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Recent Releases of https://github.com/alexslemonade/openscpca-analysis

https://github.com/alexslemonade/openscpca-analysis - 2025-09-05

What's Changed

  • Add diagnosis map TSV by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1286
  • Scripts for running SCimilarity by @allyhawkins in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1285
  • Function for formatting AnnData prior to running SCimilarity by @allyhawkins in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1288
  • Exploration of adding SCimilarity annotations to the consensus reference - part 1 by @allyhawkins in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1278
  • Add draft TSV mapping diagnosis/cell type groups by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1284
  • Notebook to compare reference/query cell counts by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1292
  • Handle multiple LCAs by using total descendants by @allyhawkins in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1293
  • Run SCimilarity in CI by @allyhawkins in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1294
  • Docker image for cell-type-scimilarity by @allyhawkins in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1306
  • Make sure conda environment has the correct name by @allyhawkins in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1308
  • More tumor cells by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1309
  • Include ontology IDs in the SCimilarity output by @allyhawkins in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1307
  • Make sure conda environment is used by default in SCimilarity image by @allyhawkins in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1311
  • Update creation of consensus reference script to include SCimilarity by @allyhawkins in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1312
  • Add conda env to path in NB-04 image by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1313
  • Add rtracklayer to environment by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1314
  • Account for new consensus cell types in the validation groups by @allyhawkins in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1315
  • Use entrypoint to set conda environments in Docker by @jashapiro in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1316
  • Update valiation group <-> diagnosis map by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1320
  • Grab marker genes for validation of broad groups and consensus cell types by @allyhawkins in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1318

Full Changelog: https://github.com/AlexsLemonade/OpenScPCA-analysis/compare/2025-08-20...2025-09-05

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Published by github-actions[bot] 6 months ago

https://github.com/alexslemonade/openscpca-analysis - 2025-08-20

What's Changed

  • Add reference cell group table by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1162
  • Add neuroblastoma CNVs to reference tsv by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1159
  • Exploratory notebook of NB normal reference options by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1161
  • Initiate NB analysis module by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1170
  • Reformat NBAtlas to SCE and AnnData objects by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1173
  • Add marker genes for NB cell type validation by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1181
  • Script to train SingleR model with NBAtlas by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1187
  • Add script to run SingleR by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1192
  • Add optparse to ETP module by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1203
  • Exploratory notebook comparing aggregated & non-aggregated by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1194
  • NB module: Docker and remove cell id script by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1205
  • Perform exploration of splitting NE cells by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1206
  • Reorganize and lay groundwork for testing gene filtering by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1208
  • Patch fix - model file name by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1209
  • Explore gene filtering NBAtlas before SingleR by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1210
  • Update code using cell-type-consensus results by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1198
  • Update which NBAtlas label we use by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1218
  • Update marker gene TSVs by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1222
  • Notebook for all singler results by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1211
  • Spelling and anndata conversion by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1225
  • Analysis module creation for Osteosarcoma celltype analysis by @rs25-code in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1224
  • Update NBAtlas anndata reference preparation by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1230
  • Update conda lock for Ewings by @allyhawkins in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1233
  • Script to prepare anndata query object by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1231
  • SingleR report: library size and PDX by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1236
  • Try to fix Ewing error by @allyhawkins in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1237
  • Add git into (non)-ETP docker by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1240
  • Add script to generate NB normal references by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1169
  • Patch the (non)-ETP-ALL modules by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1238
  • Update environment to use scANVI in CPU by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1243
  • Add scANVI training script by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1247
  • Patch for CI for wilms-06 module by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1258
  • Update sample count in docs by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1260
  • Initiate module for annotating samples with SCimilarity by @allyhawkins in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1265
  • Add scANVI query script by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1248
  • Add reference TSV file with cell type annotations and ontology IDs for SCimilarity labels by @allyhawkins in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1268
  • Add conda environment for SCimilarity by @allyhawkins in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1274
  • Add scANVI exploratory notebook by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1269
  • Add NBAtlas ontology ids by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1277
  • Remove the myeloid grouping and update accordingly by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1279
  • Final.final NB annotation notebook by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1282

New Contributors

  • @rs25-code made their first contribution in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1224

Full Changelog: https://github.com/AlexsLemonade/OpenScPCA-analysis/compare/2025-06-05...2025-08-20

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Published by github-actions[bot] 6 months ago

https://github.com/alexslemonade/openscpca-analysis - 2025-06-05

What's Changed

  • Add shell script to run SCPCP000015 by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1115
  • Add ewings infercnv template notebook by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1118
  • Add ewings palette file by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1123
  • Template notebook fix by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1124
  • Add celltype reference file by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1128
  • Add script to run inferCNV with an "internal" reference by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1126
  • Notebook text patch by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1131
  • Don't include PDX samples in the normal references by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1135
  • Add brief exploratory notebook for normal references by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1140
  • Notebook to directly compared pooled vs internal references for ewings by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1144
  • Add brief ewings conclusions to README by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1150
  • Use docker in infercnv-consensus-cell-type by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1158

Full Changelog: https://github.com/AlexsLemonade/OpenScPCA-analysis/compare/2025-05-05...2025-06-05

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Published by github-actions[bot] 9 months ago

https://github.com/alexslemonade/openscpca-analysis - 2025-05-05

What's Changed

  • Add infercnv script by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1095
  • Update infercnv script, including clustering parameters by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1103
  • Add endothelial reference by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1108

Full Changelog: https://github.com/AlexsLemonade/OpenScPCA-analysis/compare/2025-04-07...2025-05-05

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Published by github-actions[bot] 10 months ago

https://github.com/alexslemonade/openscpca-analysis - 2025-04-07

What's Changed

  • Monthly spellcheck fixes by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1075
  • Establish infercnv consensus cell type module by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1083
  • Add CNV references and Ewings cell type exploration by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1084
  • Add inferCNV gene order script by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1092
  • Add script to create ewings normal references by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1093

Full Changelog: https://github.com/AlexsLemonade/OpenScPCA-analysis/compare/2025-03-12...2025-04-07

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Published by github-actions[bot] 11 months ago

https://github.com/alexslemonade/openscpca-analysis - 2025-03-12

What's Changed

  • Add submit a cell type annotation protocol Discussions template by @jaclyn-taroni in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1059
  • Attempt to fix submit a protocol syntax by @jaclyn-taroni in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1060
  • Add exploration notebook looking at validating consensus cell types by @allyhawkins in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1056
  • Update Grant Opportunity Guidelines for 2025 by @jaclyn-taroni in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1061
  • Add data.table and complexHeatmap to renv for cell-type-consensus by @allyhawkins in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1065
  • Render validation notebooks across all projects by @allyhawkins in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1064
  • Update readme for consensus cell type references by @allyhawkins in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1068
  • 07 annotations explore cnv by @maud-p in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1030
  • CI updates for cell-type-wilms-tumor-06 by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1071

Full Changelog: https://github.com/AlexsLemonade/OpenScPCA-analysis/compare/v0.2.2...2025-03-12

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Published by github-actions[bot] 12 months ago

https://github.com/alexslemonade/openscpca-analysis - v0.2.2

This release includes minor updates to the following modules:

  • cell-type-consensus
  • cell-type-ewings
  • cell-type-wilms-06

Within the cell-type-consensus module, the reference used to assign consensus cell types has been updated to now include neuron as a possible cell type.

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Published by allyhawkins 12 months ago

https://github.com/alexslemonade/openscpca-analysis - 2025-02-06

What's Changed

  • Add merged object to AUCell workflow by @allyhawkins in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/1023

Full Changelog: https://github.com/AlexsLemonade/OpenScPCA-analysis/compare/v0.2.1...2025-02-06

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Published by github-actions[bot] about 1 year ago

https://github.com/alexslemonade/openscpca-analysis - v0.2.1

This release includes minor updates to the following modules:

  • cell-type-ewings
  • cell-type-consensus

In particular, the workflow for assigning consensus cell types has been created in the cell-type-consensus module. This workflow is now present in OpenScPCA-nf, and results will be made available to all contributors.

New FAQs covering how to work with ScPCA data as Seurat objects and using gene symbols instead of Ensembl IDs have been added to the OpenScPCA documentation.

Rcpp package versions within modules were updated for compatibility.

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Published by allyhawkins about 1 year ago

https://github.com/alexslemonade/openscpca-analysis - 2025-01-06

What's Changed

  • Add last group of cell type ontology IDs by @allyhawkins in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/928
  • Third group of cell ontology assignments by @allyhawkins in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/926
  • Update monthly GHA timing by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/930
  • Compare clusters to cell types and marker gene set expression by @allyhawkins in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/934
  • Document terms we aren't sure about in cell ontology by @allyhawkins in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/937
  • Fix broken website links by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/943
  • Initiate seurat-conversion by @jashapiro in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/946
  • hello-clusters notebook: Perform and evaluate clustering by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/874
  • Update dockerfile in consensus module to use renv by @allyhawkins in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/950
  • Add table with number of clusters to Ewing clustering report by @allyhawkins in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/938
  • Exploration notebook for creating a reference of consensus labels by @allyhawkins in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/936
  • Add Seurat conversion script by @jashapiro in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/953
  • Use docker for seurat-conversion tests by @jashapiro in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/955
  • Bump rOpenScPCA version by @jashapiro in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/956
  • Small hello-clusters notebook cleanups by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/958
  • Dictionary and spelling by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/960
  • Only skip push step in build action by @jashapiro in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/961
  • Add Changelog for 0.2.0 by @jashapiro in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/962
  • Issue title update for Docker failures by @jashapiro in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/964
  • Add example table to analysis/README by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/947
  • try to catch copykat error by @jashapiro in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/966

Full Changelog: https://github.com/AlexsLemonade/OpenScPCA-analysis/compare/2024-12-03...2025-01-06

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Published by github-actions[bot] about 1 year ago

https://github.com/alexslemonade/openscpca-analysis - v0.2.0

This release marks the first set of community-contributed analyses to the added to the repository. These modules are focused on cell type identification and annotation for specific ScPCA datasets. Note that many of these modules are still in development at this stage and may not be fully functional.

  • cell-type-dsrct
  • cell-type-ETP-ALL-03
  • cell-type-glioblastoma
  • cell-type-nonETP-ALL-03
  • cell-type-wilms-tumor-06
  • cell-type-wilms-tumor-14

This release also adds the following new modules developed by the Data Lab:

  • cell-type-consensus: a module for exploring consensus cell types across multiple annotation methods
  • hello-clusters: a demonstration module for clustering analysis using the rOpenScPCA package
  • seurat-conversion: a module for converting SingleCellExperiment objects to Seurat objects, also using the rOpenScPCA package

Other updates in this release include:

  • a new sync-results.py script to simplify uploading (and downloading) analysis results from an analysis module to a user's S3 bucket
  • changes from miniconda to miniforge for conda usage throughout the project

While not part of this repository, we do want to also note that we have created the rOpenScPCA package, which will house utility functions commonly used by analysis modules here. The goal is to centralize common functions used across analysis modules to make it easier to share code and maintain consistency across modules.

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Published by jashapiro about 1 year ago

https://github.com/alexslemonade/openscpca-analysis - 2024-12-03

What's Changed

  • Create shell script for wilms-06 workflow by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/817
  • Update the feature/wilms-tumor-azimuth-06 branch by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/823
  • Wilms 06 update: script to prepare fetal references by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/814
  • Update cell-type-wilms-tumor-06 workflow by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/827
  • Merge main into feature/wilms-tumor-06-azimuth by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/834
  • Merge main into wilms azimuth branch by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/851
  • Adapt Azimuth code for Wilms label transfer by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/843
  • 1/n: Update wilms 06 module by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/859
  • Updated wilms clustering notebooks 1/3 by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/862
  • Updated wilms clustering notebooks 2/3 by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/863
  • Updated wilms clustering notebooks 3/3 by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/864
  • Wilms 06 module: Update and re-render 04 notebook by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/867
  • Use docker image for wilms-14 CI by @jashapiro in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/842
  • Add dockerfile for metacell analysis by @jashapiro in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/869
  • Wilms-06 update CNV methods: copykat (1/3) by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/872
  • Wilms-06 update CNV methods: infercnv (2/3) by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/873
  • Update calculate_stability usage by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/871
  • Update simulate-sce to keep all metadata columns by @jashapiro in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/879
  • Account for multiplexed samples in metadata permutation by @jashapiro in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/880
  • Wilms-06 update CNV methods (3/3), and run module in CI by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/876
  • Add rOpenScPCA to renv/docker in ewing module by @allyhawkins in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/881
  • Fix wilms-06 typos by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/885
  • Add zellkonverter to wilms-06 environment by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/890
  • Merge main into feature/wilms-tumor-06-azimuth by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/891
  • Merge wilms-tumor-06-azimuth into main by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/893
  • Remove zero cells in simulations by @jashapiro in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/898
  • only warn if there are too many labels in simulations by @jashapiro in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/901
  • Initiate module for consensus cell typing by @allyhawkins in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/903
  • Update creating-vcs.md to no longer reference selecting an Availability Zone by @jaclyn-taroni in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/904
  • Use h5ad reference in cell-type-wilms-tumor-06 by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/902
  • Update clustering report to include leiden clustering by @allyhawkins in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/895
  • Shrink and fix simulated SCEs by @jashapiro in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/907
  • Fix spelling errors by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/911
  • Add workflow for evaluating clustering to Ewing's module by @allyhawkins in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/908
  • Initial assignment of cell ontology IDs to panglao cell types by @allyhawkins in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/909
  • Regenerate wilms notebooks: Code updates by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/913
  • Regenerate wilms-tumor-06 notebooks 2/N by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/916
  • Wilms tumor notebooks: next batch by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/918
  • Make sure cluster assignments are factors by @allyhawkins in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/919
  • Next batch of SCPCP000006 notebooks by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/921
  • Penultimate batch of SCPCP000006 notebooks by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/922
  • Last batch of SCPCP000006 notebooks by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/923
  • Second group of manual cell type ontology assignments by @allyhawkins in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/917
  • Add first set of manual cell ontology assignments by @allyhawkins in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/914
  • Specify number of threads used when calculating cluster stability by @allyhawkins in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/925

Full Changelog: https://github.com/AlexsLemonade/OpenScPCA-analysis/compare/2024-11-07...2024-12-03

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https://github.com/alexslemonade/openscpca-analysis - 2024-11-07

What's Changed

  • Initiate hello-clusters by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/805
  • Add biocViews to rOpenScPCA by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/807
  • Scripts to run copykat and infercnv for a subselection of Wilms tumor from SCPCP000006 by @maud-p in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/801
  • Switch to using precommit action locally by @jashapiro in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/820
  • SCPCP00000605explore_COPYKAT by @maud-p in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/813
  • cell type/tumor annotation for ETP T-ALL (SCPCP000003) by @UTSouthwesternDSSR in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/826
  • Add fetusref.SeuratData to renv by @jashapiro in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/831
  • Add rOpenScPCA install instructions by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/833
  • Exploratory CNV notebook for Wilms tumor annotation (SCPCP000014) by @JingxuanChen7 in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/825
  • Attempt to identify tumor cells in those non-ETP samples without B cells (SCPCP000003) by @UTSouthwesternDSSR in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/815
  • Included initial exploratory analysis notebook by @danhtruong in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/794
  • Add docker image for cell-type-wilms-tumor-14 by @jashapiro in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/841
  • 04- Explore the mapping scores for Wilms tumor -06 by @maud-p in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/835
  • 06 explore infercnv for Wilms tumor -06 by @maud-p in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/828
  • Adding SCTransform as an alternative to anchor transfer-Wilms tumor annotation (SCPCP000014) by @JingxuanChen7 in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/836
  • Add words to dictionary by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/845
  • Add rough tumor classification into the result table-Wilms tumor annotation (SCPCP000014) by @JingxuanChen7 in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/846
  • Update hello-python docker image by @jashapiro in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/850
  • Draft annotation by @maud-p in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/844
  • Exploratory results for inferCNV on non-ETP samples (SCPCP000003) by @UTSouthwesternDSSR in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/838
  • Submission table for cell type and tumor classification of ETP T-ALL (SCPCP000003) by @UTSouthwesternDSSR in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/847
  • Remove rOpenScPCA from this repo by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/861

Full Changelog: https://github.com/AlexsLemonade/OpenScPCA-analysis/compare/2024-10-09...2024-11-07

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https://github.com/alexslemonade/openscpca-analysis - 2024-10-09

What's Changed

  • Initiate ropenspca package by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/735
  • Merge main into ropenscpca by @jashapiro in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/753
  • Add function to perform graph-based clustering by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/749
  • Add function to extract PC matrix (1/2) by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/758
  • Add download option to sync script by @jashapiro in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/751
  • Update sync-results.py printing by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/763
  • Extract PC matrix within clustering function (2/2) by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/759
  • Start an analysis for Wilms tumor annotation (SCPCP000014) by @JingxuanChen7 in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/764
  • Add function to sweep clustering parameters by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/765
  • Wilms tumor 06- clustering exploration by @maud-p in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/750
  • Merge main into feature/ropenscpca by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/769
  • Update rOpenScPCA gha by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/770
  • initial commit by @danhtruong in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/766
  • Add silhouette and purity functions by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/777
  • Do not print messages about syncs completing when using --dryrun by @jaclyn-taroni in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/780
  • Add function for cluster stability by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/779
  • Celltype annotation for non-ETP T-ALL (SCPCP000003) by @UTSouthwesternDSSR in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/767
  • 04annotationAcrossSamplesexploration by @maud-p in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/776
  • Initiation of new Glioblastoma analysis module by @georginaalbadri in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/783
  • Anchor transfer (with Seurat) for Wilms tumor annotation (SCPCP000014) by @JingxuanChen7 in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/784
  • Add PNGs to large file exclusion by @jaclyn-taroni in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/792
  • Merge rOpenScPCA into main by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/795
  • celltype/tumor annotation for non-ETP T-ALL (SCPCP000003) by @UTSouthwesternDSSR in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/789
  • Add remaining modules with PR triggers to the run all workflow by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/798

New Contributors

  • @JingxuanChen7 made their first contribution in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/764
  • @danhtruong made their first contribution in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/766
  • @UTSouthwesternDSSR made their first contribution in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/767
  • @georginaalbadri made their first contribution in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/783

Full Changelog: https://github.com/AlexsLemonade/OpenScPCA-analysis/compare/2024-09-04...2024-10-09

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https://github.com/alexslemonade/openscpca-analysis - 2024-09-04

What's Changed

  • Update periodic release issue template to minimize steps by @jaclyn-taroni in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/707
  • Remove defaults channel from all modules and templates by @jashapiro in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/714
  • Don't have spellcheck action fail by @jashapiro in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/720
  • revert cell-type-ewings conda-lock by @jashapiro in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/718
  • Add some words to dictionary by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/721
  • 724 Update simulation scripts to handle new data formats by @jashapiro in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/725
  • Custom function in ipynb should talk about AnnData by @jaclyn-taroni in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/715
  • Fix linking to use relative links by @jashapiro in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/736
  • Run Docker build and push on a larger runner by @jaclyn-taroni in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/734
  • Update code styling workflow by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/728
  • Add README for github workflows directory by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/739
  • Update docker images and GHA to use miniforge by @jashapiro in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/740
  • 02 run azimuth before kweight by @maud-p in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/737
  • Test fix for docker actions failing after miniforge by @jashapiro in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/744
  • Propagate miniforge Docker changes by @jashapiro in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/746
  • Update documentation to remove defaults channel and suggest miniforge by @jashapiro in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/747
  • Make GHA trigger & Dockerfiles consistent by @jashapiro in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/748

Full Changelog: https://github.com/AlexsLemonade/OpenScPCA-analysis/compare/2024-08-08...2024-09-04

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Published by github-actions[bot] over 1 year ago

https://github.com/alexslemonade/openscpca-analysis - 2024-08-08

What's Changed

  • Fix docker action repository naming by @jashapiro in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/657
  • Add ensembldb to lock file and Docker by @allyhawkins in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/660
  • Fix failed GHA for building and pushing docker images by @allyhawkins in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/661
  • One more bug in the docker GHA by @allyhawkins in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/662
  • Remove prettier from precommit recommendations by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/665
  • Make sure renv is up to date by @allyhawkins in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/667
  • 610 Add script to apply SEACells to AnnData objects by @jashapiro in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/658
  • Add running SingleR to annotation workflow by @allyhawkins in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/659
  • Add module results FAQ by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/664
  • Add metacells to GHA and handle small data by @jashapiro in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/670
  • Update CODEOWNERS by @jaclyn-taroni in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/673
  • Update CODEOWNERS by @jaclyn-taroni in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/674
  • Add zellkonverter step to doublets Dockerfile by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/675
  • Assign clusters to SCPCL000822 and SCPCL000824 by @allyhawkins in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/683
  • Start wilms analysis by @maud-p in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/681
  • Add push trigger to Wilms tumor cell typing Docker build/push workflow & proposed change to template by @jaclyn-taroni in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/688
  • Test for building Ewing Docker image by @allyhawkins in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/690
  • Work around disk space limits for building Docker images by @allyhawkins in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/692
  • Disable second docker build summary by @allyhawkins in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/695
  • Add Rosetta to Docker installation instructions by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/694
  • Add template to evaluate clustering to Ewing cell typing by @allyhawkins in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/693
  • Fix some bullet spacing by @sjspielman in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/702

New Contributors

  • @maud-p made their first contribution in https://github.com/AlexsLemonade/OpenScPCA-analysis/pull/681

Full Changelog: https://github.com/AlexsLemonade/OpenScPCA-analysis/compare/v0.1.0...2024-08-08

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Published by github-actions[bot] over 1 year ago

https://github.com/alexslemonade/openscpca-analysis - v0.1.0

This is the initial versioned release of the OpenScPCA-analysis repository. The repository at this stage should be generally complete with respect to infrastructure, but the analysis is still only in the early stages.

With respect to infrastructure, the repository contains the following components:

  • detailed documentation in the docs directory explaining how to interact with the OpenScPCA project and how to set up and run analyses (published at https://openscpca.readthedocs.io/)
  • a create-analysis-module.py script for setting up new analysis modules
  • download-data.py and download-results.py scripts to download data and results from the OpenScPCA project
  • template notebooks, scripts, environment files, and Docker images for analysis modules

The repository contains the following analysis modules that are now in a relatively mature state:

  • hello-R
  • hello-python
  • simulate-sce
  • doublet-detection

The following additional modules are in active development:

  • cell-type-ewings
  • metacells

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