Transcription Factor Binding Site Identification Tool

Description

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.

Details

Copyright: Copyright (c) 2002-2016 University of California, Cornell
University, Cold Spring Harbor Laboratory.
Package: rtfbs
License: BSD_3_clause + file LICENSE
Version: 0.3.5
URL: http://compgen.cshl.edu/rtfbs
Date: 2016-08-15
Imports:
rphast,
methods
Depends:
stats
Collate:
'tfbs.R'
RoxygenNote: 5.0.1
Built: R 3.1.2; x86_64-unknown-linux-gnu; 2016-08-15 20:31:08 UTC; unix

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[.ms                    Extract, replace, reorder MS
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
output.sites            Threshold possible binding sites by Score or
                        FDR
print.ms                Prints an MS (multiple sequence) object. #'
                        @title Printing MS objects
read.mm                 Read Markov Model from file
read.ms                 Reading in sequences from file
read.pwm                Read PWM object
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

Author(s)

Nicholas Peterson, Andre Martins, Melissa Hubisz, and Adam Siepel

Maintainer: Melissa Hubisz <mjhubisz@cornell.edu>