Package: FindIT2 1.19.0
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:
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
- ATAC_normCount - ATAC normCount of E50h-72h in Chr5
- RNA_normCount - RNA normCount of E50h-72h in Chr5
- RNADiff_LEC2_GR - RNA diff result from LEC2_GR VS LEC2_DMSO
- test_featureSet - Test_featureSet
- test_geneSet - Test_geneSet
- TF_target_database - TF-target database
On BioConductor:FindIT2-1.19.0(bioc 3.24)FindIT2-1.18.0(bioc 3.23)
softwareannotationchipseqatacseqgeneregulationmultiplecomparisongenetarget
Last updated from:997663b012. Checks:1 NOTE, 9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 231 | ||
| linux-devel-x86_64 | OK | 536 | ||
| source / vignettes | OK | 381 | ||
| linux-release-x86_64 | OK | 458 | ||
| macos-release-arm64 | OK | 246 | ||
| macos-oldrel-arm64 | OK | 340 | ||
| windows-devel | OK | 377 | ||
| windows-release | OK | 481 | ||
| windows-oldrel | OK | 402 | ||
| wasm-release | OK | 186 |
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
