proBAMr: Generating SAM file for PSMs in shotgun proteomics data
Version 1.10.0

Mapping PSMs back to genome. The package builds SAM file from shotgun proteomics data The package also provides function to prepare annotation from GTF file.

AuthorXiaojing Wang
Bioconductor views MassSpectrometry Proteomics Software Visualization
Date of publicationNone
MaintainerXiaojing Wang <xiaojing.wang@vanderbilt.edu>
LicenseArtistic-2.0
Version1.10.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("proBAMr")

Popular man pages

PrepareAnnotationGENCODE: prepare annotation from GENCODE
PSMtab2SAM: Generate SAM files from PSMs.
See all...

All man pages Function index File listing

Man pages

PrepareAnnotationGENCODE: prepare annotation from GENCODE
PSMtab2SAM: Generate SAM files from PSMs.

Functions

MapCoding2genome Source code
PSMtab2SAM Man page Source code
PrepareAnnotationGENCODE Man page Source code
gen_splicmatrix Source code
peptideUnannotated Source code
proteinUnannotated Source code

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/PSMtab2SAM.R
R/PrepareAnnotationGENCODE.R
build
build/vignette.rds
inst
inst/doc
inst/doc/proBAMr.R
inst/doc/proBAMr.Rnw
inst/doc/proBAMr.pdf
inst/extdata
inst/extdata/GENCODE
inst/extdata/GENCODE/exon_anno.RData
inst/extdata/GENCODE/ids.RData
inst/extdata/GENCODE/procodingseq.RData
inst/extdata/GENCODE/proseq.RData
inst/extdata/GENCODE/txdb.sqlite
inst/extdata/coding_seq.fasta
inst/extdata/header
inst/extdata/passedPSM.tab
inst/extdata/pro_seq.fasta
inst/extdata/res
inst/extdata/res/SAM.RData
inst/extdata/res/test.sam
inst/extdata/res/test_header.bam
inst/extdata/res/test_header.sam
inst/extdata/res/test_header_sort.bam
inst/extdata/res/test_header_sort.bam.bai
inst/extdata/test.gtf
inst/unitTests
inst/unitTests/test_PSMtab2SAM.R
inst/unitTests/test_PrepareAnnotationGENCODE.R
man
man/PSMtab2SAM.Rd
man/PrepareAnnotationGENCODE.Rd
tests
tests/runTests.R
vignettes
vignettes/Fig1.jpg
vignettes/Tab1.jpg
vignettes/Tab2.jpg
vignettes/Tab3.jpg
vignettes/proBAMr.Rnw
proBAMr documentation built on May 20, 2017, 10:13 p.m.

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