mag lab predator peaks list read incorrectly#35

Open

deweycw wants to merge 209 commits into

EMSL-Computing:masterfrom

deweycw:pks-bug

Commits on Aug 12, 2024

Commits on Aug 13, 2024

Merge master into lcms_dev
kheal
committed

Commits on Aug 14, 2024

Commits on Aug 15, 2024

Commits on Aug 16, 2024

Add work towards aligning mass features
kheal
committed

Commits on Aug 19, 2024

Commits on Aug 20, 2024

Commits on Aug 26, 2024

Begin adding more dimensions to agglomerative_clustering, move to KDtree for speed
kheal
committed

Commits on Sep 12, 2024

Commits on Sep 19, 2024

Commits on Sep 20, 2024

Commits on Sep 23, 2024

Commits on Sep 24, 2024

Merge branch 'peak_shape_metrics' into lcms_dev_collection
kheal
committed

Commits on Sep 25, 2024

Add functionality for multi-batch alignment to lcms collection
kheal
committed

Commits on Sep 26, 2024

Commits on Sep 27, 2024

Add ability to add basic chromotography to lcmscollection
kheal
committed

Commits on Sep 30, 2024

Commits on Nov 18, 2024

Merge master into lcms_dev_collection
kheal
committed

Commits on Feb 12, 2025

Merge branch 'master' into lcms_dev_collection
kheal
committed

Commits on Feb 13, 2025

Clean up collection branch for distribution
kheal
committed

Commits on Feb 27, 2025

Prepare collection for distribution
kheal
committed

Commits on Mar 13, 2025

remove dask, remove extra dataframe step, block runtime warnings, set coll_mf_id column as index in add_consensus_mass_features()
Ciesielski, Danielle K
committed

Commits on Apr 14, 2025

added 2 basic plots, needs complex plot
Ciesielski, Danielle K
committed
temp working files for complex plot
Ciesielski, Danielle K
committed
added consensus plot
Ciesielski, Danielle K
committed
replacing workflow file
Ciesielski, Danielle K
committed

Commits on Apr 16, 2025

adding to docstrings, change mass feat to mz feat
Ciesielski, Danielle K
committed
modifying cluster_summary_dataframe
Ciesielski, Danielle K
committed

Commits on Apr 17, 2025

Merge master into lcms_dev_collection
kheal
committed
Move cluster_summary_df to be a property
kheal
committed
update show_all
Ciesielski, Danielle K
committed
moved plotting functions after consensus features are added
Ciesielski, Danielle K
committed
Merge branch 'lcms_dev_collection_consensusplot' into 'lcms_dev_collection'
Nellie Ciesielski
committed

Commits on Apr 30, 2025

Merge master into feature branch
kheal
committed

Commits on May 27, 2025

Merge main into lcms collection branch
kheal
committed

Commits on Jun 5, 2025

scaled distances used for clustering
danielle.ciesielski@pnnl.gov
committed

Commits on Jun 19, 2025

Add scaling to clustering distance matrix, generate figure to evaluate distance matrix
Nellie Ciesielski
committed
Merge branch 'ldc_distfigs' into 'lcms_dev_collection'
Nellie Ciesielski
committed

Commits on Jul 14, 2025

Cluster outlier frequency plot
Nellie Ciesielski
committed
Merge branch 'ldc_distfigs' into 'lcms_dev_collection'
Nellie Ciesielski
committed

Commits on Jul 18, 2025

Commits on Jul 28, 2025

Commits on Jul 29, 2025

Commits on Jul 30, 2025

Merge branch 'lcms_dev_collection_raw_data_handle' into 'lcms_dev_collection'
kheal
committed

Commits on Aug 4, 2025

Commits on Aug 13, 2025

Commits on Sep 2, 2025

Inducing mass features
Nellie Ciesielski
committed
Merge branch 'ldc_distfigs' into 'lcms_dev_collection'
Nellie Ciesielski
committed

Commits on Sep 11, 2025

Merge master into branch
kheal
committed

Commits on Sep 17, 2025

Commits on Sep 18, 2025

WIP exporter for collection
kheal
committed

Commits on Oct 2, 2025

initiating new branch for mr
danielle.ciesielski@pnnl.gov
committed
initiating new branch for mr
danielle.ciesielski@pnnl.gov
committed
Allow induced feature search to run in parallel
Nellie Ciesielski
committed
Merge branch 'ldc_parallel_mf_search' into 'lcms_dev_collection'
Nellie Ciesielski
committed
Merge remote-tracking branch 'origin/lcms_dev_collection' into ldc_pivottables
danielle.ciesielski@pnnl.gov
committed

Commits on Oct 6, 2025

first pass at pivot tables
danielle.ciesielski@pnnl.gov
committed
update docstring for mass_features_to_df
danielle.ciesielski@pnnl.gov
committed

Commits on Oct 8, 2025

Merge remote-tracking branch 'origin/lcms_dev_collection' into ldc_consensusreport
danielle.ciesielski@pnnl.gov
committed

Commits on Oct 10, 2025

working through issues processing on 1 core
danielle.ciesielski@pnnl.gov
committed

Commits on Oct 13, 2025

mostly working
danielle.ciesielski@pnnl.gov
committed
found the last bug, should be ready
danielle.ciesielski@pnnl.gov
committed
remove debugging linews
danielle.ciesielski@pnnl.gov
committed
remove more debugging lines
danielle.ciesielski@pnnl.gov
committed
Merge branch 'ldc_pivottables' of code.emsl.pnl.gov:mass-spectrometry/corems into ldc_consensusreport
danielle.ciesielski@pnnl.gov
committed
updating workflow with pivot tables
danielle.ciesielski@pnnl.gov
committed

Commits on Oct 15, 2025

first pass at consensus report, fix bug with merge
danielle.ciesielski@pnnl.gov
committed

Commits on Oct 16, 2025

update mean mode for consensus report
danielle.ciesielski@pnnl.gov
committed
update workflow, small fix, and beginning of cluster_dictionary brainstorming
danielle.ciesielski@pnnl.gov
committed

Commits on Dec 4, 2025

Commits on Jan 17, 2026

Commits on Jan 19, 2026

Commits on Jan 26, 2026

Commits on Jan 27, 2026

Commits on Jan 31, 2026

Commits on Feb 4, 2026

Modify ms2 mirror plotting to accept a list of spectral libraries
kheal
committed

Commits on Feb 9, 2026

Commits on Feb 19, 2026

Add [M]+ to ion type dictionary
kheal
committed

Commits on Feb 25, 2026

Commits on Feb 27, 2026

Commits on Mar 1, 2026

Commits on Mar 2, 2026

Add better handling for exporting with mixed TF confidence scores
kheal
committed

Commits on Mar 3, 2026

Handle ms2 scans that are outside the bounds of integration
kheal
committed

Commits on Mar 16, 2026

Merge branch 'lcms_dev_collection' into 'corems_4_0'
corilo
committed

Commits on Apr 7, 2026

Merge branch 'monet_bug_fixes_corems40' into 'corems_4_0'
kheal
committed

Commits on Apr 30, 2026

Commits on Jun 12, 2026

error with how mag lab predator files are read
deweycw
committed