rtfbs: Transcription Factor Binding Site Identification Tool

Identifies and scores possible Transcription Factor Binding Sites and allows for FDR analysis and pruning. It supports splitting of sequences based on size or a specified GFF, grouping by G+C content, and specification of Markov model order. The heavy lifting is done in C while all results are made available via R.

Install the latest version of this package by entering the following in R:
install.packages("rtfbs")
AuthorNicholas Peterson, Andre Martins, Melissa Hubisz, and Adam Siepel
Date of publication2016-08-16 19:49:30
MaintainerMelissa Hubisz <mjhubisz@cornell.edu>
LicenseBSD_3_clause + file LICENSE
Version0.3.5
http://compgen.cshl.edu/rtfbs

View on CRAN

Functions

as.pointer.ms Man page
build.mm Man page
calc.fdr Man page
concat.ms Man page
from.pointer.ms Man page
gcContent.ms Man page
groupByGC.ms Man page
is.pointer.ms Man page
label.matrix Man page
length.ms Man page
lengths.ms Man page
makeFdrPlot Man page
ms Man page
[.ms Man page
names.ms Man page
offsets.ms Man page
output.sites Man page
print.ms Man page
read.mm Man page
read.ms Man page
read.pwm Man page
rtfbs Man page
rtfbs-package Man page
score.ms Man page
sequences.ms Man page
simulate.ms Man page
split.ms Man page
summary.ms Man page
write.mm Man page
write.ms Man page

Files

inst
inst/extdata
inst/extdata/NRSF.zip
inst/doc
inst/doc/vignette.Rnw
inst/doc/vignette.pdf
inst/doc/vignette.R
configure.ac
tests
tests/calc_fdr.R tests/read_ms.R tests/read_pwm.R tests/build_mm.R tests/gcContent_ms.R tests/output_sites.R tests/groupByGC_ms.R tests/simulate_ms.R tests/makeFdrPlot.R tests/score_ms.R
src
src/queues.h
src/hmm.c
src/tfbs.c
src/phylo_p_print.h
src/hashtable.h
src/prob_vector.h
src/phylo_p.h
src/simplex_grid.h
src/bed.h
src/matrix.c
src/bed.c
src/maf.c
src/hashtable.c
src/rph_category_map.c
src/list_of_lists.c
src/indel_mod.h
src/em.h
src/fit_column.h
src/phylo_hmm.c
src/sufficient_stats.c
src/tree_model.c
src/gap_patterns.c
src/rph_phastCons.c
src/fit_column.c
src/rph_hmm.c
src/subst_distrib.c
src/stacks.h
src/pbs_code.h
src/list_of_lists.h
src/subst_mods.h
src/misc.c
src/sufficient_stats.h
src/rph_trees.c
src/complex_vector.h
src/fit_em.c
src/rph_phylo_hmm.c
src/eigen.h
src/rph_subst_mods.c
src/bd_phylo_hmm.h
src/phylo_p.c
src/phast_cons.h
src/vector.c
src/rph_phyloP.c
src/tfbs.h
src/version
src/em.c
src/subst_mods.c
src/vector.h
src/local_alignment.c
src/multi_msa.h
src/numerical_opt.c
src/misc.h
src/pssm.h
src/rph_list_of_lists.c
src/memory_handler.c
src/markov_matrix.h
src/indel_history.c
src/indel_history.h
src/lists.c
src/bgc_hmm.h
src/gff.h
src/fit_em.h
src/motif.c
src/phylo_fit.h
src/prob_matrix.h
src/rph_bgc_hmm.c
src/eigen.c
src/phylo_p_print.c
src/markov_matrix.c
src/msa.h
src/rph_tfbs.c
src/tree_likelihoods.c
src/local_alignment.h
src/rph_tree_model.c
src/gap_patterns.h
src/subst_distrib.h
src/fit_feature.c
src/complex_vector.c
src/rph_gff.c
src/complex_matrix.c
src/fit_feature.h
src/category_map.h
src/Makevars.in
src/category_map.c
src/multi_msa.c
src/maf.h
src/wig.c
src/external_libs.h
src/complex_matrix.h
src/rph_util.c
src/gff.c
src/stringsplus.c
src/dgamma.c
src/wig.h
src/numerical_opt.h
src/rph_msa.c
src/bgc_hmm.c
src/tree_model.h
src/memory_handler.h
src/rph_util.h
src/complex.h
src/rph_init.c
src/maf_block.c
src/maf_block.h
src/Makevars.win
src/trees.h
src/hmm.h
src/ms.h
src/stringsplus.h
src/genepred.h
src/motif.h
src/puzzler.h
src/rph_wig.c
src/msa.c
src/genepred.c
src/phylo_fit.c
src/indel_mod.c
src/phylo_hmm.h
src/trees.c
src/phast_cons.c
src/rph_phyloFit.c
src/dgamma.h
src/lists.h
src/tree_likelihoods.h
src/prob_matrix.c
src/prob_vector.c
src/matrix.h
NAMESPACE
R
R/tfbs.R
vignettes
vignettes/vignette.Rnw
MD5
build
build/vignette.rds
DESCRIPTION
configure
ChangeLog
man
man/read.mm.Rd man/lengths.ms.Rd man/simulate.ms.Rd man/read.pwm.Rd man/write.ms.Rd man/offsets.ms.Rd man/open-brace.ms.Rd man/summary.ms.Rd man/label.matrix.Rd man/read.ms.Rd man/calc.fdr.Rd man/rtfbs-package.Rd man/makeFdrPlot.Rd man/concat.ms.Rd man/length.ms.Rd man/as.pointer.ms.Rd man/from.pointer.ms.Rd man/score.ms.Rd man/split.ms.Rd man/ms.Rd man/is.pointer.ms.Rd man/gcContent.ms.Rd man/sequences.ms.Rd man/print.ms.Rd man/output.sites.Rd man/groupByGC.ms.Rd man/build.mm.Rd man/names.ms.Rd man/write.mm.Rd
cleanup
LICENSE

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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