Package: FindIT2 1.13.0

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_1.13.0.tar.gz
FindIT2_1.13.0.zip(r-4.5)FindIT2_1.13.0.zip(r-4.4)FindIT2_1.13.0.zip(r-4.3)
FindIT2_1.13.0.tgz(r-4.4-any)FindIT2_1.13.0.tgz(r-4.3-any)
FindIT2_1.13.0.tar.gz(r-4.5-noble)FindIT2_1.13.0.tar.gz(r-4.4-noble)
FindIT2_1.13.0.tgz(r-4.4-emscripten)FindIT2_1.13.0.tgz(r-4.3-emscripten)
FindIT2.pdf |FindIT2.html
FindIT2/json (API)
NEWS

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

Peer review:

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

Datasets:

On BioConductor:FindIT2-1.13.0(bioc 3.21)FindIT2-1.12.0(bioc 3.20)

softwareannotationchipseqatacseqgeneregulationmultiplecomparisongenetarget

5.26 score 6 stars 7 scripts 136 downloads 23 exports 111 dependencies

Last updated 22 days agofrom:30235ecd5a. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 19 2024
R-4.5-winOKNov 19 2024
R-4.5-linuxOKNov 19 2024
R-4.4-winOKNov 19 2024
R-4.4-macOKNov 19 2024
R-4.3-winOKNov 19 2024
R-4.3-macOKNov 19 2024

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:abindAnnotationDbiaskpassBHBiobaseBiocBaseUtilsBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobcachemclicodetoolscolorspacecpp11crayoncurlDBIDelayedArraydplyrfansifarverfastmapforeachformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2ggrepelglmnetgluegtablehmshttrIRangesisobanditeratorsjsonliteKEGGRESTlabelinglambda.rlatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimeMultiAssayExperimentmunsellnlmeopensslpatchworkpillarpkgconfigplogrplyrpngprettyunitsprogresspurrrqvalueR6RColorBrewerRcppRcppEigenRCurlreshape2restfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsscalesshapesnowSparseArraystringistringrSummarizedExperimentsurvivalsystibbletidyrtidyselectUCSC.utilsutf8vctrsviridisLitewithrXMLXVectoryamlzlibbioc

FindIT2:Find influential TF and influential Target

Rendered fromFindIT2.Rmdusingknitr::rmarkdownon Nov 19 2024.

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