FindIT2

DOI: 10.18129/B9.bioc.FindIT2  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see FindIT2.

find influential TF and Target based on multi-omics data

Bioconductor version: 3.17

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>

Installation

To install this package, start R (version "4.3") and enter:

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

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")

 

HTML	R Script	Introduction to FindIT2
PDF		Reference Manual
Text		NEWS

Details

biocViews	ATACSeq, Annotation, ChIPSeq, GeneRegulation, GeneTarget, MultipleComparison, Software
Version	1.6.0
In Bioconductor since	BioC 3.14 (R-4.1) (2 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
LinkingTo
Suggests	BiocStyle, knitr, rmarkdown, sessioninfo, testthat (>= 3.0.0), TxDb.Athaliana.BioMart.plantsmart28
SystemRequirements
Enhances
URL	https://github.com/shangguandong1996/FindIT2
BugReports	https://support.bioconductor.org/t/FindIT2
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	FindIT2_1.6.0.tar.gz
Windows Binary	FindIT2_1.6.0.zip
macOS Binary (x86_64)	FindIT2_1.6.0.tgz
macOS Binary (arm64)	FindIT2_1.6.0.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