NEWS.md
In MoTrPAC/MotrpacBicQC: QC/QA functions for the MoTrPAC community
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: provide QC support for TMT-18
MotrpacBicQC 0.9.4 (2024-05-16)
- Enhance and improve
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 it is not recommended)
- Improve detecting the source of errors
- Improve verbosity and feedback to the user
MotrpacBicQC 0.9.3 (2024-03-25)
- Critical update
validate_refmetname: ensure checking the refmet standarized name. Update refmet tests
- Update
get_and_validate_mdd()
- Update REST service url
- Update Documentation
- Remove dependency on data.table
- Enhance: only one
metadata_phase file allowed
- Enhance
dl_read_gcp: replace data table by read_delim
- Enhance
open_file: accept 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 assays:
PROT_OX
- Fix package conflicts
- OLINK: write release adjustments
MotrpacBicQC 0.9.0 (2024-01-04)
- Add support for OLINK datasets (check
olink_qc vignette to find out more)
- Adjust function to download data from GCP (
dl_read_gcp):
it 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)
- Fix bug preventing the processing of BICRESULTS folders (proteomics)
- Make clear that the metadata_phase.txt file is required
- Other enhancements
MotrpacBicQC 0.8.8 (2023-06-15)
- Add 24 hours time support for the
acquisition_date (MM/DD/YYYY HH:MM:SS)
MotrpacBicQC 0.8.7 (2023-05-22)
- Add QC for the new required batching variables
- Replace deprecated
ggplot function
- Fix 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)
- Add new
dl_read_gcp
- Replace dplyr
summarise function (deprecated) by reframe
- Fix bug affecting
proteomics_plots
MotrpacBicQC 0.8.3 (2023-02-08)
- Fix typo
MotrpacBicQC 0.8.1 and 0.8.2 (2023-02-08)
- Fix bug affecting IMM assays
MotrpacBicQC 0.8.0 (2023-02-05)
- New metabolomics targeted assays (IMM_GLC, IMM_INS, IMM_CTR)
- Remove exception of non-unique raw files allowed for CONV assays, and added to IMM assays
- Improve metabolomics documentation
MotrpacBicQC 0.7.9 (2023-01-12)
- Add exception: unique raw files are now not required for metabolomics CONV assay
- Update
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)
- Improve DMAQC validation
MotrpacBicQC 0.7.5 (2022-10-21)
- Update
write_proteomics according to latest updates on data/file structure
- Fix 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
- Update
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)
- Update a package's dependency
MotrpacBicQC 0.7.1 (2022-09-17)
Updates affecting the proteomics validation:
validate_proteomics: rename argument run_by_bic to check_only_results. Default is still FALSE (it does not affect CAS)- Adjust 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)
- Update 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)
- Refactor 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: add mz/rt density plots
MotrpacBicQC 0.6.6 (2022-03-03)
- Improve reporting and handling of required files
- Fix minor bugs
MotrpacBicQC 0.6.5 (2022-02-28)
- Metabolomics: fix manifest checks.
MotrpacBicQC 0.6.4 (2022-02-27)
- Metabolomics: adjust metabolomic plots to deal with a large number of samples
- Metabolomics new plot: sum of intensity/concentration
- Metabolomics: detects negative values
- Metabolomics: update vignette
MotrpacBicQC 0.6.3 (2022-02-25)
- Proteomics: support for tmt16
- Metabolomics: Improve verbosity for wrong tissue code
MotrpacBicQC 0.6.2 (2021-12-07)
- Fix bug affecting the validation of refmet_names
- Update data objects (immunoassay added)
MotrpacBicQC 0.6.1 (2021-09-06)
- Refactor the validation of refmet_name. It now checks on at the time
using the RefMet API. It also validates multipeak isoforms
- The function
get_and_validate_mdd() donwload the entire RefMet database (warning, >15MB)
- The
metabolomics_data_dictionary data object will be soon deprecated.
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)
- Update: add human tissue codes
MotrpacBicQC 0.5.4 (2021-07-16)
- Improved version for checking the file manifest from metabolomics submissions
- Enable 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: Replace
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
MotrpacBicQC 0.5.0 (2021-04-29)
- Update data dictionary (GTech's kegg revision)
MotrpacBicQC 0.4.9 (2021-04-27)
- Bug fixes
- Update readme
MotrpacBicQC 0.4.8 (2021-04-20)
- Proteomics QC: enable option to check data processed at the BIC
- Bug fixes (color code)
MotrpacBicQC 0.4.7 (2021-04-02)
- Proteomics QC: update warnings affecting
gene_symbol and entrez_id when missing ids
- Fix issue affecting Windows machines (Pierre J-B)
- Several Color code fixes * 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)
- Update metabolomics data dictionary, including:
- Broad Metabolomics revision (39 new kegg ids * minor corrections)
- targeted refmet_name
- Fix text in warning in case of missing manifest file
- Add and improve tests
MotrpacBicQC 0.4.4 (2021-03-22)
- Fix and improve check (new required)
manifest file for untargeted metabolomics datasets
MotrpacBicQC 0.4.3 (2021-03-16)
- Update
tissue_cols data object (Nicole Gay)
MotrpacBicQC 0.4.2 (2021-03-10)
- Fix 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 return 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: restore previous version of
bic_animal_tissue_code
MotrpacBicQC 0.3.8 (2021-02-03)
- Add new assays
MotrpacBicQC 0.3.5 (2020-10-20)
- Bug fix on DMAQC to deal with missing data in DMAQC table
- Proteomics: Address 130C missing channel issue affecting the Broad
- Proteomics: add an additional QC check point to validate that all values in vial_label column are unique
- Proteomics:
write_proteomics updated (only required columns selected)
- Fix bugs and typos
MotrpacBicQC 0.3.4 (2020-10-15)
- Add a check point when expected files are not available in the manifest file
MotrpacBicQC 0.3.3 (2020-10-14)
- Fix 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
MoTrPAC/MotrpacBicQC documentation built on Sept. 26, 2024, 11:10 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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: provide QC support for TMT-18
MotrpacBicQC 0.9.4 (2024-05-16)
- Enhance and improve
dl_read_gcp: - Check if
gsutilpath is correct and report back to the user if it is not - Handle spaces in folder names (although it is not recommended)
- Improve detecting the source of errors
- Improve verbosity and feedback to the user
MotrpacBicQC 0.9.3 (2024-03-25)
- Critical update
validate_refmetname: ensure checking the refmet standarized name. Update refmet tests - Update
get_and_validate_mdd() - Update REST service url
- Update Documentation
- Remove dependency on data.table
- Enhance: only one
metadata_phasefile allowed - Enhance
dl_read_gcp: replace data table by read_delim - Enhance
open_file: accept 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 assays:
PROT_OX - Fix package conflicts
- OLINK: write release adjustments
MotrpacBicQC 0.9.0 (2024-01-04)
- Add support for OLINK datasets (check
olink_qcvignette to find out more) - Adjust function to download data from GCP (
dl_read_gcp): it automatically detects the operating system (argumentsignore_std_errandignore_std_outdeprecated) - Multiple fixes and enhancements
MotrpacBicQC 0.8.9 (2023-07-07)
- Fix bug preventing the processing of BICRESULTS folders (proteomics)
- Make clear that the metadata_phase.txt file is required
- Other enhancements
MotrpacBicQC 0.8.8 (2023-06-15)
- Add 24 hours time support for the
acquisition_date(MM/DD/YYYY HH:MM:SS)
MotrpacBicQC 0.8.7 (2023-05-22)
- Add QC for the new required batching variables
- Replace deprecated
ggplotfunction - Fix 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)
- Add new
dl_read_gcp - Replace dplyr
summarisefunction (deprecated) byreframe - Fix bug affecting
proteomics_plots
MotrpacBicQC 0.8.3 (2023-02-08)
- Fix typo
MotrpacBicQC 0.8.1 and 0.8.2 (2023-02-08)
- Fix bug affecting IMM assays
MotrpacBicQC 0.8.0 (2023-02-05)
- New metabolomics targeted assays (IMM_GLC, IMM_INS, IMM_CTR)
- Remove exception of non-unique raw files allowed for CONV assays, and added to IMM assays
- Improve metabolomics documentation
MotrpacBicQC 0.7.9 (2023-01-12)
- Add exception: unique raw files are now not required for metabolomics CONV assay
- Update
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)
- Improve DMAQC validation
MotrpacBicQC 0.7.5 (2022-10-21)
- Update
write_proteomicsaccording to latest updates on data/file structure - Fix bugs affecting
metabolomics_qcand checks onfile_manifest
MotrpacBicQC 0.7.4 (2022-10-09)
- Metabolomics plots: check if enough compounds to generate plots
- Update
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)
- Update a package's dependency
MotrpacBicQC 0.7.1 (2022-09-17)
Updates affecting the proteomics validation:
validate_proteomics: rename argumentrun_by_bictocheck_only_results. Default is stillFALSE(it does not affect CAS)- Adjust size of pdf output depending on the number of samples
- Support
BICRESULTS_YYYYMMDDfolder validation (similar to the currently supportedRESULTS_YYYYMMDDandPROCESSED_YYYYMMDDfolders). This folder is the output of the proteomics pipeline run by the BIC
MotrpacBicQC 0.7.0 (2022-08-25)
- Update 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)
- Refactor 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-06might be submitted but the input folder name isPASS1A-06)
MotrpacBicQC 0.6.7 (2022-03-11)
- DMAQC validation: print out missing vial labels
- Metabolomics QC: add mz/rt density plots
MotrpacBicQC 0.6.6 (2022-03-03)
- Improve reporting and handling of required files
- Fix minor bugs
MotrpacBicQC 0.6.5 (2022-02-28)
- Metabolomics: fix manifest checks.
MotrpacBicQC 0.6.4 (2022-02-27)
- Metabolomics: adjust metabolomic plots to deal with a large number of samples
- Metabolomics new plot: sum of intensity/concentration
- Metabolomics: detects negative values
- Metabolomics: update vignette
MotrpacBicQC 0.6.3 (2022-02-25)
- Proteomics: support for tmt16
- Metabolomics: Improve verbosity for wrong tissue code
MotrpacBicQC 0.6.2 (2021-12-07)
- Fix bug affecting the validation of refmet_names
- Update data objects (immunoassay added)
MotrpacBicQC 0.6.1 (2021-09-06)
- Refactor the validation of refmet_name. It now checks on at the time using the RefMet API. It also validates multipeak isoforms
- The function
get_and_validate_mdd()donwload the entire RefMet database (warning, >15MB) - The
metabolomics_data_dictionarydata object will be soon deprecated.
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)
- Update: add human tissue codes
MotrpacBicQC 0.5.4 (2021-07-16)
- Improved version for checking the file manifest from metabolomics submissions
- Enable 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: Replace
prettydocbyrmdformats - 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
MotrpacBicQC 0.5.0 (2021-04-29)
- Update data dictionary (GTech's kegg revision)
MotrpacBicQC 0.4.9 (2021-04-27)
- Bug fixes
- Update readme
MotrpacBicQC 0.4.8 (2021-04-20)
- Proteomics QC: enable option to check data processed at the BIC
- Bug fixes (color code)
MotrpacBicQC 0.4.7 (2021-04-02)
- Proteomics QC: update warnings affecting
gene_symbolandentrez_idwhen missing ids - Fix issue affecting Windows machines (Pierre J-B)
- Several Color code fixes * 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)
- Update metabolomics data dictionary, including:
- Broad Metabolomics revision (39 new kegg ids * minor corrections)
- targeted refmet_name
- Fix text in warning in case of missing manifest file
- Add and improve tests
MotrpacBicQC 0.4.4 (2021-03-22)
- Fix and improve check (new required) manifest file for untargeted metabolomics datasets
MotrpacBicQC 0.4.3 (2021-03-16)
- Update
tissue_colsdata object (Nicole Gay)
MotrpacBicQC 0.4.2 (2021-03-10)
- Fix bug in
validate_metabolomicsaffecting 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 return 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: restore previous version of
bic_animal_tissue_code
MotrpacBicQC 0.3.8 (2021-02-03)
- Add new assays
MotrpacBicQC 0.3.5 (2020-10-20)
- Bug fix on DMAQC to deal with missing data in DMAQC table
- Proteomics: Address 130C missing channel issue affecting the Broad
- Proteomics: add an additional QC check point to validate that all values in vial_label column are unique
- Proteomics:
write_proteomicsupdated (only required columns selected) - Fix bugs and typos
MotrpacBicQC 0.3.4 (2020-10-15)
- Add a check point when expected files are not available in the manifest file
MotrpacBicQC 0.3.3 (2020-10-14)
- Fix 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
R Package Documentation
Browse R Packages
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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