FindIT2

DOI: 10.18129/B9.bioc.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 (3.15)

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 "4.2") and enter:

if (!requireNamespace("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")

 

HTML R Script Introduction to FindIT2
PDF   Reference Manual
Text   NEWS

Details

biocViews ATACSeq, Annotation, ChIPSeq, GeneRegulation, GeneTarget, MultipleComparison, Software
Version 1.1.2
In Bioconductor since BioC 3.14 (R-4.1) (< 6 months)
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_1.1.2.tar.gz
Windows Binary
macOS 10.13 (High Sierra) FindIT2_1.1.2.tgz
Source Repository git clone https://git.bioconductor.org/packages/FindIT2
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/FindIT2
Package Short Url https://bioconductor.org/packages/FindIT2/
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