sapFinder: A package for variant peptides detection and visualization in shotgun proteomics.

sapFinder is developed to automate (1) variation-associated database construction, (2) database searching, (3) post-processing, (4) HTML-based report generation in shotgun proteomics.

Author
Shaohang Xu, Bo Wen
Date of publication
None
Maintainer
Shaohang Xu <xsh.skye@gmail.com>, Bo Wen <wenbo@genomics.cn>
License
GPL-2
Version
1.12.0

View on Bioconductor

Man pages

dbCreator
dbCreator
easyRun
easyRun
parserGear
parserGear
reportCreator
reportCreator
runTandem
run xtandem

Files in this package

sapFinder/DESCRIPTION
sapFinder/NAMESPACE
sapFinder/R
sapFinder/R/basic.r
sapFinder/R/main.r
sapFinder/R/rchtml.r
sapFinder/R/rdhtml.r
sapFinder/R/rghtml.r
sapFinder/R/rhhtml.r
sapFinder/R/rihtml.r
sapFinder/R/rshtml.r
sapFinder/R/searchEngine.r
sapFinder/R/spplot.r
sapFinder/build
sapFinder/build/vignette.rds
sapFinder/inst
sapFinder/inst/CITATION
sapFinder/inst/NEWS
sapFinder/inst/css
sapFinder/inst/css/content.css
sapFinder/inst/css/index.css
sapFinder/inst/css/jquery.qtip.css
sapFinder/inst/css/jquery.qtip.min.css
sapFinder/inst/css/left.css
sapFinder/inst/doc
sapFinder/inst/doc/sapFinder.R
sapFinder/inst/doc/sapFinder.Rnw
sapFinder/inst/doc/sapFinder.pdf
sapFinder/inst/extdata
sapFinder/inst/extdata/sapFinder_test.mgf
sapFinder/inst/extdata/sapFinder_test.vcf
sapFinder/inst/extdata/sapFinder_test_BioMart.Xref.txt
sapFinder/inst/extdata/sapFinder_test_ensGene.txt
sapFinder/inst/extdata/sapFinder_test_ensGeneMrna.fa
sapFinder/inst/images
sapFinder/inst/images/bg_bar.png
sapFinder/inst/images/head_right.png
sapFinder/inst/images/help_images
sapFinder/inst/images/help_images/help1.png
sapFinder/inst/images/help_images/help2.png
sapFinder/inst/images/help_images/help3.png
sapFinder/inst/images/help_images/help4.png
sapFinder/inst/images/help_images/help5.png
sapFinder/inst/images/help_images/help6.png
sapFinder/inst/images/help_images/help7.png
sapFinder/inst/images/help_images/help8.png
sapFinder/inst/images/li_bg.gif
sapFinder/inst/images/minus.gif
sapFinder/inst/images/plus.gif
sapFinder/inst/images/seq_ctl_topbg.gif
sapFinder/inst/images/seq_foot_bg.gif
sapFinder/inst/images/seq_tool_bg.gif
sapFinder/inst/images/sequence.png
sapFinder/inst/images/spectral_thumb.gif
sapFinder/inst/images/spectral_thumb.png
sapFinder/inst/js
sapFinder/inst/js/content.js
sapFinder/inst/js/index.js
sapFinder/inst/js/index2.js
sapFinder/inst/js/jquery-1.10.2.min.js
sapFinder/inst/js/jquery.qtip.min.js
sapFinder/inst/parser4sapFinder.jar
sapFinder/inst/savdbcreate.v1.2.jar
sapFinder/inst/unitTests
sapFinder/inst/unitTests/test_TestFiles.R
sapFinder/man
sapFinder/man/dbCreator.Rd
sapFinder/man/easyRun.Rd
sapFinder/man/parserGear.Rd
sapFinder/man/reportCreator.Rd
sapFinder/man/runTandem.Rd
sapFinder/src
sapFinder/src/Makevars
sapFinder/src/Makevars.win
sapFinder/src/dataHandle.cpp
sapFinder/tests
sapFinder/tests/runTests.R
sapFinder/vignettes
sapFinder/vignettes/biomart.png
sapFinder/vignettes/sapFinder.Rnw
sapFinder/vignettes/sapFinder.bib