InTAD
This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see InTAD.
Search for correlation between epigenetic signals and gene expression in TADs
Bioconductor version: 3.17
The package is focused on the detection of correlation between expressed genes and selected epigenomic signals (i.e. enhancers obtained from ChIP-seq data) either within topologically associated domains (TADs) or between chromatin contact loop anchors. Various parameters can be controlled to investigate the influence of external factors and visualization plots are available for each analysis step.
Author: Konstantin Okonechnikov, Serap Erkek, Lukas Chavez
Maintainer: Konstantin Okonechnikov <k.okonechnikov at gmail.com>
citation("InTAD")):
Installation
To install this package, start R (version "4.3") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("InTAD")
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("InTAD")| Correlation of epigenetic signals and genes in TADs | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | ChIPSeq, Epigenetics, GeneExpression, HiC, ImmunoOncology, RNASeq, Sequencing, Software |
| Version | 1.20.0 |
| In Bioconductor since | BioC 3.7 (R-3.5) (6 years) |
| License | GPL (>=2) |
| Depends | R (>= 3.5), methods, S4Vectors, IRanges, GenomicRanges, MultiAssayExperiment, SummarizedExperiment, stats |
| Imports | BiocGenerics, Biobase, rtracklayer, parallel, graphics, mclust, qvalue, ggplot2, utils, ggpubr |
| System Requirements | |
| URL |
See More
| Suggests | testthat, BiocStyle, knitr, rmarkdown |
| 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 | InTAD_1.20.0.tar.gz |
| Windows Binary | InTAD_1.20.0.zip |
| macOS Binary (x86_64) | InTAD_1.20.0.tgz |
| macOS Binary (arm64) | InTAD_1.20.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/InTAD |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/InTAD |
| Bioc Package Browser | https://code.bioconductor.org/browse/InTAD/ |
| Package Short Url | https://bioconductor.org/packages/InTAD/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.17 | Source Archive |