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Changelog

Source: NEWS.md

MotrpacBicQC 1.4.0 (2025-12-12)

Bug Fixes

  • PDF Plot Generation: Fixed critical issue where PDF plots were not being created when running validate_lab from scripts. Changed from invisible(gridExtra::grid.arrange()) to gridExtra::arrangeGrob() + grid::grid.draw() pattern, which properly renders to PDF device without printing TableGrob output to console

  • DMAQC Extra Samples: Fixed bug where extra samples (submitted but not expected in DMAQC) were reported but not counted as issues. Now properly sets ic = "FAIL" when extra samples are detected

  • Release Writer: Fixed bug in write_lab_releases where results data was accessed as lab_df$r instead of the correct lab_df$r_o (matching the key returned by load_lab_batch)

Improvements

  • DMAQC Validation Summary: Added informative summary message showing expected, submitted, and matched sample counts (e.g., “DMAQC summary: 761 expected, 967 submitted, 761 matched”)

  • DMAQC Extra Samples Message: Improved message to show count of extra samples (e.g., “CAS SITE IS PROVIDING 206 SAMPLE IDS THAT ARE NOT IN DMAQC”)

  • Code Optimization: Simplified multiple grepl() calls with alternation pattern (e.g., grepl("PH|AC|UB|OX", assay) instead of chained | operators)

MotrpacBicQC 1.3.0 (2025-12-06)

New Features

  • Human Study Support: Enhanced handling of HUMAN phase formats, including main and pre-COVID tranches, for more accurate validation of human study submissions

Bug Fixes

  • DMAQC Validation: Fixed a critical bug where DMAQC validation failures were not being counted in the total issues. The check_viallabel_dmaqc function returns a string status ("OK", "FAIL"), which was incorrectly checked with is.numeric(). Now properly increments the issue count when validation fails
  • Proteomics: Fixed missing sample labels when reference (Ref) channels are absent in proteomics datasets
  • Metabolomics: Fixed incorrect variable assignment in write_metabolomics_releases where cleaned sample metadata was incorrectly assigned to m_s_u instead of m_s_n
  • LAB QC Plots: Fixed plot layout issues in plot_basic_lab_qc that caused plots to print to console instead of saving to PDF. Refactored to use gridExtra::grid.arrange() properly

Improvements

  • QC Date Format: Standardized QC date format to YYYYMMDD across all validation modules (validate_lab, validate_metabolomics, validate_olink, validate_proteomics), ensuring consistency in output filenames and reports
  • Phase Parsing: Improved phase parsing in check_viallabel_dmaqc to handle complex HUMAN phase formats (e.g., HUMAN-MAIN-TR04) correctly
  • Release Writer: Added handling for human-main phase in release folder logic for proper directory structure generation
  • PDF Output: Improved plot output flow—suppresses console noise when saving to PDF and logs saved file locations

Internal Changes

  • Updated .Rbuildignore to use explicit regex patterns for more reliable build process
  • Various code refactoring for better maintainability

MotrpacBicQC 1.2.0 (2025-07-30)

New Features

  • Assay Codes: Added new assay code for Whole Genome Sequencing (WGS) to inst/extdata/assay_codes.csv

Improvements

  • Assay Codes Updates: Populated submission_code values for several existing transcriptomics and epigenomics entries; corrected typo for ‘Phosphoproteomics’
  • File Location Enforcement: Modified set_phase function to enforce that metadata_phase.txt must be located directly within the batch folder (changed recursive parameter from TRUE to FALSE)

MotrpacBicQC 1.1.0 (2025-05-01)

Improvements

  • Updated the data object assay_codes:
    • Updated omics_text values to omics technologies
    • Added ome_text for the “omes”: the complete set of a given biological entity (all genes, all proteins, etc.)
    • Added assay as a copy of assay_code

MotrpacBicQC 1.0.0 (2025-04-23)

New Features

  • Updated the data object assay_codes with 2 new variables:
    • assay_short_text: Abbreviated name specific to the assay for use in graphs and tables
    • ome_text: Omic class measured by the given assay

Improvements

  • Updated style of the vignettes

MotrpacBicQC 0.9.9 (2025-04-22)

  • Fixed minor issue with dl_read_gcp

MotrpacBicQC 0.9.8 (2025-04-10)

  • Updated dl_read_gcp: now supports gcloud in addition to gsutil

MotrpacBicQC 0.9.7 (2025-03-16)

New Features

  • Clinical Chemistry Support: Added QC support for clinical chemistry assays: glucagon, insulin, cortisol, and creatine kinase
  • Conventional metabolites (previously metab-t-conv) now expected as a new assay within this category (lab-conv)

Bug Fixes

  • Numerous bug fixes and enhancements

MotrpacBicQC 0.9.6 (2024-09-23)

  • Download and read file from GCP function can create recursive folders (@christopherjin)
  • Adjustments in metabolomics metadata sample files QC to enable processing of old submissions (before batch related variables were required)

MotrpacBicQC 0.9.5 (2024-05-22)

  • Proteomics: Added QC support for TMT-18

MotrpacBicQC 0.9.4 (2024-05-16)

  • Enhanced and improved dl_read_gcp:
    • Check if gsutil path is correct and report back to the user if it is not
    • Handle spaces in folder names (although not recommended)
    • Improved error source detection
    • Improved verbosity and feedback to the user

MotrpacBicQC 0.9.3 (2024-03-25)

  • Critical Update: Fixed validate_refmetname to ensure checking the refmet standardized name; updated refmet tests
  • Updated get_and_validate_mdd():
    • Updated REST service URL
    • Updated documentation
    • Removed dependency on data.table
  • Enhanced: only one metadata_phase file allowed
  • Enhanced dl_read_gcp: replaced data.table by read_delim
  • Enhanced open_file: accepts only tab-delimited files

MotrpacBicQC 0.9.2 (2024-03-04)

  • Critical Update: Resolved an issue where the validation of refmet names was compromised due to updates to the Metabolomics Workbench REST service. This version introduces adjustments to ensure accurate validation of refmet names.

MotrpacBicQC 0.9.1 (2024-02-02)

  • New assay: PROT_OX
  • Fixed package conflicts
  • OLINK: write release adjustments

MotrpacBicQC 0.9.0 (2024-01-04)

New Features

  • Added support for OLINK datasets (check olink_qc vignette to find out more)

Improvements

  • Adjusted function to download data from GCP (dl_read_gcp): automatically detects the operating system (arguments ignore_std_err and ignore_std_out deprecated)
  • Multiple fixes and enhancements

MotrpacBicQC 0.8.9 (2023-07-07)

  • Fixed bug preventing the processing of BICRESULTS folders (proteomics)
  • Made clear that the metadata_phase.txt file is required
  • Other enhancements

MotrpacBicQC 0.8.8 (2023-06-15)

  • Added 24-hour time support for the acquisition_date (MM/DD/YYYY HH:MM:SS)

MotrpacBicQC 0.8.7 (2023-05-22)

  • Added QC for the new required batching variables
  • Replaced deprecated ggplot function
  • Fixed issues with dl_read_gcp
  • Other adjustments

MotrpacBicQC 0.8.6 (2023-04-21)

  • Minor adjustments

MotrpacBicQC 0.8.5 (2023-03-18)

  • New tissue codes, abbreviations, and colors available for lateral Gastrocnemius and vena cava

MotrpacBicQC 0.8.4 (2023-02-20)

  • Added new dl_read_gcp
  • Replaced dplyr summarise function (deprecated) by reframe
  • Fixed bug affecting proteomics_plots

MotrpacBicQC 0.8.3 (2023-02-08)

  • Fixed typo

MotrpacBicQC 0.8.1 and 0.8.2 (2023-02-08)

  • Fixed bug affecting IMM assays

MotrpacBicQC 0.8.0 (2023-02-05)

New Features

  • New metabolomics targeted assays (IMM_GLC, IMM_INS, IMM_CTR)

Bug Fixes

  • Removed exception of non-unique raw files allowed for CONV assays, and added to IMM assays

Improvements

  • Improved metabolomics documentation

MotrpacBicQC 0.7.9 (2023-01-12)

  • Added exception: unique raw files are now not required for metabolomics CONV assay
  • Updated assay_codes: immunoassay/IMMUNO added. The table now also includes assay hex colours and assay abbreviation

MotrpacBicQC 0.7.8 (2022-12-13)

  • Bug fix

MotrpacBicQC 0.7.7 (2022-12-08)

  • Better handling of large proteomics datasets:
    • Proteomics RII plots are skipped if the dataset is too large
    • Larger PDF size for proteomics ratio plots
  • Several improvements and enhancements

MotrpacBicQC 0.7.6 (2022-10-27)

  • Improved DMAQC validation

MotrpacBicQC 0.7.5 (2022-10-21)

  • Updated write_proteomics according to latest updates on data/file structure
  • Fixed bugs affecting metabolomics_qc and checks on file_manifest

MotrpacBicQC 0.7.4 (2022-10-09)

  • Metabolomics plots: check if enough compounds to generate plots
  • Updated assay_codes: conventional assays code added (CONV)

MotrpacBicQC 0.7.3 (2022-10-02)

  • Adjustments to generate data releases (deal with pass1a/1c)
  • Version number will be added to upcoming releases

MotrpacBicQC 0.7.2 (2022-09-22)

  • Updated a package’s dependency

MotrpacBicQC 0.7.1 (2022-09-17)

Updates affecting the proteomics validation:

  • validate_proteomics: renamed argument run_by_bic to check_only_results. Default is still FALSE (does not affect CAS)
  • Adjusted size of PDF output depending on the number of samples
  • Support BICRESULTS_YYYYMMDD folder validation (similar to the currently supported RESULTS_YYYYMMDD and PROCESSED_YYYYMMDD folders). This folder is the output of the proteomics pipeline run by the BIC

MotrpacBicQC 0.7.0 (2022-08-25)

  • Updated MoTrPAC color abbreviations

MotrpacBicQC 0.6.9 (2022-07-09)

  • Metabolomics: new density plots
  • Code optimizations
  • Bug fixes affecting file manifest checks

MotrpacBicQC 0.6.8 (2022-04-11)

  • Refactored the DMAQC validation. A new file will be required when:
    • Two phases are combined in the same batch (e.g., PASS1A-06|PASS1C-06)
    • The phase content is different from the input folder name (e.g., PASS1C-06 might be submitted but the input folder name is PASS1A-06)

MotrpacBicQC 0.6.7 (2022-03-11)

  • DMAQC validation: print out missing vial labels
  • Metabolomics QC: added mz/rt density plots

MotrpacBicQC 0.6.6 (2022-03-03)

  • Improved reporting and handling of required files
  • Fixed minor bugs

MotrpacBicQC 0.6.5 (2022-02-28)

  • Metabolomics: fixed manifest checks

MotrpacBicQC 0.6.4 (2022-02-27)

  • Metabolomics: adjusted metabolomic plots to deal with a large number of samples
  • Metabolomics new plot: sum of intensity/concentration
  • Metabolomics: detects negative values
  • Metabolomics: updated vignette

MotrpacBicQC 0.6.3 (2022-02-25)

  • Proteomics: support for TMT-16
  • Metabolomics: improved verbosity for wrong tissue code

MotrpacBicQC 0.6.2 (2021-12-07)

  • Fixed bug affecting the validation of refmet_names
  • Updated data objects (immunoassay added)

MotrpacBicQC 0.6.1 (2021-09-06)

  • Refactored the validation of refmet_name. It now checks one at a time using the RefMet API. It also validates multipeak isoforms
  • The function get_and_validate_mdd() downloads the entire RefMet database (warning: >15MB)
  • The metabolomics_data_dictionary data object will be deprecated soon

MotrpacBicQC 0.6.0 (2021-09-06)

  • Support DMAQC validation of human submissions

MotrpacBicQC 0.5.9 (2021-08-10)

  • Adjustments for PASS1C-06
  • Bug fixes affecting HUMAN phase processing

MotrpacBicQC 0.5.8 (2021-08-06)

  • New Metabolomics QC plots: number and proportion of named vs unnamed features identified

MotrpacBicQC 0.5.7 (2021-08-05)

  • New proteomics QC plots for protein coverage

MotrpacBicQC 0.5.6 (2021-07-22)

  • Bug fix

MotrpacBicQC 0.5.5 (2021-07-21)

  • Added human tissue codes

MotrpacBicQC 0.5.4 (2021-07-16)

  • Improved version for checking the file manifest from metabolomics submissions
  • Enabled DMAQC validation for submissions combining multiple phases (e.g. PASS1A-06 + PASS1C-06)

MotrpacBicQC 0.5.3 (2021-06-25)

  • Metabolomics QC: new metabolomics QC plots, including number of IDs per sample, intensity distribution, and percentage of NA values
  • Markdown: replaced prettydoc by rmdformats
  • New assay code: CONV (Targeted Conventional metabolites or clinical analytes, provided by Duke)

MotrpacBicQC 0.5.2 (2021-06-23)

  • New Phase: HUMAN (name of the new project folder for the human studies)
  • Proteomics QC: new proteomics QC plot, number of unique IDs per sample
  • Proteomics QC: improved QC plots

MotrpacBicQC 0.5.1 (2021-05-03)

  • New metabolomics sample_type: QC-ReCAS, Global reference biological material prepared at CAS

MotrpacBicQC 0.5.0 (2021-04-29)

  • Updated data dictionary (GTech’s KEGG revision)

MotrpacBicQC 0.4.9 (2021-04-27)

  • Bug fixes
  • Updated README

MotrpacBicQC 0.4.8 (2021-04-20)

  • Proteomics QC: enabled option to check data processed at the BIC
  • Bug fixes (color code)

MotrpacBicQC 0.4.7 (2021-04-02)

  • Proteomics QC: updated warnings affecting gene_symbol and entrez_id when missing IDs
  • Fixed issue affecting Windows machines (Pierre J-B)
  • Several color code fixes for assay (Nicole G)
  • Bug fixes

MotrpacBicQC 0.4.6 (2021-03-26)

  • New QC checks for the new proteomics requirements

MotrpacBicQC 0.4.5 (2021-03-25)

  • Updated metabolomics data dictionary, including:
    • Broad Metabolomics revision (39 new KEGG IDs + minor corrections)
    • Targeted refmet_name
  • Fixed text in warning in case of missing manifest file
  • Added and improved tests

MotrpacBicQC 0.4.4 (2021-03-22)

  • Fixed and improved check for new required manifest file for untargeted metabolomics datasets

MotrpacBicQC 0.4.3 (2021-03-16)

  • Updated tissue_cols data object (Nicole Gay)

MotrpacBicQC 0.4.2 (2021-03-10)

  • Fixed bug in validate_metabolomics affecting unnamed sample check

MotrpacBicQC 0.4.1 (2021-03-08)

  • Improved QC for the required manifest file (proteomics and metabolomics)

MotrpacBicQC 0.4.0 (2021-03-04)

  • Metabolomics data dictionary available as a data object: metabolomics_data_dictionary
  • The function get_and_validate_mdd() still works, but does not pull the data from Metabolomics Workbench. Just returns metabolomics_data_dictionary
  • Bug fix: the manifest issue count now properly displays the number of issues detected

MotrpacBicQC 0.3.9 (2021-02-10)

  • Bug fix: restored previous version of bic_animal_tissue_code

MotrpacBicQC 0.3.8 (2021-02-03)

  • Added new assays

MotrpacBicQC 0.3.5 (2020-10-20)

  • Bug fix on DMAQC to deal with missing data in DMAQC table
  • Proteomics: addressed 130C missing channel issue affecting the Broad
  • Proteomics: added additional QC check point to validate that all values in vial_label column are unique
  • Proteomics: write_proteomics updated (only required columns selected)
  • Fixed bugs and typos

MotrpacBicQC 0.3.4 (2020-10-15)

  • Added check point when expected files are not available in the manifest file

MotrpacBicQC 0.3.3 (2020-10-14)

  • Fixed bugs affecting manifest files
  • Adjustments when files don’t meet requirements

MotrpacBicQC 0.3.2 (2020-10-06)

  • Check new required manifest file in both proteomics and metabolomics submissions
  • Raw file manifest now optional

MotrpacBicQC 0.3.1 (2020-10-04)

  • Proteomics write proteomics
  • Proteomics load metabolomics

MotrpacBicQC 0.3.0 (2020-09-21)

  • Proteomics QC support

MotrpacBicQC 0.2.2 (2020-08-09)

  • New assays

MotrpacBicQC 0.2.1 (2020-06-03)

  • Bug fixes