Basics | Install FindIT2 | Citation | Acknowledgments | Introduction | Multi-peak multi-gene annotation | annotate peak using nearest mode | find realted peak using gene Bound mode | find related peak using gene scan mode | Calculate regulation potential(RP) | calculate RP using mmAnno | Calculate RP using bw file | Calculate RP using mmAnno result and peakScore matrix | Find influential target | Find influential TF | Find IT of input peak based on wilcox test | Find IT of input peak based on fisher test | Find IT of input genes based on fisher test | Find IT of input genes based on TF hit | Find IT of input genes based on region RP | Find IT of input genes based on motif activity response | integrate result | Calculate feature correlation | Calculate peak gene correlation | Calculate enhancer promoter correlation | Integrate result | Session info | References
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:
FindIT2_1.19.0.tar.gz
FindIT2_1.19.0.zip(r-4.7-any)FindIT2_1.19.0.zip(r-4.6-any)FindIT2_1.19.0.zip(r-4.5-any)
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✨
DESCRIPTION |NEWS
card.svg |card.png
FindIT2/json (API)
| # 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:
- 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 | 232 | ||
| linux-devel | OK | 529 | ||
| source / vignettes | OK | 383 | ||
| linux-release | OK | 539 | ||
| macos-release | OK | 369 | ||
| macos-oldrel | OK | 310 | ||
| windows-devel | OK | 365 | ||
| windows-release | OK | 401 | ||
| windows-oldrel | OK | 372 | ||
| wasm-release | OK | 192 |
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
