Package: FindIT2 1.19.0

Guandong Shang

FindIT2: find influential TF and Target based on multi-omics data

This package implements functions to find influential TF and target based on different input type. It have five module: Multi-peak multi-gene annotaion(mmPeakAnno module), Calculate regulation potential(calcRP module), Find influential Target based on ChIP-Seq and RNA-Seq data(Find influential Target module), Find influential TF based on different input(Find influential TF module), Calculate peak-gene or peak-peak correlation(peakGeneCor module). And there are also some other useful function like integrate different source information, calculate jaccard similarity for your TF.

Authors:Guandong Shang [aut, cre]

FindIT2_1.19.0.tar.gz
FindIT2_1.19.0.zip(r-4.7)FindIT2_1.19.0.zip(r-4.6)FindIT2_1.19.0.zip(r-4.5)
FindIT2_1.19.0.tgz(r-4.6-any)FindIT2_1.19.0.tgz(r-4.5-any)
FindIT2_1.19.0.tar.gz(r-4.7-any)FindIT2_1.19.0.tar.gz(r-4.6-any)
FindIT2_1.19.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html
card.svg |card.png
FindIT2/json (API)
NEWS

# Install 'FindIT2' in R:
install.packages('FindIT2', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/shangguandong1996/findit2/issues

Datasets:

On BioConductor:FindIT2-1.19.0(bioc 3.24)FindIT2-1.18.0(bioc 3.23)

softwareannotationchipseqatacseqgeneregulationmultiplecomparisongenetarget

5.26 score 6 stars 7 scripts 384 downloads 23 exports 103 dependencies

Last updated from:997663b012. Checks:1 NOTE, 9 OK. Indexed: yes.

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bioc-checksNOTE231
linux-devel-x86_64OK536
source / vignettesOK381
linux-release-x86_64OK458
macos-release-arm64OK246
macos-oldrel-arm64OK340
windows-develOK377
windows-releaseOK481
windows-oldrelOK402
wasm-releaseOK186

Exports:calcRP_coveragecalcRP_regioncalcRP_TFHitenhancerPromoterCorfindIT_enrichFisherfindIT_enrichWilcoxfindIT_MARAfindIT_regionRPfindIT_TFHitfindIT_TTPairgetAssocPairNumberintegrate_ChIP_RNAintegrate_replicatesjaccard_findIT_enrichFisherjaccard_findIT_TTpairloadPeakFilemm_geneBoundmm_geneScanmm_nearestGenepeakGeneCorplot_annoDistanceplot_peakGeneAlias_summaryplot_peakGeneCor

Dependencies:abindAnnotationDbiaskpassBHBiobaseBiocBaseUtilsBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobcachemcigarilloclicodetoolscpp11crayoncurlDBIDelayedArraydplyrfarverfastmapforeachformatRfutile.loggerfutile.optionsgenericsGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2ggrepelglmnetgluegtablehmshttrIRangesisobanditeratorsjsonliteKEGGRESTlabelinglambda.rlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeMultiAssayExperimentopensslpatchworkpillarpkgconfigplyrpngprettyunitsprogresspurrrqvalueR6RColorBrewerRcppRcppEigenRCurlreshape2restfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsS7scalesSeqinfoshapesnowSparseArraystringistringrSummarizedExperimentsurvivalsystibbletidyrtidyselectutf8vctrsviridisLitewithrXMLXVectoryaml

FindIT2:Find influential TF and influential Target

Rendered fromFindIT2.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2022-05-10
Started: 2021-06-08

Readme and manuals

Help Manual

Help pageTopics
ATAC normCount of E50h-72h in Chr5ATAC_normCount
calcRP_coveragecalcRP_coverage
calcRP_regioncalcRP_region
calcRP_TFHitcalcRP_TFHit
enhancerPromoterCorenhancerPromoterCor
findI(nfluential)T(F)_enrichFisherfindIT_enrichFisher
findIT_enrichWilcoxfindIT_enrichWilcox
findIT_MARAfindIT_MARA
findI(nfluential)T(F)_regionRPfindIT_regionRP
findI(nfluential)T(F)_TFHitfindIT_TFHit
findI(nfluential)T(F)_T(F)T(arget)PairfindIT_TTPair
getAssocPairNumbergetAssocPairNumber
integrate_ChIP_RNAintegrate_ChIP_RNA
integrate_replicatesintegrate_replicates
jaccard_findIT_enrichFisherjaccard_findIT_enrichFisher
jaccard_findIT_TTpairjaccard_findIT_TTpair
loadPeakFileloadPeakFile
mm_geneBoundmm_geneBound
mm_geneScanmm_geneScan
mm_nearestGenemm_nearestGene
peakGeneCorpeakGeneCor
plot_annoDistanceplot_annoDistance
plot_peakGeneAlias_summaryplot_peakGeneAlias_summary
plot_peakGeneCorplot_peakGeneCor
RNA normCount of E50h-72h in Chr5RNA_normCount
RNA diff result from LEC2_GR VS LEC2_DMSORNADiff_LEC2_GR
test_featureSettest_featureSet
test_geneSettest_geneSet
TF-target databaseTF_target_database