Lnanderson patch 1 #46
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Update read_study_design.R
Ms2 to Ms3 linking
fix tool2suffix typo
Upgrade/prune dms tools
…le_imports Bugfix/missing datatable imports
…b_to_matrix Convert crosstab to matrix before constructing MSnSet
…tools Removed DMS functionality from study design tools
…support Added UniProt support to MoTrPAC BIC functions
Greatly reduce computation time and memory. The filter object only requires an MSnID with columns to calculate FDR and columns used for filtering.
Update motrpac_bic_funtions.R
Bugfix: multiple PTM types on same sequence
Fix separation of Specie into protein_id and sequence columns when PTMs are denoted by '@'
Include more robust checks for study design tables
Update how results are written to tables (set na to empty strings) and save RData files with compression
Version change from 0.4.1 to 0.5.0. Update run_plexedpiper and its helper functions to allow for the processing of redox proteomics data. Also increase the minimum MSnID version number to prevent 'function not in namespace' errors caused by installation of the Bioconductor version.
Update test-remap_accessions_refseq_to_gene_fasta to use specific conversion table to ensure reproducibility.
Replace get_study_design_by_dataset_package with read_study_design_from_DMS.
Capitalize MSFragger. Reflow text. Remove ... parameter, which was a carry-over from filter_msgf_data. Align code.
Add input checks. Improve readability with switch. Add global variables.
Fix checks for valid TMT layout.
Remove tidyselect import: the where function is now imported from dplyr.
Replace get_AScore_results with read_AScore_results_from_DMS.
Only run when a new release is published or upon workflow dispatch.
Only keep current release machines.
…r_redox Add redox processing capability to run_plexedpiper
Added Zenodo DOI badge and "Citation Guidance" section to include full citation.
vladpetyuk
approved these changes
Jan 21, 2025
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Add updated Zenodo DOI badge and "Citation Guidance" to include full citation.