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.

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

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Files in this package

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

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