Files in CambridgeCentreForProteomics/camprotR
Processing, analysing and visualising CCP proteomics data
.Rbuildignore
.github/.gitignore
.github/workflows/check-bioc.yml
.gitignore
DESCRIPTION
LICENSE
NAMESPACE
R/append_fasta.R
R/camprotR-package.R
R/combine_runs.R
R/count_features_per_protein.R
R/dep_gene2cat.R
R/dep_results.R
R/download_ccp_crap.R
R/estimate_incorporation.R
R/filter_TMT_PSMs.R
R/get_cat_palette.R
R/get_ratio.R
R/go.R
R/lfq_oops_rnase.R
R/make_fasta.R
R/modifications.R
R/normalise.R
R/parse_features.R
R/pep_oops_1.R
R/pep_oops_2.R
R/pep_oops_3.R
R/pep_oops_4.R
R/pep_silac_p0.R
R/pep_silac_p4.R
R/psm_oops_1.R
R/psm_oops_2.R
R/psm_oops_3.R
R/psm_oops_4.R
R/psm_silac_p4.R
R/psm_tmt_phospho.R
R/psm_tmt_total.R
R/ptm.R
R/qc_plots.R
R/restrict_features_per_protein.R
R/silac.R
R/silac_psm_seq_int.R
R/theme_camprot.R
R/theme_csd.R
R/tmt_qc_plots.R
R/utilities.R
README.Rmd
README.md
_pkgdown.yml
camprotR.Rproj
codecov.yml
data-raw/dep_gene2cat.R
data-raw/dep_results.R
data-raw/lfq_oops_rnase.R
data-raw/pep_silac_p0.R
data-raw/pep_silac_p4.R
data-raw/psm_silac_p4.R
data-raw/psm_tmt_phospho.R
data-raw/psm_tmt_total.R
data-raw/silac_comparison.R
data-raw/silac_p4.R
data/dep_gene2cat.rda
data/dep_results.rda
data/lfq_oops_rnase_pep.rda
data/lfq_oops_rnase_psm.rda
data/pep_oops_1.rda
data/pep_oops_2.rda
data/pep_oops_3.rda
data/pep_oops_4.rda
data/pep_silac_p0.rda
data/pep_silac_p4.rda
data/psm_oops_1.rda
data/psm_oops_2.rda
data/psm_oops_3.rda
data/psm_oops_4.rda
data/psm_silac_p4.rda
data/psm_tmt_phospho.rda
data/psm_tmt_total.rda
inst/extdata/cRAP_20190401.fasta.gz
inst/extdata/cRAP_GPM.fasta.gz
inst/extdata/commercial_reagents.fasta
inst/extdata/contaminants.fasta.gz
man/add_PTM_positions.Rd
man/add_peptide_positions.Rd
man/add_site_sequence.Rd
man/append_fasta.Rd
man/camprotR-package.Rd
man/center_normalise_to_ref.Rd
man/check_uniprot_release.Rd
man/compare_IDs.Rd
man/compare_sequences_per_protein.Rd
man/compare_single_master.Rd
man/count_features_per_protein.Rd
man/dep_gene2cat.Rd
man/dep_results.Rd
man/determine_ancestor_function.Rd
man/determine_offspring_function.Rd
man/download_ccp_crap.Rd
man/estimate_go_overrep.Rd
man/estimate_incorporation.Rd
man/expand_terms.Rd
man/filter_TMT_PSMs.Rd
man/get_all_mappings.Rd
man/get_ancestor_go.Rd
man/get_cat_palette.Rd
man/get_ccp_crap.Rd
man/get_enriched_go.Rd
man/get_incorporation.Rd
man/get_medians.Rd
man/get_notch_per_protein.Rd
man/get_parsimony_pep2prot.Rd
man/get_psm_metrics.Rd
man/get_psm_silac_mod_regex.Rd
man/get_ratio.Rd
man/get_sequence.Rd
man/get_sequence2protein.Rd
man/lfq_oops_rnase_pep.Rd
man/lfq_oops_rnase_psm.Rd
man/make_fasta.Rd
man/match_proteins.Rd
man/parse_PTM_scores.Rd
man/parse_features.Rd
man/pep_oops_1.Rd
man/pep_oops_2.Rd
man/pep_oops_3.Rd
man/pep_oops_4.Rd
man/pep_silac_p0.Rd
man/pep_silac_p4.Rd
man/plot_TMT_notch.Rd
man/plot_below_notch_per_prot.Rd
man/plot_fraction_below_notch_per_prot.Rd
man/plot_go.Rd
man/plot_incorporation.Rd
man/plot_missing_SN.Rd
man/plot_missing_SN_per_sample.Rd
man/plot_quant.Rd
man/psm_oops_1.Rd
man/psm_oops_2.Rd
man/psm_oops_3.Rd
man/psm_oops_4.Rd
man/psm_silac_p4.Rd
man/psm_tmt_phospho.Rd
man/psm_tmt_total.Rd
man/psm_to_peptide_style_modifications.Rd
man/read_infiles.Rd
man/remove_dots.Rd
man/remove_redundant_go.Rd
man/remove_silac_modifications.Rd
man/remove_x.Rd
man/restrict_features_per_protein.Rd
man/silac_psm_seq_int.Rd
man/sub_crap.Rd
man/theme_camprot.Rd
man/theme_csd.Rd
man/update_average_sn.Rd
tests/testthat.R
tests/testthat/_snaps/combine_runs/parsimony.txt
tests/testthat/_snaps/count_features_per_protein/feature_count.txt
tests/testthat/_snaps/estimate_incorporation/estimate-incorporation-hl-correlation.svg
tests/testthat/_snaps/estimate_incorporation/estimate-incorporation-peptide.svg
tests/testthat/_snaps/estimate_incorporation/estimate-incorporation-protein.svg
tests/testthat/_snaps/estimate_incorporation/estimate-incorporation-table
tests/testthat/_snaps/filter_TMT_PSMs/filter_TMT_PSMs_exprs.txt
tests/testthat/_snaps/filter_TMT_PSMs/filter_TMT_PSMs_fData.txt
tests/testthat/_snaps/filter_TMT_PSMs/update_average_sn.txt
tests/testthat/_snaps/go.md
tests/testthat/_snaps/go/plot-go.svg
tests/testthat/_snaps/normalise/center_normalise_to_ref.txt
tests/testthat/_snaps/parse_features/psm_tmt_total_parsed.txt
tests/testthat/_snaps/parse_features/small_pep_silac_p4_parsed.txt
tests/testthat/_snaps/ptm/psm_tmt_phospho_parsed.txt
tests/testthat/_snaps/ptm/psm_tmt_phospho_scored.txt
tests/testthat/_snaps/qc_plots/plot-quant-method-box.svg
tests/testthat/_snaps/qc_plots/plot-quant-method-density-facet.svg
tests/testthat/_snaps/qc_plots/plot-quant-method-density.svg
tests/testthat/_snaps/qc_plots/plot-quant-method-histogram.svg
tests/testthat/_snaps/restrict_features_per_protein/restrict-features-histogram.svg
tests/testthat/_snaps/restrict_features_per_protein/restrict-features-msnset.txt
tests/testthat/_snaps/silac/plot-incorporation-mix.svg
tests/testthat/_snaps/silac/plot-incorporation-no-mix.svg
tests/testthat/_snaps/silac_psm_seq_int/silac_psm_seq_int.txt
tests/testthat/_snaps/theme_camprot/theme-camprot-base-size-10.svg
tests/testthat/_snaps/theme_camprot/theme-camprot-default.svg
tests/testthat/_snaps/theme_camprot/theme-camprot-no-border.svg
tests/testthat/_snaps/theme_camprot/theme-camprot-not-square.svg
tests/testthat/_snaps/theme_camprot/theme-camprot-sans-serif.svg
tests/testthat/_snaps/tmt_qc_plots/notch_per_protein.txt
tests/testthat/_snaps/tmt_qc_plots/plot-below-notch-default.svg
tests/testthat/_snaps/tmt_qc_plots/plot-fraction-below-notch-default.svg
tests/testthat/_snaps/tmt_qc_plots/plot-missing-sn-per-sample.svg
tests/testthat/_snaps/tmt_qc_plots/plot-missing-sn.svg
tests/testthat/_snaps/tmt_qc_plots/plot-tmt-notch-default.svg
tests/testthat/_snaps/tmt_qc_plots/plot-tmt-notch-facet.svg
tests/testthat/setup.R
tests/testthat/test-append_fasta.R
tests/testthat/test-combine_runs.R
tests/testthat/test-count_features_per_protein.R
tests/testthat/test-download_ccp_crap.R
tests/testthat/test-estimate_incorporation.R
tests/testthat/test-filter_TMT_PSMs.R
tests/testthat/test-get_cat_palette.R
tests/testthat/test-get_ratio.R
tests/testthat/test-go.R
tests/testthat/test-modifications.R
tests/testthat/test-normalise.R
tests/testthat/test-parse_features.R
tests/testthat/test-ptm.R
tests/testthat/test-qc_plots.R
tests/testthat/test-restrict_features_per_protein.R
tests/testthat/test-setup.R
tests/testthat/test-silac.R
tests/testthat/test-silac_psm_seq_int.R
tests/testthat/test-theme_camprot.R
tests/testthat/test-tmt_qc_plots.R
tests/testthat/test-utilities.R
vignettes/.gitignore
vignettes/LFQ_parse_qc_protein_inference.Rmd
vignettes/SILAC.Rmd
vignettes/TMT_PSM_QC_Summarisation.Rmd
vignettes/camprotR.json
vignettes/crap.Rmd
vignettes/figures/msnset.png
vignettes/figures/msnset.pptx
vignettes/msnset.Rmd
