v0.5.0

What's Changed

• Take into account that chromosomes may be removed when specifying manual reference by @grst in #135
• Feat: Feature gene annotation by @grantn5 in #132

New Contributors

• @lorenzoamir made their first contribution in #131
• @grantn5 made their first contribution in #132

Full Changelog: v0.4.5...v0.5.0

v0.4.5

What's Changed

• Add cell_line and window_size parameters to copykat by @josephreplogle in #124
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #120

New Contributors

• @josephreplogle made their first contribution in #124

Full Changelog: v0.4.4...v0.4.5

v0.4.4

What's Changed

• template update icbi lab infercnvpy v0.3.0 by @grst in #119
• Update gtfparse version requirement by @jpintar in #118

Full Changelog: v0.4.3...v0.4.4

v0.4.3

What's Changed

• Fix codecov CI and update template by @grst in #85
• added mouse functinality for copyKAT by @abyssum in #92
• scverse cookiecutter template update v0.2.22 by @grst in #111
• Fix heatmap passing of uns data to scanpy.pl.heatmap by @jpintar in #110
• Fix support for vmax/vmin parameters for heatmaps by @grst in #113
• Pin gtfparse < 2 by @grst in #112

New Contributors

• @jpintar made their first contribution in #110

Full Changelog: v0.4.2...v0.4.3

v0.4.2

Fixes

• allow heatmap to use user's dendrogram by @mmfalco in #72

Chore

• Automated template update from cookiecutter-scverse by @github-actions in #67
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #68

New Contributors

• @mmfalco made their first contribution in #72

Full Changelog: v0.4.1...v0.4.2

v0.4.1

Fixes

• Fix incompatibility with gtfparse>=2 by @grst in #66

v0.4.0

Fixes

• Heatmaps look for existing colors in adata.uns by @codyheiser in #46
• Fixing the filter sizes by @redst4r in #51

Other changes

• Switch to cookiecutter-scverse template by @grst in #42. This implies
  • change of the build system to hatch
  • move documentation from github pages to readthedocs.

v0.3.0

Additions

• It is now possible to read and process results of SCEVAN (#32)
• ITHCNA and ITHGEX metrics (#30 by @elisapanizzolo and @grst)
• The copyKAT wrapper now takes the norm_cell_names parameter and returns tumor/normal predictions (#25 by @jingxinfu)

Fixes

• Don't hardcode copykat column names in results data frame (#24 by @abyssum)

v0.2.0

Additions

• Add wrapper for copyKAT (#21 by @abyssum)
• Update CI to test R-based functions (#21)

Fixes

• Fix use_rep parameter in pl.chromosome_heatmap (#20).

v0.1.2

Fixes

• Plotting a chromosome_heatmap_summary now works even if the matrix in obsm is in dense format.