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Lnanderson patch 1#46

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lnanderson wants to merge 129 commits intovladpetyuk:mastervladpetyuk/PlexedPiper:masterfrom PNNL-Comp-Mass-Spec:lnanderson-patch-1PNNL-Comp-Mass-Spec/PlexedPiper:lnanderson-patch-1Copy head branch name to clipboard

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Commits on May 13, 2021

• Merge pull request #2 from PNNL-Comp-Mass-Spec/improve/read_study_design

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Commits on Jun 7, 2021

• Ms2 to Ms3 linking

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• Merge pull request #3 from CamiloPosso/Camilo-dev

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Commits on Jun 11, 2021

• fix typo

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• Merge pull request #4 from PNNL-Comp-Mass-Spec/dev

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Commits on Jun 21, 2021

• Update README.md

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Commits on Jun 23, 2021

• removed DMS functionality

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• updated documentation

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• added PNNL.DMS.utils dependencies to vignettes

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Commits on Jun 24, 2021

• update function names

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• Update DESCRIPTION

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• Update README.md

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• migrated some functionality to MSnID

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• Update DESCRIPTION

  

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• Merge branch 'master' into upgrade/prune-DMS-tools

  

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• Delete make_results_ratio_ph_debug.R

  

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• Delete tmt_pipeline_global_PNNL_DMS.Rmd

  

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• Delete tmt_pipeline_global_PNNL_DMS_MoTrPAC.html

  

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Commits on Jun 25, 2021

• Merge pull request #6 from PNNL-Comp-Mass-Spec/upgrade/prune-DMS-tools

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Commits on Jul 29, 2021

• Added missing data.table import

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• Updated NAMESPACE

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• Convert crosstab to matrix before constructing MSnSet

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• Merge pull request #7 from PNNL-Comp-Mass-Spec/bugfix/missing_datatable_imports

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• Merge pull request #8 from PNNL-Comp-Mass-Spec/bugfix/convert_crosstab_to_matrix

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Commits on Sep 22, 2021

• Removed DMS functionality from study design tools

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• Merge pull request #9 from PNNL-Comp-Mass-Spec/bugfix/prune-more-DMS-tools

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Commits on Oct 14, 2021

• Added UniProt support to MoTrPAC BIC functions

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• Merge pull request #10 from PNNL-Comp-Mass-Spec/dev2/motrpac-uniprot-support

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Commits on Jan 29, 2022

• Update filter_msgf_data.R

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• Import all of data.table

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• Fix imports

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• Minor bugfix

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• Merge pull request #12 from PNNL-Comp-Mass-Spec/update/filter_msgf_data

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Commits on Feb 9, 2022

• Add R-CMD-check

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Commits on Feb 10, 2022

• Clean up vignettes

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• Remove old functions

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Commits on Feb 11, 2022

• Update FASTA remapping functions

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Commits on Mar 30, 2022

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• Update test-remap_accessions_uniprot_to_gene_fasta.R

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Commits on Apr 12, 2022

• Merge pull request #13 from PNNL-Comp-Mass-Spec/bugfix/fix-checks

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Commits on Apr 13, 2022

• Add run_plexedpiper

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• Update run_plexedpiper.R

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• Update example

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• Update vignettes

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Commits on Apr 14, 2022

• Update run_plexedpiper

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• Merge pull request #16 from PNNL-Comp-Mass-Spec/feature/run-plexedpiper

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Commits on Apr 16, 2022

• Update DESCRIPTION

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• Add pkgdown website

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• Update run_plexedpiper docs

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• Create NEWS.md

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• Merge pull request #17 from PNNL-Comp-Mass-Spec/dev/pkgdown

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• Update README.md

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Commits on Apr 28, 2022

• Add infer_parsimonious_accessions related arguments to run_plexedpiper

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• Update DESCRIPTION: new version

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Commits on Apr 30, 2022

• Clean up vignettes folder

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• Update DESCRIPTION

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• Merge pull request #18 from PNNL-Comp-Mass-Spec/feature/add-msnid-related-options

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Commits on May 26, 2022

• adding SiteID to the filter docs

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Commits on Jul 1, 2022

• Add prefix argument to read_study_design

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• Add option to read mzid files

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• Merge pull request #21 from PNNL-Comp-Mass-Spec/trigger_workflow_run

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Commits on Jul 6, 2022

• Add prefix argument to run_plexedpiper

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Commits on Aug 6, 2022

• Update create_crosstab.R

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• Update version

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• Merge pull request #22 from PNNL-Comp-Mass-Spec/check-study-design

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• Update run_plexedpiper.R

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• Update MoTrPAC BIC functions

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• Version updates

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Commits on Nov 3, 2022

• Fix GENCODE errors

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Commits on Nov 4, 2022

• GENCODE fixes

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• Update motrpac_bic_funtions.R

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• Update motrpac_bic_functions

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• Update to v0.4.0

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• Update NEWS.md

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Commits on Jan 10, 2023

• Merge pull request #23 from PNNL-Comp-Mass-Spec/update/add-gencode

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• Remove redundant GENCODE IDs

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Commits on Jan 14, 2023

• Shorten UniProt headers in run_plexedpiper output

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Commits on Jan 23, 2023

• Merge pull request #24 from PNNL-Comp-Mass-Spec/update/run_plexedpiper

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• Merge pull request #25 from PNNL-Comp-Mass-Spec/update/run_plexedpiper

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• Update to 0.4.1

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Commits on Apr 19, 2023

• Update read study design

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• Create msfragger filtering function based on filter_msgf_data

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