v.1.2.0

What's Changed

• Update multimodal integration documentation by @wlason in #302
• Update pipeline.yml by @bio-la in #305
• Update run_filter.py by @deevdevil88 in #298
• Update run_scib.py by @JarneBelien in #303
• LSI-enabled BBKNN by @wlason in #301
• Update run_scanpyQC_rna.py by @wlason in #317
• Fix dsb background by @wlason in #314
• Add Run option params LISI and SCIB metrics for pipeline_integration.py by @deevdevil88 in #321
• added check for duplicated rows in submission file by @bio-la in #324
• Threads documentation by @giuliaelgarcia in #288
• Update qc.md by @bio-la in #327
• PlotQC.R errors on making plots when you have many samples, adding LimitSize=False by @deevdevil88 in #323
• From MuData to SpatialData by @SarahOuologuem in #319

New Contributors

• @JarneBelien made their first contribution in #303

Full Changelog: v.1.1.0...v.1.20

v.1.1.0

What's Changed

• Now running matplotlib 3.9: update matplotlib and change imports by @bio-la in #287
• MultiVI default training param adversarial_mixing changed to False (for updates see scvi-tools) : update multivi by @bio-la in #291

Full Changelog: v1.0.0...v.1.1.0

v1.0.0

What's Changed

• Update run_scanpyQC_rna.py to fix scrublet merge issue in ingest by @deevdevil88 in #277
• Fc matplotlib by @bio-la in #282
• minor hashing_ab bug fix by @deevdevil88 in #284
• Fixed threads number in pipeline_integration.py by @giuliaelgarcia in #279
• Fc matplotlib by @bio-la in #285

Full Changelog: v0.5.0...v1.0.0

v0.5.0

added

• added Tangram to deconvolution_spatial
• added scib metrics calculation to integration, using the scib-metrics package
• extra documentation

fixed

• fixed error in vis
  • error occurred when only wanting to plot continuous or categorical variables (or neither), not both
• fixed error in refmap
  • high threads was not recognised, now fixed.

dependencies

• All the dependencies have been updated.
  • Python>=3.10 required
• added seeds to all scvi tasks for reproducibility

v0.4.1

What's Changed

• Update assess_background.py by @deevdevil88 in #109
• Mome tenxmetrics by @bio-la in #129
• Mome tenxmetrics by @bio-la in #130
• changes to fix missing tutorials by @bio-la in #118
• Restructure usage docs by @crichgriffin in #131
• Fc sparsedocsfix by @bio-la in #133
• LSI recomputation panpipes_clustering by @SarahOuologuem in #114
• readthedocs by @SarahOuologuem in #121
• Fc sparsedocsfix by @bio-la in #134
• Fc sparsedocsfix by @bio-la in #135
• Fc fixesrefmap by @bio-la in #99
• fixed parsing solver for PCA by @bio-la in #138
• added refmap link by @bio-la in #139
• fixed info custom gene lists by @bio-la in #140
• Fc sparsedocsfix by @bio-la in #141
• rephrase index by @bio-la in #142
• Fc sparsedocsfix by @bio-la in #143
• Small code fixes in panpipes_ingest by @SarahOuologuem in #144
• call R install script by @crichgriffin in #145
• Fc sparsedocsfix by @bio-la in #146
• Mdsync by @bio-la in #147

Full Changelog: v0.4.0...v0.4.1

v0.4.0

v0.4.0

Big Change! the submission files for the ingest workflow have now changed! we require the paths to the Gene expression (RNA/GEX) and Protein (ADT) to have the following headers.

sample_id	rna_path	rna_filetype	prot_path	prot_filetype
sampleX	path/to/rna	10X_h5	path/to/prot	10x_h5

See tutorials for examples of submission files.

added

• merged PR #111:
  • LSI in panpipes_preprocess is run on the highly variable features
  • n_comp for LSI

fixed

• changed all instances of ADT into PROT
• changed all instances of GEX to RNA
• changed the params to fix plotting as mentioned in issue #41
• typo in readme
• set default seaborn <=0.12.2 to avoid issue #104, #126

auto-generated releases

What's Changed

• renaming by @bio-la in #110
• Run LSI on HVFs by @SarahOuologuem in #111
• Seaborn by @bio-la in #128
• Fc namescheck by @bio-la in #115

Full Changelog: v0.3.1...v0.4.0

v0.3.1

Updated pyproject toml to manage matplitlib version.
"matplotlib<=3.7.3" required for compatibility

What's Changed

• modify installation by @bio-la in #105
• added some description by @bio-la in #107
• testing matplotlib by @bio-la in #106

Full Changelog: v0.3.0...v0.3.1

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

v0.2.0

Merge pull request #78 from DendrouLab/fc_docs

Fc docs

v0.1.3

Various bug fixes, and small improvements.

What's Changed

• Fix R and python script paths by @crichgriffin in #14
• these changes to pipeline_vis got lost in the restructure by @crichgriffin in #16
• Improved comments and logging by @crichgriffin in #17
• [clustering] Missing script! by @crichgriffin in #19
• batch correct merge fix by @crichgriffin in #20
• Fix pyproject.toml and upgrades to documentation by @crichgriffin in #22
• remove github installs by @crichgriffin in #23
• update requirements file by @crichgriffin in #24
• Fixes #18 by @crichgriffin in #26
• [integration] Fixes the error where umaps don't plot because there are too many categories by @crichgriffin in #27
• Implement batch key argument in sc.pp.highly_variable_genes by @crichgriffin in #28
• barcode metadata df shouldnt be used for bg concat by @deevdevil88 in #29
• Update installation_rescomp.md by @crichgriffin in #30
• Update pipeline.yml by @crichgriffin in #31
• minor code fix by @deevdevil88 in #32
• Brining tenx metrics aggregation and plotting back by @crichgriffin in #33
• [QC_MM] Multiple different ADT libraries by @crichgriffin in #34
• add bbknn for prot, by @crichgriffin in #35

Full Changelog: 0.1.2...0.1.3