Releases · theislab/scib

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