Files in peterblattmann/SWATH2stats
Transform and Filter SWATH Data for Statistical Packages
.Rbuildignore
.github/.gitignore
.github/workflows/pkgdown.yaml
.gitignore
DESCRIPTION
NAMESPACE
NEWS
R/JPP_update.R
R/assess_decoy_rate.R
R/assess_fdr_byrun.R
R/assess_fdr_overall.R
R/convert4MSstats.R
R/convert4PECA.R
R/convert4aLFQ.R
R/convert4mapDIA.R
R/convert4pythonscript.R
R/convert_protein_ids.R
R/count_analytes.R
R/data.R
R/disaggregate.R
R/filter_all_peptides.R
R/filter_mscore.R
R/filter_mscore_condition.R
R/filter_mscore_fdr.R
R/filter_mscore_freqobs.R
R/filter_on_max_peptides.R
R/filter_on_min_peptides.R
R/filter_proteotypic_peptides.R
R/import_data.R
R/mscore4assayfdr.R
R/mscore4pepfdr.R
R/mscore4protfdr.R
R/plot.fdr_cube.R
R/plot.fdr_table.R
R/plot_correlation_between_samples.R
R/plot_variation.R
R/plot_variation_vs_total.R
R/reduce_OpenSWATH_output.R
R/removeDecoyProteins.R
R/sample_annotation.R
R/transform_MSstats_OpenSWATH.R
R/unifyProteinGroupLabels.R
R/validate_columns.R
R/write_matrix_peptides.R
R/write_matrix_proteins.R
README.Rmd
README.md
_pkgdown.yml
data/MSstats_data.txt.gz
data/OpenSWATH_data.txt.gz
data/Spyogenes.rda
data/Study_design.txt.gz
inst/CITATION
inst/scripts/featurealigner2msstats_withRT.py
man/JPP_update.Rd
man/MSstats_data.Rd
man/OpenSWATH_data.Rd
man/Spyogenes.Rd
man/Study_design.Rd
man/add_genesymbol.Rd
man/assess_decoy_rate.Rd
man/assess_fdr_byrun.Rd
man/assess_fdr_overall.Rd
man/convert4MSstats.Rd
man/convert4PECA.Rd
man/convert4aLFQ.Rd
man/convert4mapDIA.Rd
man/convert4pythonscript.Rd
man/convert_protein_ids.Rd
man/count_analytes.Rd
man/disaggregate.Rd
man/filter_all_peptides.Rd
man/filter_mscore.Rd
man/filter_mscore_condition.Rd
man/filter_mscore_fdr.Rd
man/filter_mscore_freqobs.Rd
man/filter_on_max_peptides.Rd
man/filter_on_min_peptides.Rd
man/filter_proteotypic_peptides.Rd
man/import_data.Rd
man/load_mart.Rd
man/mscore4assayfdr.Rd
man/mscore4pepfdr.Rd
man/mscore4protfdr.Rd
man/plot.fdr_cube.Rd
man/plot.fdr_table.Rd
man/plot_correlation_between_samples.Rd
man/plot_variation.Rd
man/plot_variation_vs_total.Rd
man/reduce_OpenSWATH_output.Rd
man/removeDecoyProteins.Rd
man/rmDecoyProt.Rd
man/sample_annotation.Rd
man/transform_MSstats_OpenSWATH.Rd
man/unifyProteinGroupLabels.Rd
man/validate_columns.Rd
man/write_matrix_peptides.Rd
man/write_matrix_proteins.Rd
tests/test-all.R
tests/testthat/test_FDRfunctions.R
tests/testthat/test_biomart.R
tests/testthat/test_convert.R
tests/testthat/test_filtering.R
tests/testthat/test_loading.R
tests/testthat/test_matrixwriting.R
tests/testthat/test_plots.R
vignettes/SWATH2stats_example_script.Rmd
vignettes/SWATH2stats_vignette.Rnw
