2.5.4

What's Changed

• Bump werkzeug from 2.2.3 to 3.0.1 in /devtools by @dependabot in #330
• Bump aiohttp from 3.8.5 to 3.9.0 in /devtools by @dependabot in #332
• Bump urllib3 from 1.26.8 to 1.26.18 in /devtools by @dependabot in #328
• Bump pillow from 9.3.0 to 10.0.1 in /devtools by @dependabot in #327
• Update doc-tests.yml by @kohleman in #333
• Updated dblabels to correspond to db by @swalpe in #336
• updated versioneer by @kohleman in #348
• Bump fonttools from 4.29.1 to 4.43.0 in /devtools by @dependabot in #334
• Bump jinja2 from 3.0.3 to 3.1.3 in /devtools by @dependabot in #335
• Bump aiohttp from 3.9.0 to 3.9.2 in /devtools by @dependabot in #338
• Bump grpcio from 1.53.0 to 1.53.2 in /devtools by @dependabot in #339
• Bump urllib3 from 1.26.18 to 1.26.19 in /devtools by @dependabot in #351
• Bump aiohttp from 3.9.2 to 3.10.2 in /devtools by @dependabot in #355
• Bump tornado from 6.3.3 to 6.4.1 in /devtools by @dependabot in #354
• Bump requests from 2.31.0 to 2.32.2 in /devtools by @dependabot in #356
• Bump certifi from 2023.7.22 to 2024.7.4 in /devtools by @dependabot in #350
• Bump pillow from 10.0.1 to 10.3.0 in /devtools by @dependabot in #343
• Update CellNames_scseqCMs6_Extrasigs.mouse.gmt by @swalpe in #340
• Bump idna from 3.3 to 3.7 in /devtools by @dependabot in #360
• Bump tqdm from 4.63.0 to 4.66.3 in /devtools by @dependabot in #359
• Bump jinja2 from 3.1.3 to 3.1.4 in /devtools by @dependabot in #358
• Bump werkzeug from 3.0.1 to 3.0.3 in /devtools by @dependabot in #357
• Bump zipp from 3.7.0 to 3.19.1 in /devtools by @dependabot in #349
• Bump scikit-learn from 1.0.2 to 1.5.0 in /devtools by @dependabot in #352
• Bump torch from 1.13.1 to 2.2.0 in /devtools by @dependabot in #353
• Sinfo by @kohleman in #361
• Bump numexpr from 2.8.1 to 2.8.5 in /devtools by @dependabot in #362

Full Changelog: https://github.com/bedapub/besca/commits/2.5.4

Besca 2.5.3

What's Changed

• #262 modified regex to accept '-' in gene names by @kohleman in #263
• Update _read.py by @hatjek in #264

Full Changelog: 2.5.2...2.5.3

Besca 2.5.2

What's Changed

• Bump protobuf from 3.19.4 to 3.19.5 in /devtools by @dependabot in #258
• Bump joblib from 1.1.0 to 1.2.0 in /devtools by @dependabot in #259
• #260 homologs folder is not installed by @kohleman in #261

Full Changelog: 2.5.1...2.5.2

Besca 2.5.1

What's Changed

• #253 replace parameter bbbox_inches with bbox_inches by @kohleman in #254
• #252 added matplotlib version to print_software_versions by @kohleman in #255
• Bump mako from 1.1.6 to 1.2.2 in /devtools by @dependabot in #256
• Bump oauthlib from 3.2.0 to 3.2.1 in /devtools by @dependabot in #257

Full Changelog: 2.5...2.5.1

Besca 2.5

What's Changed

• Bump numpy from 1.21.5 to 1.22.0 in /devtools by @dependabot in #210
• updated setup.py to create pypi packages, updated README.md to install besca from pypi by @yannik-benndorf in #209
• modified setup.py by @paulgeser in #212
• Fix for #166 / refactored subset_data function by @paulgeser in #214
• Add pytest to environment.yml by @paulgeser in #211
• fixed typo / resolve #187 by @paulgeser in #213
• Added width/height to plotting functions by @paulgeser in #216
• GitHub action to deploy besca to PyPI on new release by @yannik-benndorf in #220
• Update _celltype_quantification.py by @hatjek in #198
• Besca issue#3 by @kohleman in #221
• replaced bc.st.regress_out with sc.pp.scale by @kohleman in #222
• 185 bcplupdate qualitative palette is not working proprely by @kohleman in #224
• 197 the r code in function valoutlier needs modification by @kohleman in #225
• #167 added a replace after reading in metadata.tsv by @kohleman in #227
• Bump mistune from 0.8.4 to 2.0.3 in /devtools by @dependabot in #231
• Added check for var_names in citeseq part of sw fixing #149 by @swalpe in #230
• fix bug in bc.pl.dot_heatmap_split by @yannik-benndorf in #233
• Updated Python version by @yannik-benndorf in #235
• Bump nbconvert from 6.4.2 to 6.5.1 in /devtools by @dependabot in #236
• Bug Fix: in commit f6c914a, regress_out was removed and only scaling … by @Accio in #234
• Removed double space in Neutro signature (between FCGR3B and CXCR2) by @llumdi in #232
• Critical Bug fix: in highly_variable_genes by @Accio in #238
• Fix for issue #159 by @paulgeser in #239
• #240 using random anndata to run test by @kohleman in #241
• 12 import functions currently do not check for correct standard formatting by @kohleman in #237
• Fix for issue #100 by @paulgeser in #242
• Changed author in setup.py by @paulgeser in #244
• updated environment.lock.yml by @paulgeser in #245
• 217 omit or replace r functions by @kohleman in #243
• Fix for issue #176 by @paulgeser in #246
• 2.5 dev by @kohleman in #247
• Update standard_workflow_besca2.ipynb by @swalpe in #248
• Modified mtx read function as fix #167 introduced a bug by @swalpe in #249
• Std workflow 2.5 by @hatjek in #250

New Contributors

• @yannik-benndorf made their first contribution in #209

Full Changelog: 2.4.6...2.5

Besca 2.4

Major changes includes:

• dependencies to rpy2 and R libraries

• Rwrappers functions :
  + dsb_normalize
  + deviance for HVG selection
  + maxLikGlobalDimEst for data dimensionnality
  + valOutlier (Estimates and returns the thresholds to use for gene/cell filtering)
  + scTransform

• auto-annot comparison reports is now generic and include a riverplot

• R called into the notebooks + installation procedures

Bug / warning fixed:

• if bbknn batch call contains only one category, waring is set up #112
• exporting of a unique labelling is possible #105

Additional improvements:

• default datasets is now Kotliarov for the different notebooks.
• Small function to convert undirected signatures dictionary to signed one to use combined_signature_score as a routine;
• Updating URLs for Granja datasets (new Zenodo upload).
• some code refactoring in particular in export functions.

Besca 2.3

New implementations and bug fixes including:

New features:

• number of hvgs now take into account the batches
• geometric mean vs arithmetic mean
• riverplot display to compare 2 categories

Dependencies:

• Scanpy 1.6

Signatures and Nomenclatures

• update of the neuron nomenclature
• platelet signature added

Fixes:

• bug fix in the pseudo bulk function
• export fix for the FAIR export. cp10K exported to help upload in mongodb database (no dependency of the reformat C program)

Standard workflow:

• Standard workflow renamed (from 2.0 to 2)
• Standard workflow is automatically exported with the analysis name as an html file.

Besca 2.2

Release of Besca 2.2:

• Batch correction default is BBKNN

• Cite-Seq in standard workflow

• auto_annot merged in

• Bescape interface available

• Sig-Annot with parameters output

• Improved Sig Annot for epithelial like cells

• DBLabel annotation for interoperability of the annotations

• Making GEMS connection possible

• Sig-Annot graph visualization

• Versionneer

• Link to all datasets in Zenodo and check function to output required URL