Besca

What's Changed
* 262 modified regex to accept '-' in gene names by kohleman in https://github.com/bedapub/besca/pull/263
* Update _read.py by hatjek in https://github.com/bedapub/besca/pull/264


**Full Changelog**: https://github.com/bedapub/besca/compare/2.5.2...2.5.3

What's Changed
* Bump protobuf from 3.19.4 to 3.19.5 in /devtools by dependabot in https://github.com/bedapub/besca/pull/258
* Bump joblib from 1.1.0 to 1.2.0 in /devtools by dependabot in https://github.com/bedapub/besca/pull/259
* 260 homologs folder is not installed by kohleman in https://github.com/bedapub/besca/pull/261


**Full Changelog**: https://github.com/bedapub/besca/compare/2.5.1...2.5.2

What's Changed
* 253 replace parameter bbbox_inches with bbox_inches by kohleman in https://github.com/bedapub/besca/pull/254
* 252 added matplotlib version to print_software_versions by kohleman in https://github.com/bedapub/besca/pull/255
* Bump mako from 1.1.6 to 1.2.2 in /devtools by dependabot in https://github.com/bedapub/besca/pull/256
* Bump oauthlib from 3.2.0 to 3.2.1 in /devtools by dependabot in https://github.com/bedapub/besca/pull/257


**Full Changelog**: https://github.com/bedapub/besca/compare/2.5...2.5.1

What's Changed
* Bump numpy from 1.21.5 to 1.22.0 in /devtools by dependabot in https://github.com/bedapub/besca/pull/210
* updated setup.py to create pypi packages, updated README.md to install besca from pypi by yannik-benndorf in https://github.com/bedapub/besca/pull/209
* modified setup.py by paulgeser in https://github.com/bedapub/besca/pull/212
* Fix for 166 / refactored subset_data function by paulgeser in https://github.com/bedapub/besca/pull/214
* Add pytest to environment.yml by paulgeser in https://github.com/bedapub/besca/pull/211
* fixed typo / resolve 187 by paulgeser in https://github.com/bedapub/besca/pull/213
* Added width/height to plotting functions by paulgeser in https://github.com/bedapub/besca/pull/216
* GitHub action to deploy besca to PyPI on new release by yannik-benndorf in https://github.com/bedapub/besca/pull/220
* Update _celltype_quantification.py by hatjek in https://github.com/bedapub/besca/pull/198
* Besca issue3 by kohleman in https://github.com/bedapub/besca/pull/221
* replaced bc.st.regress_out with sc.pp.scale by kohleman in https://github.com/bedapub/besca/pull/222
* 185 bcplupdate qualitative palette is not working proprely by kohleman in https://github.com/bedapub/besca/pull/224
* 197 the r code in function valoutlier needs modification by kohleman in https://github.com/bedapub/besca/pull/225
* 167 added a replace after reading in metadata.tsv by kohleman in https://github.com/bedapub/besca/pull/227
* Bump mistune from 0.8.4 to 2.0.3 in /devtools by dependabot in https://github.com/bedapub/besca/pull/231
* Added check for var_names in citeseq part of sw fixing 149 by swalpe in https://github.com/bedapub/besca/pull/230
* fix bug in bc.pl.dot_heatmap_split by yannik-benndorf in https://github.com/bedapub/besca/pull/233
* Updated Python version by yannik-benndorf in https://github.com/bedapub/besca/pull/235
* Bump nbconvert from 6.4.2 to 6.5.1 in /devtools by dependabot in https://github.com/bedapub/besca/pull/236
* Bug Fix: in commit f6c914a, regress_out was removed and only scaling … by Accio in https://github.com/bedapub/besca/pull/234
* Removed double space in Neutro signature (between FCGR3B and CXCR2) by llumdi in https://github.com/bedapub/besca/pull/232
* Critical Bug fix: in highly_variable_genes by Accio in https://github.com/bedapub/besca/pull/238
* Fix for issue 159 by paulgeser in https://github.com/bedapub/besca/pull/239
* 240 using random anndata to run test by kohleman in https://github.com/bedapub/besca/pull/241
* 12 import functions currently do not check for correct standard formatting by kohleman in https://github.com/bedapub/besca/pull/237
* Fix for issue 100 by paulgeser in https://github.com/bedapub/besca/pull/242
* Changed author in setup.py by paulgeser in https://github.com/bedapub/besca/pull/244
* updated environment.lock.yml by paulgeser in https://github.com/bedapub/besca/pull/245
* 217 omit or replace r functions by kohleman in https://github.com/bedapub/besca/pull/243
* Fix for issue 176 by paulgeser in https://github.com/bedapub/besca/pull/246
* 2.5 dev by kohleman in https://github.com/bedapub/besca/pull/247
* Update standard_workflow_besca2.ipynb by swalpe in https://github.com/bedapub/besca/pull/248
* Modified mtx read function as fix 167 introduced a bug by swalpe in https://github.com/bedapub/besca/pull/249
* Std workflow 2.5 by hatjek in https://github.com/bedapub/besca/pull/250

New Contributors
* yannik-benndorf made their first contribution in https://github.com/bedapub/besca/pull/209

**Full Changelog**: https://github.com/bedapub/besca/compare/2.4.6...2.5

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.

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.