Files in lgatto/synapter
Label-free data analysis pipeline for optimal identification and quantitation

.Rbuildignore
.gitignores/all
.gitignores/devel
.travis.yml
DESCRIPTION
NAMESPACE
NEWS
NEWS.md R/AllClasses.R R/AllGenerics.R R/MSnbase-extensions.R R/exported_tools.R R/fasta.R R/figures.R R/fragmentlibrary-functions.R R/fragmentmatching-functions.R R/fragments-functions.R R/gui.R R/master.R R/readcsv-functions.R R/requantify-functions.R R/spectrum-functions.R R/synapter-class.R R/synapter-interface.R R/synergise.R R/update.R R/utils.R R/zzz.R README.md
data/synapterTiny.rda
docs/articles/Bugs.md
docs/articles/Dotfiles/synapter2workflow.dot
docs/articles/Figures/PLGS_create_databank1.jpg
docs/articles/Figures/PLGS_create_databank2.jpg
docs/articles/Figures/PLGS_db_search_options.jpg
docs/articles/Figures/PLGS_output_files1.jpg
docs/articles/Figures/PLGS_output_files2.jpg
docs/articles/Figures/PLGS_output_files3.jpg
docs/articles/Figures/synapter2workflow.png
docs/articles/Foreword.md
docs/articles/fragmentmatching.html
docs/articles/fragmentmatching_files/figure-html/filterfragmentsplot-1.png
docs/articles/fragmentmatching_files/figure-html/filterfragmentsplot-2.png
docs/articles/fragmentmatching_files/figure-html/plotfm22-1.png
docs/articles/fragmentmatching_files/figure-html/plotfmid-1.png
docs/articles/fragmentmatching_files/figure-html/plotfmid-2.png
docs/articles/fragmentmatching_files/figure-html/plotfmperformance-1.png
docs/articles/fragmentmatching_files/figure-html/plotfmseq-1.png
docs/articles/fragmentmatching_files/figure-html/plotfmseq-2.png
docs/articles/index.html
docs/articles/synapter.bib
docs/articles/synapter.html
docs/articles/synapter2.html
docs/articles/synapter2_files/figure-html/filtering-1.png
docs/articles/synapter2_files/figure-html/filtering-2.png
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docs/articles/synapter2_files/figure-html/gridsearch-1.png
docs/articles/synapter2_files/figure-html/intmodel-1.png
docs/articles/synapter2_files/figure-html/intmodel-2.png
docs/articles/synapter2_files/figure-html/rtmodel-1.png
docs/articles/synapter2_files/figure-html/rtmodel-2.png
docs/articles/synapter2_files/figure-html/rtmodel-3.png
docs/articles/synapter_cache/html/__packages
docs/articles/synapter_cache/html/masterFdr_cbf016498a85714ca20e500c29127beb.RData
docs/articles/synapter_cache/html/masterFdr_cbf016498a85714ca20e500c29127beb.rdb
docs/articles/synapter_cache/html/masterFdr_cbf016498a85714ca20e500c29127beb.rdx
docs/articles/synapter_cache/html/master_1784a75ed4415975cf4303536506bb2c.RData
docs/articles/synapter_cache/html/master_1784a75ed4415975cf4303536506bb2c.rdb
docs/articles/synapter_cache/html/master_1784a75ed4415975cf4303536506bb2c.rdx
docs/articles/synapter_files/figure-html/estimateFdrPlot-1.png
docs/articles/synapter_files/figure-html/hmap-1.png
docs/articles/synapter_files/figure-html/volcano-1.png
docs/authors.html
docs/docsearch.css
docs/docsearch.js
docs/index.html
docs/jquery.sticky-kit.min.js
docs/link.svg
docs/news/index.html
docs/pkgdown.css
docs/pkgdown.js
docs/pkgdown.yml
docs/reference/MasterFdrResults-class.html
docs/reference/MasterPeptides-class.html
docs/reference/Res-MatchedEMRTs.csv
docs/reference/Res-MergedPeptides.csv
docs/reference/Synapter-1.png
docs/reference/Synapter-10.png
docs/reference/Synapter-11.png
docs/reference/Synapter-12.png
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docs/reference/Synapter-6.png
docs/reference/Synapter-7.png
docs/reference/Synapter-8.png
docs/reference/Synapter-9.png
docs/reference/Synapter.html
docs/reference/createUniquePeptideDbRds.html
docs/reference/defunct.html
docs/reference/estimateMasterFdr.html
docs/reference/index.html
docs/reference/inspectPeptideScores.html
docs/reference/makeMaster.html
docs/reference/myIdentPeptides.csv
docs/reference/myQuantPeptides.csv
docs/reference/myresults.csv
docs/reference/myresults2.csv
docs/reference/plotCrossMatching.html
docs/reference/requantify.html
docs/reference/rescaleForTop3.html
docs/reference/synapter-package.html
docs/reference/synapterGuide.html
docs/reference/synapterPlgsAgreement.html
docs/reference/synapterTinyData.html
docs/reference/synergise.html
docs/reference/synergise2.html
inst/CITATION
inst/doc/Bugs.md inst/doc/Foreword.md
inst/extdata/04_test_database.fasta
inst/extdata/synapter.css
inst/reports/scripts/synergise.R inst/reports/synergise1.Rmd inst/reports/synergise2.Rmd inst/scripts/run_test_report.R man/MasterFdrResults-class.Rd man/MasterPeptides-class.Rd man/Synapter.Rd man/createUniquePeptideDbRds.Rd man/defunct.Rd man/estimateMasterFdr.Rd man/inspectPeptideScores.Rd man/makeMaster.Rd man/plotCrossMatching.Rd man/requantify.Rd man/rescaleForTop3.Rd man/synapter-package.Rd man/synapterGuide.Rd man/synapterPlgsAgreement.Rd man/synapterTinyData.Rd man/synergise.Rd man/synergise2.Rd tests/testthat.R tests/testthat/test_MSnbase-extensions.R tests/testthat/test_fragmentlibrary-functions.R tests/testthat/test_fragments-functions.R tests/testthat/test_master-functions.R tests/testthat/test_readcsv-functions.R tests/testthat/test_requantify.R tests/testthat/test_spectrum-functions.R tests/testthat/test_utils.R vignettes/Bugs.md
vignettes/Dotfiles/synapter2workflow.dot
vignettes/Figures/PLGS_create_databank1.jpg
vignettes/Figures/PLGS_create_databank2.jpg
vignettes/Figures/PLGS_db_search_options.jpg
vignettes/Figures/PLGS_output_files1.jpg
vignettes/Figures/PLGS_output_files2.jpg
vignettes/Figures/PLGS_output_files3.jpg
vignettes/Figures/synapter2workflow.png
vignettes/Foreword.md vignettes/fragmentmatching.Rmd vignettes/synapter.Rmd
vignettes/synapter.bib
vignettes/synapter2.Rmd
lgatto/synapter documentation built on Sept. 4, 2018, 6:57 a.m.