rtfbs: Transcription Factor Binding Site Identification Tool

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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.

Author
Nicholas Peterson, Andre Martins, Melissa Hubisz, and Adam Siepel
Date of publication
2016-08-16 19:49:30
Maintainer
Melissa Hubisz <mjhubisz@cornell.edu>
License
BSD_3_clause + file LICENSE
Version
0.3.5
URLs

View on CRAN

Man pages

as.pointer.ms
MS To Pointer
build.mm
Build Markov Model to represent sequences in an MS object
calc.fdr
Calculate FDR
concat.ms
Concat MS
from.pointer.ms
MS From Pointer
gcContent.ms
Get GC content of each sequence in an MS object
groupByGC.ms
Group sequences by GC
is.pointer.ms
Data in R or C
label.matrix
Name PWM & MM rows and columns
length.ms
Length of MS object
lengths.ms
MS sequence lengths
makeFdrPlot
Plot FDR
ms
Multiple Sequence (MS) Objects
names.ms
MS Sequence Names
offsets.ms
Get index offsets
open-brace.ms
Extract, replace, reorder MS
output.sites
Threshold possible binding sites by Score or FDR
print.ms
Prints an MS (multiple sequence) object. #' @title Printing...
read.mm
Read Markov Model from file
read.ms
Reading in sequences from file
read.pwm
Read PWM object
rtfbs-package
Transcription Factor Binding Site Identification Tool
score.ms
Score sequences against a PWM
sequences.ms
Get sequences
simulate.ms
Generate sequence from Markov Model
split.ms
Split sequences
summary.ms
MS Summary
write.mm
Write Markov Model to file
write.ms
Writing MS Object to FASTA file

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