FindIT2
find influential TF and Target based on multi-omics data
Bioconductor version: Release (3.20)
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("FindIT2")):
Installation
To install this package, start R (version "4.4") 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")| Introduction to FindIT2 | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | ATACSeq, Annotation, ChIPSeq, GeneRegulation, GeneTarget, MultipleComparison, Software |
| Version | 1.12.0 |
| 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 |
See More
| Suggests | BiocStyle, knitr, rmarkdown, sessioninfo, testthat (>= 3.0.0), TxDb.Athaliana.BioMart.plantsmart28 |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | FindIT2_1.12.0.tar.gz |
| Windows Binary (x86_64) | FindIT2_1.12.0.zip (64-bit only) |
| macOS Binary (x86_64) | FindIT2_1.12.0.tgz |
| macOS Binary (arm64) | FindIT2_1.11.0.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 |