Package: FindIT2 1.13.0
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_1.13.0.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)
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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')) |
Bug tracker:https://github.com/shangguandong1996/findit2/issues
- ATAC_normCount - ATAC normCount of E50h-72h in Chr5
- RNADiff_LEC2_GR - RNA diff result from LEC2_GR VS LEC2_DMSO
- RNA_normCount - RNA normCount of E50h-72h in Chr5
- TF_target_database - TF-target database
- test_featureSet - Test_featureSet
- test_geneSet - Test_geneSet
On BioConductor:FindIT2-1.13.0(bioc 3.21)FindIT2-1.12.0(bioc 3.20)
softwareannotationchipseqatacseqgeneregulationmultiplecomparisongenetarget
Last updated 2 months agofrom:30235ecd5a. Checks:OK: 7. Indexed: yes.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Dec 19 2024 |
R-4.5-win | OK | Dec 19 2024 |
R-4.5-linux | OK | Dec 19 2024 |
R-4.4-win | OK | Dec 19 2024 |
R-4.4-mac | OK | Dec 19 2024 |
R-4.3-win | OK | Dec 19 2024 |
R-4.3-mac | OK | Dec 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