v0.2.4

This release includes a minor update to the cell-type-consensus module.
The reference used to assign consensus cell types has been updated to now assign a consensus cell type when two of the three automated cell type methods (SingleR, CellAssign, and SCimilarity) agree, but the third method is unable to classify a cell.

2026-01-06

What's Changed

• Use bigger disk for scimilarity by @allyhawkins in #1369
• Update GHAs to quarterly by @sjspielman in #1372
• Fix hello-clusters by @sjspielman in #1377
• Add hello-clusters to the run all GHA by @sjspielman in #1378
• Add typos to precommit by @sjspielman in #1375
• Fix some typos by @sjspielman in #1381
• Bigger disk for NB module by @sjspielman in #1383

Full Changelog: 2025-11-05...2026-01-06

2025-11-05

What's Changed

• Update cell type diagnosis notebook by @sjspielman in #1357
• Monthly spellcheck by @sjspielman in #1359

Full Changelog: 2025-10-06...2025-11-05

v0.2.3

The following includes the new modules developed by the Data Lab:

• infercnv-consensus-cell-type: a module for exploring different strategies to use consensus cell types as a normal reference when running InferCNV
• cell-type-neuroblastoma-04: a module for annotating the Neuroblastoma samples in SCPCP000004
• cell-type-scimilarity: a module for annotating cells using SCimilarity

The cell-type-consensus module was updated to now incorporate annotations from the cell-type-scimilarity module such that consensus cell types are now assigned if 2 out of 3 methods agree (SingleR, CellAssign, and SCimilarity).

This release includes minor updates to the following modules:

• cell-type-wilms-06
• cell-type-ETP-ALL-03
• cell-type-nonETP-ALL-03
• cell-type-ewings

The following community-contributed analysis modules have been initiated and are in active development:

• cell-type-osteosarcoma-23

2025-10-06

What's Changed

• Add scimilarity annotations to assigning consensus cell types by @allyhawkins in #1323
• Remove spaces from diagnosis celltypes file by @sjspielman in #1322
• Compare SCimilarity results to existing consensus cell type annotations by @allyhawkins in #1321
• Fix typos for release by @allyhawkins in #1329
• Changelog for v0.2.3 by @allyhawkins in #1331
• Account for multiple sample types in consensus cell type assignment by @allyhawkins in #1332
• Make sure the new modules are included in the run all workflow by @allyhawkins in #1334
• GHA infercnv module fixes by @sjspielman in #1336
• Add notebook comparing consensus cell type outputs by @allyhawkins in #1339
• Add duckplyr to consensus renv for use with validation notebooks by @allyhawkins in #1340
• Add leukemias to dictionary by @sjspielman in #1343
• Clean up assigning consensus cell type script by @allyhawkins in #1337
• Regenerate validation notebooks by @allyhawkins in #1344
• Replace rols in renv by @allyhawkins in #1348
• Use ontologyIndex to grab CL ids by @allyhawkins in #1349
• Add cell-type-scimilarity to build all docker images by @allyhawkins in #1350

Full Changelog: 2025-09-05...2025-10-06

2025-09-05

What's Changed

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

Full Changelog: 2025-08-20...2025-09-05

2025-08-20

What's Changed

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

New Contributors

• @rs25-code made their first contribution in #1224

Full Changelog: 2025-06-05...2025-08-20

2025-06-05

What's Changed

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

Full Changelog: 2025-05-05...2025-06-05

2025-05-05

What's Changed

• Add infercnv script by @sjspielman in #1095
• Update infercnv script, including clustering parameters by @sjspielman in #1103
• Add endothelial reference by @sjspielman in #1108

Full Changelog: 2025-04-07...2025-05-05

2025-04-07

What's Changed

• Monthly spellcheck fixes by @sjspielman in #1075
• Establish infercnv consensus cell type module by @sjspielman in #1083
• Add CNV references and Ewings cell type exploration by @sjspielman in #1084
• Add inferCNV gene order script by @sjspielman in #1092
• Add script to create ewings normal references by @sjspielman in #1093

Full Changelog: 2025-03-12...2025-04-07