FindIT2
This is the released version of FindIT2; for the devel version, see FindIT2.
find influential TF and Target based on multi-omics data
Bioconductor version: Release (3.23)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | 1.18.0 |
| In Bioconductor since | BioC 3.14 (R-4.1) (5 years) |
| License | Artistic-2.0 |
| Depends | GenomicRanges, R (>= 3.5.0) |
| Imports | withr, BiocGenerics, Seqinfo, 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_1.18.0.tar.gz |
| Windows Binary (x86_64) | FindIT2_1.18.0.zip |
| macOS Binary (big-sur-x86_64) | FindIT2_1.18.0.tgz |
| macOS Binary (sonoma-arm64) | FindIT2_1.18.0.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 |