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.
Copyright: | Copyright (c) 2002-2020 University of California, Cornell |
University, Cold Spring Harbor Laboratory. | |
Package: | rtfbs |
License: | BSD_3_clause + file LICENSE |
Version: | 0.3.15 |
URL: | http://compgen.cshl.edu/rtfbs |
Date: | 2020-01-21 |
Imports: | |
rphast, | |
methods | |
Depends: | |
stats | |
Collate: | |
'tfbs.R' | |
RoxygenNote: | 5.0.1 |
SystemRequirements: | PCRE |
Built: | R 3.1.2; x86_64-unknown-linux-gnu; 2020-01-21 20:50:12 UTC; unix |
Index:
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 | [.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
|
Nicholas Peterson, Andre Martins, Melissa Hubisz, and Adam Siepel
Maintainer: Ritika Ramani<rramani@cshl.edu>
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