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) 2002-2016 University of California, Cornell|
|University, Cold Spring Harbor Laboratory.|
|License:||BSD_3_clause + file LICENSE|
|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
Nicholas Peterson, Andre Martins, Melissa Hubisz, and Adam Siepel
Maintainer: Melissa Hubisz <email@example.com>
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