TFBSTools: an R/bioconductor package for transcription factor binding site analysis
By Ge Tan, Boris Lenhard. Bioinform., 2016
344 citations recorded by the source corpus.
Summary: The ability to efficiently investigate transcription factor binding sites (TFBSs) genome-wide is central to computational studies of gene regulation. TFBSTools is an R/Bioconductor package for the analysis and manipulation of TFBSs and their associated transcription factor profile matrices. TFBStools provides a toolkit for handling TFBS profile matrices, scanning sequences and alignments including whole genomes, and querying the JASPAR database. The functionality of the package can be easily extended to include advanced statistical analysis, data visualization and data integration. Availability and implementation: The package is implemented in R and available under GPL-2 license from the Bioconductor website (http://bioconductor.org/packages/TFBSTools/). Contact: ge.tan09@imperial.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online.
Subfields: Molecular Biology
View Paper: https://www.semanticscholar.org/paper/7952b7c68b33972d5f8483cf7742efaed6396357
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Citations in the corpus
- JASPAR 2024: 20th anniversary of the open-access database of transcription factor binding profiles (2023, methodology): “We further provide different interfaces ranging from straightforward web-interface to programmatic access through various packages in Perl ( 16 ), Python ( 17 ), R / Bioconductor ( 18 ), and Ruby ( 12 ).”
- Evolution of Superinfection Immunity in Cluster A Mycobacteriophages (2019, methodology): “Pairwise PWM-normalized Euclidean distances were computed using the PWMSimilarity function, and larger distances represent more dissimilar PWMs (46, 47).”