Releases: bedapub/besca
Releases · bedapub/besca
2.5.5
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
Contributors
kohleman, dependabot, and swalpe
Assets 2
Besca 2.5.3
Contributors
kohleman and hatjek
Assets 2
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
Contributors
kohleman and dependabot
Assets 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
Contributors
kohleman and dependabot
Assets 2
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
Contributors
Accio, kohleman, and 6 other contributors
Assets 2
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