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Recent Releases of panpipes

panpipes - v.1.2.0

What's Changed

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

New Contributors

  • @JarneBelien made their first contribution in https://github.com/DendrouLab/panpipes/pull/303

Full Changelog: https://github.com/DendrouLab/panpipes/compare/v.1.1.0...v.1.20

- Python
Published by bio-la about 1 year ago

panpipes - v.1.1.0

What's Changed

  • Now running matplotlib 3.9: update matplotlib and change imports by @bio-la in https://github.com/DendrouLab/panpipes/pull/287
  • MultiVI default training param adversarial_mixing changed to False (for updates see scvi-tools) : update multivi by @bio-la in https://github.com/DendrouLab/panpipes/pull/291

Full Changelog: https://github.com/DendrouLab/panpipes/compare/v1.0.0...v.1.1.0

- Python
Published by bio-la almost 2 years ago

panpipes - v1.0.0

What's Changed

  • Update runscanpyQCrna.py to fix scrublet merge issue in ingest by @deevdevil88 in https://github.com/DendrouLab/panpipes/pull/277
  • Fc matplotlib by @bio-la in https://github.com/DendrouLab/panpipes/pull/282
  • minor hashing_ab bug fix by @deevdevil88 in https://github.com/DendrouLab/panpipes/pull/284
  • Fixed threads number in pipeline_integration.py by @giuliaelgarcia in https://github.com/DendrouLab/panpipes/pull/279
  • Fc matplotlib by @bio-la in https://github.com/DendrouLab/panpipes/pull/285

Full Changelog: https://github.com/DendrouLab/panpipes/compare/v0.5.0...v1.0.0

- Python
Published by crichgriffin almost 2 years ago

panpipes - v0.5.0

added

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

- Python
Published by crichgriffin about 2 years ago

panpipes - v0.4.1

What's Changed

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

Full Changelog: https://github.com/DendrouLab/panpipes/compare/v0.4.0...v0.4.1

- Python
Published by crichgriffin over 2 years ago

panpipes - 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.

| sampleid | rnapath | rnafiletype | protpath | protfiletype | | --------- | ----------- | ------------ | ------------ | ------------- | | sampleX | path/to/rna | 10Xh5 | 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 https://github.com/DendrouLab/panpipes/pull/110
  • Run LSI on HVFs by @SarahOuologuem in https://github.com/DendrouLab/panpipes/pull/111
  • Seaborn by @bio-la in https://github.com/DendrouLab/panpipes/pull/128
  • Fc namescheck by @bio-la in https://github.com/DendrouLab/panpipes/pull/115

Full Changelog: https://github.com/DendrouLab/panpipes/compare/v0.3.1...v0.4.0

- Python
Published by crichgriffin over 2 years ago

panpipes - 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 https://github.com/DendrouLab/panpipes/pull/105
  • added some description by @bio-la in https://github.com/DendrouLab/panpipes/pull/107
  • testing matplotlib by @bio-la in https://github.com/DendrouLab/panpipes/pull/106

Full Changelog: https://github.com/DendrouLab/panpipes/compare/v0.3.0...v0.3.1

- Python
Published by crichgriffin over 2 years ago

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

Full Changelog: https://github.com/DendrouLab/panpipes/compare/v0.2.0...v0.3.0

- Python
Published by crichgriffin over 2 years ago

panpipes - v0.2.0

- Python
Published by crichgriffin over 2 years ago

panpipes - v0.1.3

Various bug fixes, and small improvements.

What's Changed

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

Full Changelog: https://github.com/DendrouLab/panpipes/compare/0.1.2...0.1.3

- Python
Published by crichgriffin about 3 years ago

panpipes - Restructured the repo so it installs with pip

This means that when the mudata version be need is added to PyPi, we can also add panpipes to PyPi

What's Changed

  • restructured to allow for install from pip by @crichgriffin in https://github.com/DendrouLab/panpipes/pull/12

Full Changelog: https://github.com/DendrouLab/panpipes/compare/0.1.1...0.1.2

- Python
Published by crichgriffin about 3 years ago

panpipes - freeze code prior to file restructure

This is to freeze the code before it gets restructured to be able to install with pip.

What's Changed

  • improved pipeline.yml documentation by @deevdevil88 in https://github.com/DendrouLab/panpipes/pull/7
  • update panpipes branch to match development branch by @crichgriffin in https://github.com/DendrouLab/panpipes/pull/6
  • X_scVI read in by @crichgriffin in https://github.com/DendrouLab/panpipes/pull/4
  • Crg compat with panpipes dev by @crichgriffin in https://github.com/DendrouLab/panpipes/pull/10
  • updating with scpipelinemuon_dev by @crichgriffin in https://github.com/DendrouLab/panpipes/pull/13

@crichgriffin merged in @bio-la's code to the repo

Full Changelog: https://github.com/DendrouLab/panpipes/compare/0.1.0...0.1.1

- Python
Published by crichgriffin about 3 years ago

panpipes - v0.1.0

First release of panpipes for manuscript.

- Python
Published by crichgriffin over 3 years ago