sapFinder: A package for variant peptides detection and visualization in shotgun proteomics.
Version 1.14.0

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

AuthorShaohang Xu, Bo Wen
Bioconductor views MassSpectrometry Proteomics RNASeq ReportWriting SNP Visualization
Date of publicationNone
MaintainerShaohang Xu <xsh.skye@gmail.com>, Bo Wen <wenbo@genomics.cn>
LicenseGPL-2
Version1.14.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("sapFinder")

Popular man pages

dbCreator: dbCreator
easyRun: easyRun
parserGear: parserGear
reportCreator: reportCreator
runTandem: run xtandem
See all...

All man pages Function index File listing

Man pages

dbCreator: dbCreator
easyRun: easyRun
parserGear: parserGear
reportCreator: reportCreator
runTandem: run xtandem

Functions

Sys.which2 Source code
blank Source code
concat Source code
ctag Source code
dataHandle_R Source code
dbCreator Man page Source code
db_link_switch Source code
easyRun Man page Source code
java.executable Source code
mut_freq_heatmap Source code
mut_highlight Source code
mut_pro_dist Source code
parserGear Man page Source code
pepsummary Source code
precursor_error_hist Source code
rchtml Source code
rdhtml Source code
reportCreator Man page Source code
rghtml Source code
rhhtml Source code
rihtml Source code
rshtml Source code
runTandem Man page Source code
spplot Source code
tag Source code
wm_charge_bar Source code
wm_evalue_hist Source code
wm_mass_hist Source code
write Source code
writeBody_c Source code
writeBody_d Source code
writeBody_g Source code
writeBody_h Source code
writeBody_i Source code
writeBody_s Source code
writeHead_c Source code
writeHead_d Source code
writeHead_g Source code
writeHead_h Source code
writeHead_i Source code
writeHead_s Source code
writeHtml_c Source code
writeHtml_d Source code
writeHtml_g Source code
writeHtml_h Source code
writeHtml_i Source code
writeHtml_s Source code
writeSeq_c Source code
writeTable Source code

Files

DESCRIPTION
NAMESPACE
R
R/basic.r
R/main.r
R/rchtml.r
R/rdhtml.r
R/rghtml.r
R/rhhtml.r
R/rihtml.r
R/rshtml.r
R/searchEngine.r
R/spplot.r
build
build/vignette.rds
inst
inst/CITATION
inst/NEWS
inst/css
inst/css/content.css
inst/css/index.css
inst/css/jquery.qtip.css
inst/css/jquery.qtip.min.css
inst/css/left.css
inst/doc
inst/doc/sapFinder.R
inst/doc/sapFinder.Rnw
inst/doc/sapFinder.pdf
inst/extdata
inst/extdata/sapFinder_test.mgf
inst/extdata/sapFinder_test.vcf
inst/extdata/sapFinder_test_BioMart.Xref.txt
inst/extdata/sapFinder_test_ensGene.txt
inst/extdata/sapFinder_test_ensGeneMrna.fa
inst/images
inst/images/bg_bar.png
inst/images/head_right.png
inst/images/help_images
inst/images/help_images/help1.png
inst/images/help_images/help2.png
inst/images/help_images/help3.png
inst/images/help_images/help4.png
inst/images/help_images/help5.png
inst/images/help_images/help6.png
inst/images/help_images/help7.png
inst/images/help_images/help8.png
inst/images/li_bg.gif
inst/images/minus.gif
inst/images/plus.gif
inst/images/seq_ctl_topbg.gif
inst/images/seq_foot_bg.gif
inst/images/seq_tool_bg.gif
inst/images/sequence.png
inst/images/spectral_thumb.gif
inst/images/spectral_thumb.png
inst/js
inst/js/content.js
inst/js/index.js
inst/js/index2.js
inst/js/jquery-1.10.2.min.js
inst/js/jquery.qtip.min.js
inst/parser4sapFinder.jar
inst/savdbcreate.v1.2.jar
inst/unitTests
inst/unitTests/test_TestFiles.R
man
man/dbCreator.Rd
man/easyRun.Rd
man/parserGear.Rd
man/reportCreator.Rd
man/runTandem.Rd
src
src/Makevars
src/Makevars.win
src/dataHandle.cpp
tests
tests/runTests.R
vignettes
vignettes/biomart.png
vignettes/sapFinder.Rnw
vignettes/sapFinder.bib
sapFinder documentation built on May 20, 2017, 9:22 p.m.

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