DOI: 10.18129/B9.bioc.FindIT2  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see FindIT2.

find influential TF and Target based on multi-omics data

Bioconductor version: 3.16

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.

Author: Guandong Shang [aut, cre]

Maintainer: Guandong Shang <shangguandong1996 at>

Citation (from within R, enter citation("FindIT2")):


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biocViews ATACSeq, Annotation, ChIPSeq, GeneRegulation, GeneTarget, MultipleComparison, Software
Version 1.4.0
In Bioconductor since BioC 3.14 (R-4.1) (1.5 years)
License Artistic-2.0
Depends GenomicRanges, R (>= 3.5.0)
Imports withr, BiocGenerics, GenomeInfoDb, rtracklayer, S4Vectors, GenomicFeatures, dplyr, rlang, patchwork, ggplot2, BiocParallel, qvalue, stringr, utils, stats, ggrepel, tibble, tidyr, SummarizedExperiment, MultiAssayExperiment, IRanges, progress, purrr, glmnet, methods
Suggests BiocStyle, knitr, rmarkdown, sessioninfo, testthat (>= 3.0.0), TxDb.Athaliana.BioMart.plantsmart28
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