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.
Last updated 29 days ago
motifannotationgeneregulationmotifdiscoverytranscriptionalignment
12.00 score 25 stars 18 packages 1000 scripts 7.1k downloadsCNEr - CNE Detection and Visualization
Large-scale identification and advanced visualization of sets of conserved noncoding elements.
Last updated 29 days ago
generegulationvisualizationdataimport
9.27 score 3 stars 19 packages 34 scripts 5.9k 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 It is an interface to code originally made available by Helene Touzet and Jean-Stephane Varre, 2007, Algorithms Mol Biol:2, 15.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>.
Last updated 2 years ago
5.60 score 1 stars 20 packages 13 scripts 3.4k downloads