Package: FindIT2 1.11.0

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]

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

On BioConductor:FindIT2-1.11.0(bioc 3.20)FindIT2-1.10.0(bioc 3.19)

bioconductor-package

23 exports 0.61 score 111 dependencies

Last updated 2 months agofrom:f468499064

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