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FindIT2

This is the development version of FindIT2; for the stable release version, see FindIT2.

find influential TF and Target based on multi-omics data


Bioconductor version: Development (3.19)

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 163.com>

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

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("FindIT2")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("FindIT2")
Introduction to FindIT2 HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews ATACSeq, Annotation, ChIPSeq, GeneRegulation, GeneTarget, MultipleComparison, Software
Version 1.9.0
In Bioconductor since BioC 3.14 (R-4.1) (2.5 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
System Requirements
URL https://github.com/shangguandong1996/FindIT2
Bug Reports https://support.bioconductor.org/t/FindIT2
See More
Suggests BiocStyle, knitr, rmarkdown, sessioninfo, testthat (>= 3.0.0), TxDb.Athaliana.BioMart.plantsmart28
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package FindIT2_1.9.0.tar.gz
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64) FindIT2_1.9.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/FindIT2
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/FindIT2
Bioc Package Browser https://code.bioconductor.org/browse/FindIT2/
Package Short Url https://bioconductor.org/packages/FindIT2/
Package Downloads Report Download Stats