TFBSTools - Software Package for Transcription Factor Binding Site (TFBS) Analysis
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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motifannotationgeneregulationmotifdiscoverytranscriptionalignment
10.28 score 38 stars 19 dependents 12 scripts 9.1k downloadsTFMPvalue - Efficient and Accurate P-Value Computation for Position Weight Matrices
In putative Transcription Factor Binding Sites (TFBSs) identification from sequence/alignments, we are interested in the significance of certain match score. TFMPvalue provides the accurate calculation of P-value with score threshold for Position Weight Matrices, or the score with given P-value. It is an interface to code originally made available by Helene Touzet and Jean-Stephane Varre, 2007, Algorithms Mol Biol:2, 15. <doi:10.1186/1748-7188-2-15>.
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cpp
6.38 score 2 stars 23 dependents 16 scripts 3.6k downloadsJASPAR2014 - Data package for JASPAR
Data package for JASPAR 2014. To search this databases, please use the package TFBSTools.
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experimentdatasequencingdatadatapkg
3.07 score 59 scriptsJASPAR2016 - Data package for JASPAR 2016
Data package for JASPAR 2016. To search this databases, please use the package TFBSTools (>= 1.8.1).
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experimentdatamotifannotationgeneregulationdatapkg
3.03 score 54 scripts