InTAD
This package is for version 3.9 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: 3.9
The package is focused on the detection of correlation between expressed genes and selected epigenomic signals i.e. enhancers obtained from ChIP-seq data within topologically associated domains (TADs). 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 "3.6") 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 | 1.4.0 |
| 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_1.4.0.tar.gz |
| Windows Binary | InTAD_1.4.0.zip |
| Mac OS X 10.11 (El Capitan) | InTAD_1.4.0.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 3.9 | Source Archive |