Files in ftwkoopmans/msdap
Mass Spectrometry Downstream Analysis Pipeline

.Rbuildignore

.gitignore

DESCRIPTION

LICENSE

NAMESPACE

R/dataset.R R/dea.R R/export_data_tables.R R/export_stats_genesummary.R R/filter_peptides.R R/gene_idmapping.R R/merge_replicate_samples.R R/msdap-package.R R/msqrobsum__bugfix.R R/normalize_vwmb.R R/parse_encyclopedia.R R/parse_expressionset.R R/parse_fragpipe.R R/parse_fragpipe_legacy.R R/parse_longformat_generic.R R/parse_maxquant.R R/parse_metamorpheus.R R/parse_openms.R R/parse_peaks.R R/parse_proteomediscoverer_txt.R R/plot_benchmark.R R/plot_differential_detect.R R/plot_missing_values.R R/plot_normalization.R R/plot_peptide_data.R R/plot_protein_stats.R R/plot_retention_time.R R/plot_sample_metadata.R R/plot_sample_pca.R R/plot_score_distributions.R R/plot_variance_explained.R R/plot_volcano.R R/process_peptide_data.R R/quickstart.R R/report_as_rmarkdown.R R/rollup.R R/sample_metadata.R R/stats_differential_abundance.R R/stats_differential_detect.R R/stats_summary.R R/util_expressionset.R R/util_fasta.R R/util_files.R R/util_generic.R R/util_infer_metadata_from_file.R R/util_log.R R/util_normalization.R R/util_rmarkdown.R README.Rmd README.md doc/custom_limma.Rmd doc/custom_limma.md doc/custom_norm_dea.Rmd doc/custom_norm_dea.md doc/differential_detection.Rmd doc/differential_detection.md doc/differential_expression_analysis.Rmd doc/differential_expression_analysis.md doc/docker.Rmd doc/docker.md

doc/images/DEA-workflow.png

doc/images/custnorm-venn-1.png

doc/images/customlimma-validation-1.png

doc/images/dd-zscore-hist-1.png

doc/images/dd-zscore-roc-1.png

doc/images/intro-PXD007683-rt-histogram-1.png

doc/images/msdap-overview.png

doc/images/msdap_docker_cartoon.png

doc/images/msdap_docker_cartoon.svg

doc/images/qc-cov_loo_outlier.png

doc/images/qc-detect_counts.png

doc/images/qc-foldchange_outlier.png

doc/images/qc-pca_color_codes.png

doc/images/qc-pca_outlier.png

doc/images/qc-rt_ko5_outlier.png

doc/images/qc-rt_wt4_typical.png

doc/images/qc-rt_wt5_outlier.png

doc/images/qc-stat-fc-density_Klaassen_shisa6ip.png

doc/images/qc-volcano_Klaassen_shisa6ip.png

doc/intro.Rmd doc/intro.md

doc/logo/msdap_logo.svg

doc/logo/msdap_logo_small.png

doc/misc/FragPipe_Quant_MS1.png

doc/misc/FragPipe_database.png

doc/misc/FragPipe_workflow_by-filename.png

doc/misc/FragPipe_workflow_exp-biorep.png

doc/misc/MS-DAP Format.rs

doc/misc/Spectronaut_report.png

doc/misc/openms_lfq_workflow_v0.2.bat

doc/misc/peaks_config.png

doc/rpackage.Rmd doc/rpackage.md doc/userguide.Rmd doc/userguide.md

docker/Dockerfile

docker/msdap_launcher_unix.sh

docker/msdap_launcher_windows.ps1

examples/data/Bader2020_pmid32485097_report.pdf examples/data/Klaassen2018_pmid26931375_report.pdf examples/data/OConnel2018_pmid29635916_report.pdf

examples/data/dataset_Klaassen2018_pmid26931375.zip

examples/example_Klaassen2018_pmid26931375.R examples/example_OConnel2018_pmid29635916.R

inst/CITATION

inst/extdata/Skyline_HYE124_TTOF5600_64var_it2.tsv.gz

msdap.Rproj

tests/exploration/msempire_debug_false_negative_results.R tests/exploration/msempire_feedback.R tests/exploration/msempire_reproducibility_needs_set-seed.R tests/exploration/msqrob_pvalue_histogram.R tests/prepare_test_datasets.R tests/testthat.R tests/testthat/helper.R tests/testthat/test_dea_reproducibility.R tests/testthat/test_filtering.R tests/testthat/test_fragpipe_parser.R tests/testthat/test_normalization.R tests/testthat/test_normalization_reproducibility.R tests/testthat/test_pipeline-vs-msempire.R tests/testthat/test_pipeline-vs-msqrob.R

ftwkoopmans/msdap documentation built on March 5, 2025, 12:15 a.m.

rdrr.io home R language documentation Run R code online

CRAN packages Bioconductor packages R-Forge packages GitHub packages

Note that we can't provide technical support on individual packages. You should contact the package authors for that.

ftwkoopmans/msdap
Mass Spectrometry Downstream Analysis Pipeline

Files in ftwkoopmans/msdap
Mass Spectrometry Downstream Analysis Pipeline

R Package Documentation

Browse R Packages

We want your feedback!

ftwkoopmans/msdap Mass Spectrometry Downstream Analysis Pipeline

Files in ftwkoopmans/msdap Mass Spectrometry Downstream Analysis Pipeline

R Package Documentation

Browse R Packages

We want your feedback!

ftwkoopmans/msdap
Mass Spectrometry Downstream Analysis Pipeline

Files in ftwkoopmans/msdap
Mass Spectrometry Downstream Analysis Pipeline