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 (3.21)

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] (ORCID: )

Maintainer: Guandong Shang <shangguandong1996 at 163.com>

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

Installation

To install this package, start R (version "4.5") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	ATACSeq, Annotation, ChIPSeq, GeneRegulation, GeneTarget, MultipleComparison, Software
Version	1.13.0
In Bioconductor since	BioC 3.14 (R-4.1) (3 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

Suggests	BiocStyle, knitr, rmarkdown, sessioninfo, testthat (>= 3.0.0), TxDb.Athaliana.BioMart.plantsmart28
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Build Report	Build Report

Package Archives

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

Source Package	FindIT2_1.13.0.tar.gz
Windows Binary (x86_64)	FindIT2_1.13.0.zip
macOS Binary (x86_64)
macOS Binary (arm64)
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