v0.3.0 - the spatial transcriptomics update

News

• spatial transcriptomics is now supported with the following workflows
  • panpipes qc_spatial
  • panpipes preprocess_spatial
  • panpipes deconvolution_spatial

Checkout the documentation at https://panpipes-pipelines.readthedocs.io/ and tutorials at https://panpipes-tutorials.readthedocs.io/en/latest/

The other important change is that the qc_mm workflow was renamed ingest to better reflect that the workflow loads and concatenates data, and computes QC metrics but does not filter the data, so the output data of ingest is not QC'd data

What's Changed

• load_mudatas fix by @crichgriffin in #58
• Update install.md by @deevdevil88 in #79
• Merging in the documentation for the website by @crichgriffin in #57
• fixed assess_background.py to account for unequal samples in rna & prot by @deevdevil88 in #61
• Fc docs by @bio-la in #81
• update for spatial by @crichgriffin in #82
• add contribute instructions to index by @crichgriffin in #83
• Update index.md by @crichgriffin in #85
• Merge pull request #85 from DendrouLab/crichgriffin-readthedocs-patch1 by @crichgriffin in #86
• Update integration.md by @deevdevil88 in #88
• cleanup for clustering yml by @bio-la in #91
• documentation ingest fix by @crichgriffin in #94
• missing package openpyxl - checked on new PyPy installation by @crichgriffin in #95
• specify same packages as conda by @crichgriffin in #96
• Fc so spatial by @bio-la in #72
• change to index by @bio-la in #97
• Fc test multimodal by @bio-la in #90

Full Changelog: v0.2.0...v0.3.0