proBAMr: Generating SAM file for PSMs in shotgun proteomics data

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.

Author
Xiaojing Wang
Date of publication
None
Maintainer
Xiaojing Wang <xiaojing.wang@vanderbilt.edu>
License
Artistic-2.0
Version
1.8.0

View on Bioconductor

Man pages

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

Files in this package

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