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To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("TFBSTools")
In most cases, you don't need to download the package archive at all.
TFBSTools
|
This package is for version 3.3 of Bioconductor; for the stable, up-to-date release version, see TFBSTools.
Software Package for Transcription Factor Binding Site (TFBS) Analysis
Bioconductor version: 3.3
TFBSTools is a package for the analysis and manipulation of transcription factor binding sites. It includes matrices conversion between Position Frequency Matirx (PFM), Position Weight Matirx (PWM) and Information Content Matrix (ICM). It can also scan putative TFBS from sequence/alignment, query JASPAR database and provides a wrapper of de novo motif discovery software.
Author: Ge Tan [aut, cre]
Maintainer: Ge Tan <ge.tan09 at imperial.ac.uk>
Citation (from within R,
enter citation("TFBSTools")):
Installation
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("TFBSTools")
Documentation
| HTML | R Script | Transcription factor binding site (TFBS) analysis with the "TFBSTools" package |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | Alignment, GeneRegulation, MotifAnnotation, MotifDiscovery, Software, Transcription |
| Version | 1.10.4 |
| In Bioconductor since | BioC 2.13 (R-3.0) (3 years) |
| License | GPL-2 |
| Depends | R (>= 3.2.2) |
| Imports | Biobase(>= 2.28), Biostrings(>= 2.36.4), BiocGenerics(>= 0.14.0), BiocParallel(>= 1.2.21), BSgenome(>= 1.36.3), caTools (>= 1.17.1), CNEr(>= 1.4.0), DirichletMultinomial(>= 1.10.0), GenomeInfoDb(>= 1.6.1), GenomicRanges(>= 1.20.6), gtools (>= 3.5.0), grid, IRanges(>= 2.2.7), methods, RSQLite (>= 1.0.0), rtracklayer(>= 1.28.10), seqLogo(>= 1.34.0), S4Vectors(>= 0.9.25), TFMPvalue (>= 0.0.5), XML (>= 3.98-1.3), XVector(>= 0.8.0) |
| LinkingTo | |
| Suggests | BiocStyle(>= 1.7.7), JASPAR2014(>= 1.4.0), knitr (>= 1.11), testthat, JASPAR2016(>= 1.0.0) |
| SystemRequirements | |
| Enhances | |
| URL | https://github.com/ge11232002/TFBSTools |
| BugReports | https://github.com/ge11232002/TFBSTools/issues |
| Depends On Me | |
| Imports Me | MatrixRider |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | TFBSTools_1.10.4.tar.gz |
| Windows Binary | TFBSTools_1.10.4.zip (32- & 64-bit) |
| Mac OS X 10.9 (Mavericks) | TFBSTools_1.10.4.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/TFBSTools/tree/release-3.3 |
| Package Short Url | http://bioconductor.org/packages/TFBSTools/ |
| Package Downloads Report | Download Stats |
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