopics
Metadata data frameARNT.metadata
ChIP-Seq datasetARNT.peaks.bed
TF-gene binding binary matrixChIPDB
Computes 2x2 contingency matricescontingency_matrix
DHS databseDnaseHS_db
List of Entrez Gene IDsEntrez.gene.IDs
Translates gene IDs from Gene Symbol or Ensemble ID to Entrez ID.GeneID2entrez
List of Entrez Gene IDsGenes.Upreg
Creates df containing accessions of ChIP-Seq datasets and TF.get_chip_index
Plots a color bar from log2(Fold Change) values.get_LFC_bar
Generate statistical parameters from a contingency_matrix outputgetCMstats
List of one ChIP-Seq datasetgr.list
Computes the weighted GSEA score of gene.set in gene.list.GSEA_EnrichmentScore
Calculate enrichment scores for a permutation test.GSEA_ESpermutations
Function to run a GSEA analysisGSEA_run
Output of the function GSEA.run from the TFEA.ChIP packageGSEA.result
Highlight certain transcription factors in a plotly graph.highlight_TF
RNA-Seq experimenthypoxia
RNA-Seq experimenthypoxia_DESeq
List of Entrez Gene IDslog2.FC
Make a ChIP - target databasemakeChIPGeneDB
Re-formatting ChIP-Gene databasematrixDB_to_listDB
TF-gene binding DB metadataMetaData
Makes an interactive html plot from an enrichment table.plot_CM
Plots Enrichment Score from the output of GSEA.run.plot_ES
Plots all the RES stored in a GSEA_run output.plot_RES
Extracts data from a DESeqResults object or a data frame.preprocessInputData
Rank the TFs in the output from 'getCMstats'rankTFs
Extracts genes according to logFoldChange and p-val limitsSelect_genes
Sets the data objects as default.set_user_data
Function to filter a ChIP-Seq input.txt2GR