Files in MiguelCos/fragNterminomics
Annotation and processing of peptides from FragPipe search results
.Rbuildignore
.gitignore
.vscode/tasks.json
CITATION.cff
DESCRIPTION
NAMESPACE
R/annotate_nterm.R
R/annotate_peptides.R
R/best_modified_peptides_from_psm_file.R
R/categorize_nterm.R
R/count_location_nterm.R
R/data.R
R/feature_specific_fdr.R
R/get_cleave_area.R
R/helper_functions.R
R/normalize_peptide_abund_by_protein_abund.R
R/peptide2matrix.R
R/protein_quant_sum_from_best_psms.R
R/purify_n_normalize.R
R/summarize_peptide_counts.R
README.md
data-raw/DATASET.R
data-raw/abundance_peptide_MD.tsv
data-raw/abundance_protein_MD.tsv
data-raw/annotation.csv
data-raw/annotation.txt
data-raw/peptide.tsv
data-raw/protein.fas
data-raw/protein.tsv
data-raw/psm.tsv
data/fasta.rda
data/pept_abund_mat.rda
data/pept_ident.rda
data/prot_abund_mat.rda
data/prot_ident.rda
data/sample_annotation.rda
fragNterminomics.Rproj
man/annotate_nterm.Rd
man/annotate_peptides.Rd
man/categorize_nterm.Rd
man/count_location_nterm.Rd
man/fasta.Rd
man/feature_fdr_correction.Rd
man/get_cleave_area.Rd
man/list_peptides.Rd
man/pept_abund_mat.Rd
man/pept_ident.Rd
man/peptide2protein_normalization.Rd
man/peptide_matrix_count.Rd
man/prot_abund_mat.Rd
man/prot_ident.Rd
man/proteins_from_psms.Rd
man/psmtsv_to_modified_peptides.Rd
man/purify_n_normalize.Rd
man/sample_annotation.Rd
man/sample_proteins.Rd
man/summarize_peptide_counts.Rd
report/outputs/annotated_best_psm_modified_peptide.tsv
report/outputs/limma_merged_terminomics_and_proteomics.tsv
report/outputs/uniprot_features_pkd.rds
terminomics_analysis_workflow.md
terminomics_analysis_workflow.qmd
terminomics_analysis_workflow_files/figure-commonmark/unnamed-chunk-13-1.png
terminomics_analysis_workflow_files/figure-commonmark/unnamed-chunk-18-1.png
terminomics_analysis_workflow_files/figure-commonmark/unnamed-chunk-23-1.png
terminomics_analysis_workflow_files/figure-commonmark/unnamed-chunk-46-1.png
terminomics_analysis_workflow_files/figure-commonmark/unnamed-chunk-51-1.png
terminomics_analysis_workflow_files/figure-commonmark/unnamed-chunk-57-1.png
terminomics_analysis_workflow_files/figure-commonmark/unnamed-chunk-59-1.png
terminomics_analysis_workflow_files/figure-gfm/unnamed-chunk-13-1.png
terminomics_analysis_workflow_files/figure-gfm/unnamed-chunk-18-1.png
terminomics_analysis_workflow_files/figure-gfm/unnamed-chunk-23-1.png
terminomics_analysis_workflow_files/figure-gfm/unnamed-chunk-46-1.png
terminomics_analysis_workflow_files/figure-gfm/unnamed-chunk-51-1.png
terminomics_analysis_workflow_files/figure-gfm/unnamed-chunk-57-1.png
terminomics_analysis_workflow_files/figure-gfm/unnamed-chunk-59-1.png
terminomics_analysis_workflow_files/figure-gfm/unnamed-chunk-65-1.png
