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