Scanpy-scripts

* Automatically adjust PCA n_comps to deal with low cell numbers https://github.com/ebi-gene-expression-group/scanpy-scripts/pull/78

* Address bugs in highly variable genes option handling https://github.com/ebi-gene-expression-group/scanpy-scripts/pull/75

* Always calculate basic stats when filtering: https://github.com/ebi-gene-expression-group/scanpy-scripts/commit/4635a6370f5d9d187441c464f28260138e847d13
* Filter on boolean variables as catetorical: https://github.com/ebi-gene-expression-group/scanpy-scripts/commit/e1e74d3634a7dfdee998b917668a06c5db9ea734

- A variety of Scanpy's plotting functions for differential expression added:

- Violin plots: https://github.com/ebi-gene-expression-group/scanpy-scripts/pull/62
- Dot plots: https://github.com/ebi-gene-expression-group/scanpy-scripts/pull/63
- Matrix plots: https://github.com/ebi-gene-expression-group/scanpy-scripts/pull/64
- Heatmaps: https://github.com/ebi-gene-expression-group/scanpy-scripts/pull/65

- rank_genes_groups variants of these plots (see e.g. https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.rank_genes_groups_matrixplot.html#scanpy.pl.rank_genes_groups_matrixplot) made accessible via --rgg.: https://github.com/ebi-gene-expression-group/scanpy-scripts/pull/66

- Category-wise negative filtering for cells (https://github.com/ebi-gene-expression-group/scanpy-scripts/pull/68) and genes (https://github.com/ebi-gene-expression-group/scanpy-scripts/pull/70)

* Allow deactivation of log transform at normalisation

Allow specifying cell/gene prefix for all filtering attributes (59)
Make exchangeable loom more compatible with loom3 spec(56)
Allow passing additional arguments to sc.read_loom() (54)