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