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TFBSTools (version 1.10.3)

Software Package for Transcription Factor Binding Site (TFBS) Analysis

Description

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.

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Version

Version

1.10.3

License

GPL-2

Issues

Pull Requests

Stars

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Maintainer

Ge Tan

Last Published

February 15th, 2017

Functions in TFBSTools (1.10.3)

SiteSet

Class "SiteSet"
MotifSet

Class "MotifSet"
SitePairSetList-class

Class "SitePairSetList"
getEmissionProb

Get the emission distribution parameters.
TFFM

The TFFM class
writeGFF3-methods

writeGFF3, writeGFF2 functions
getMatrixByID

Basic JASPAR database search functionis getMatrixByID, getMatrixByName
readXMLTFFM

readXMLTFFM
dmmEM-methods

dmmEM method
toGRangesList-methods

toGRangesList function
searchAln

searchAln method
searchSeq

searchSeq method
permuteMatrix-methods

permuteMatrix method
calConservation-methods

calConservation method
getPosProb

Get the emission probabilities of nucleotides
searchPairBSgenome-methods

searchPairBSgenome method
seqLogo

Plot a sequence logo
TFBSTools-package

TFBS software package.
MA0004.1

Some example PFM matrices.
SitePairSet

Class "SitePairSet"
shannon.entropy

Calculate the Shannon entropy
runMEME

Wrapper function for MEME
deleteMatrixHavingID

JASPAR database operations
sampleRanges

sampleRanges
IUPAC2Matrix

IUPAC2Matrix
XMatrix

"XMatrix" objects
toICM

toICM method
toPWM

toPWM method
PFMSimilarity-methods

PFMSimilarity method
PWMSimilarity-methods

PWMSimilarity method
SiteSetList

Class "SiteSetList"
XMatrixList

Class "XMatrixList"
rPWMDmm-methods

rPWMDmm method
makeFlatFileDir

Generate "FlatFileDir" directory
getMatrixSet

Advanced JASPAR database search functions get_MatrixSet