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rtfbs (version 0.3.15)

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.

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Version

Install

install.packages('rtfbs')

Monthly Downloads

10

Version

0.3.15

License

BSD_3_clause + file LICENSE

Maintainer

Ritika Ramani

Last Published

January 21st, 2020

Functions in rtfbs (0.3.15)

offsets.ms

Get index offsets
lengths.ms

MS sequence lengths
makeFdrPlot

Plot FDR
read.mm

Read Markov Model from file
score.ms

Score sequences against a PWM
sequences.ms

Get sequences
read.ms

Reading in sequences from file
is.pointer.ms

Data in R or C
ms

Multiple Sequence (MS) Objects
simulate.ms

Generate sequence from Markov Model
output.sites

Threshold possible binding sites by Score or FDR
print.ms

Prints an MS (multiple sequence) object. #' @title Printing MS objects
[.ms

Extract, replace, reorder MS
summary.ms

MS Summary
write.ms

Writing MS Object to FASTA file
write.mm

Write Markov Model to file
split.ms

Split sequences
names.ms

MS Sequence Names
read.pwm

Read PWM object
rtfbs-package

Transcription Factor Binding Site Identification Tool
calc.fdr

Calculate FDR
concat.ms

Concat MS
label.matrix

Name PWM & MM rows and columns
as.pointer.ms

MS To Pointer
build.mm

Build Markov Model to represent sequences in an MS object
length.ms

Length of MS object
groupByGC.ms

Group sequences by GC
from.pointer.ms

MS From Pointer
gcContent.ms

Get GC content of each sequence in an MS object