- Home
- Bioconductor 3.5
- Software Packages
- TFBSTools
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
|
|
|
|
|
Software Package for Transcription Factor Binding Site (TFBS) Analysis
Bioconductor version: Release (3.5)
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 | 1.14.2 |
| In Bioconductor since | BioC 2.13 (R-3.0) (4 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, DBI (>= 0.6), 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.
| Source Package | TFBSTools_1.14.2.tar.gz |
| Windows Binary | TFBSTools_1.14.2.zip (32- & 64-bit) |
| Mac OS X 10.11 (El Capitan) | TFBSTools_1.14.2.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/TFBSTools |
| Package Short Url | http://bioconductor.org/packages/TFBSTools/ |
| Package Downloads Report | Download Stats |
Documentation »
Bioconductor
- Package vignettes and manuals.
- Workflows for learning and use.
- Course and conference material.
- Videos.
- Community resources and tutorials.
R / CRAN packages and documentation
Support »
Please read the posting guide. Post questions about Bioconductor to one of the following locations:
- Support site - for questions about Bioconductor packages
- Bioc-devel mailing list - for package developers
