Releases: theislab/scib
Releases · theislab/scib
v1.0.2
Contributors
danielStrobl and mumichae
Assets 4
v1.0.1
What's Changed
- Added embed to opt_louvain in metrics function (#277) by @lauradmartens in #281
- [WIP] fixed clisi scaling bug by @LuckyMD in #287
- Remove
,inboolvar by @johnarevalo in #295 - Update dependency versions by @mumichae in #294
New Contributors
- @lauradmartens made their first contribution in #281
- @johnarevalo made their first contribution in #295
Full Changelog: v1.0.0...v1.0.1
Contributors
johnarevalo, LuckyMD, and 2 other contributors
Assets 4
v1.0.0
What's Changed
- Add igraph to dependencies by @scottgigante in #134
- [WIP] DESC integration by @LuckyMD in #131
- Add louvain dependency by @scottgigante in #135
- Add fastMNN prototype by @lazappi in #126
- added saucie by @danielStrobl in #129
- don't overwrite adata.X in combat integration by @danielStrobl in #138
- Add scGen to data integration benchmark by @LuckyMD in #127
- Error for saucie if input is dense by @danielStrobl in #139
- Unintegrated metrics by @mumichae in #133
- Removed undefined palette definition by @danielStrobl in #142
- Rescale lisi (updated to latest master) by @mumichae in #143
- scIB not compatible with scanpy >= 1.5 by @scottgigante in #144
- Update metrics.py by @danielStrobl in #146
- added log-transform argument to normalize function by @LisaSikkema in #149
- add scanvi to scib by @danielStrobl in #132
- Improve documentation for isolated label score by @mumichae in #152
- Update integration.py by @danielStrobl in #151
- Fixing F1 isolated label score by @mumichae in #154
- Enable Bioconductor 3.11 compatibility by @LuckyMD in #162
- Revert "Enable Bioconductor 3.11 compatibility" by @LuckyMD in #163
- Update scran normalization for bioc 3.11, closes #141 by @scottgigante in #157
- changed trajectory metric to only consider largest connected component by @danielStrobl in #165
- Modify how embeddings are stored in Seurat objects by @lazappi in #167
- Catch metrics errors by @danielStrobl in #161
- added Seurat RPCA mode by @LuckyMD in #172
- [WIP] Free memory after running normalize by @LuckyMD in #156
- Coerce to Csparsematrix for C++ conversion efficiency by @scottgigante in #164
- added new methods names by @martaint in #174
- Update runMethods.R by @danielStrobl in #176
- Fix small bug in scanvi function by @danielStrobl in #181
- Fix finding optimal resolution for clustering by @mumichae in #184
- Merge benchmarks into a single output file by @lazappi in #179
- Include LISI files during package installation by @mumichae in #186
- Add UMAP plots to metrics by @lazappi in #169
- Isolated label fix by @mumichae in #187
- Check for empty files when merging benchmarks by @lazappi in #190
- Added error checks for scran normalization by @LuckyMD in #194
- Handle empty input files when saving embedding plots by @lazappi in #193
- Bugfix in PCA regression by @mumichae in #197
- Fix LISI error for small values by @mbuttner in #188
- change adata to adata_tmp in LISI_graph by @mbuttner in #201
- Deactivate anndata2ri after preprocessing by @scottgigante in #202
- Analysis notebook updates by @LuckyMD in #206
- further analysis notebook update by @LuckyMD in #207
- Update scIB-python.yml by @danielStrobl in #147
- fix bug in silhouete calculation by @Hrovatin in #212
- updated version of plotting function by @martaint in #199
- Tidy my plotting functions by @lazappi in #214
- Isolated label asw embed by @mumichae in #213
- Fix: Anndata concatenate causes shuffled batches by @mumichae in #215
- GitHub actions integration by @mumichae in #205
- [WIP] Remove scanpy<1.5 requirement by @danielStrobl in #218
- Remove method dependencies by @danielStrobl in #223
- Remove locked dependencies by @danielStrobl in #224
- Update integration.py by @danielStrobl in #231
- add mapping orthologous genes by @martaint in #234
- Update README.md by @danielStrobl in #232
- update scanpy and anndata by @LuckyMD in #243
- Remove redundant cc score code by @mumichae in #241
- Moving files to scib-pipeline and scib-reproducibility by @mumichae in #217
- Allow specific pseudotime column for TI metric by @mumichae in #249
- Update docstring for get_root by @mumichae in #250
- Fix TI metric by @mumichae in #251
- Allow CSR sparse matrix for PCR by @mumichae in #252
- Catch RootCellError and return score of 0 by @mumichae in #254
- Refactor metrics by @mumichae in #256
- fix missing metrics module by @mumichae in #258
- fix kbet metric by @mbuttner in #257
- Check dependies in functions by @mumichae in #262
- Reimplement ARI by @mumichae in #263
- Check kbet lisi by @mbuttner in #264
- Refactor metrics by @mumichae in #265
- Check metrics by @mumichae in #268
- add per batch trajectory score by @danielStrobl in #273
- Packaging by @mumichae in #272
New Contributors
- @scottgigante made their first contribution in #134
- @LisaSikkema made their first contribution in #149
- @Hrovatin made their first contribution in #212
Full Changelog: 0.2.0...v1.0.0
Contributors
lazappi, scottgigante, and 7 other contributors