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Releases: bedapub/besca

2.5.5

10 Oct 13:44
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Full Changelog: 2.5.4...2.5.5

2.5.4

01 Oct 06:29
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Full Changelog: https://github.com/bedapub/besca/commits/2.5.4

Besca 2.5.3

10 Nov 16:41
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Full Changelog: 2.5.2...2.5.3

Besca 2.5.2

20 Oct 12:45
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Full Changelog: 2.5.1...2.5.2

Besca 2.5.1

19 Sep 12:51
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Full Changelog: 2.5...2.5.1

Besca 2.5

15 Sep 16:09
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Full Changelog: 2.4.6...2.5

Besca 2.4

19 Feb 13:04
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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

24 Nov 14:53
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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

07 Aug 15:35
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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