DESCRIPTION

Package: TFBSTools
Version: 1.45.1
Date: 2024-12-23
Title: 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.
Authors@R: person("Ge", "Tan", email="ge_tan@live.com",
                  role = c("aut", "cre"))
VignetteBuilder: knitr
Imports: Biobase(>= 2.28),
         Biostrings(>= 2.36.4),
         pwalign,
         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),
         parallel
Depends: R (>= 3.2.2)
Suggests: BiocStyle(>= 1.7.7),
          JASPAR2014(>= 1.4.0),
          knitr(>= 1.11),
          testthat,
          JASPAR2016(>= 1.0.0),
          JASPAR2018(>= 1.0.0),
          rmarkdown
License: GPL-2
URL: https://github.com/ge11232002/TFBSTools
BugReports: https://github.com/ge11232002/TFBSTools/issues
Type: Package
biocViews: MotifAnnotation, GeneRegulation, MotifDiscovery, Transcription, 
           Alignment
NeedsCompilation: yes
LazyData: yes
Collate: AllGenerics.r AllClasses.r show-methods.r util-methods.r
         XMatrix-methods.r XMatrixList-methods.r
         SiteSet-methods.r
         coercion-methods.r DB-methods.r
         JASPAR.R
         PairwiseAlignment-methods.r
         ICM-methods.r PWM-methods.r 
         Motif-methods.r PFM-methods.r
         Wrappers-methods.r DirichletMixture.r
         TFFM.R TFFMseqLogo.R IO.R Enrichment.R