v0.2.0

This release marks the first set of community-contributed analyses to the added to the repository.
These modules are focused on cell type identification and annotation for specific ScPCA datasets.
Note that many of these modules are still in development at this stage and may not be fully functional.

• cell-type-dsrct
• cell-type-ETP-ALL-03
• cell-type-glioblastoma
• cell-type-nonETP-ALL-03
• cell-type-wilms-tumor-06
• cell-type-wilms-tumor-14

This release also adds the following new modules developed by the Data Lab:

• cell-type-consensus: a module for exploring consensus cell types across multiple annotation methods
• hello-clusters: a demonstration module for clustering analysis using the rOpenScPCA package
• seurat-conversion: a module for converting SingleCellExperiment objects to Seurat objects, also using the rOpenScPCA package

Other updates in this release include:

• a new sync-results.py script to simplify uploading (and downloading) analysis results from an analysis module to a user's S3 bucket
• changes from miniconda to miniforge for conda usage throughout the project

While not part of this repository, we do want to also note that we have created the rOpenScPCA package, which will house utility functions commonly used by analysis modules here.
The goal is to centralize common functions used across analysis modules to make it easier to share code and maintain consistency across modules.

2024-12-03

What's Changed

• Create shell script for wilms-06 workflow by @sjspielman in #817
• Update the feature/wilms-tumor-azimuth-06 branch by @sjspielman in #823
• Wilms 06 update: script to prepare fetal references by @sjspielman in #814
• Update cell-type-wilms-tumor-06 workflow by @sjspielman in #827
• Merge main into feature/wilms-tumor-06-azimuth by @sjspielman in #834
• Merge main into wilms azimuth branch by @sjspielman in #851
• Adapt Azimuth code for Wilms label transfer by @sjspielman in #843
• 1/n: Update wilms 06 module by @sjspielman in #859
• Updated wilms clustering notebooks 1/3 by @sjspielman in #862
• Updated wilms clustering notebooks 2/3 by @sjspielman in #863
• Updated wilms clustering notebooks 3/3 by @sjspielman in #864
• Wilms 06 module: Update and re-render 04 notebook by @sjspielman in #867
• Use docker image for wilms-14 CI by @jashapiro in #842
• Add dockerfile for metacell analysis by @jashapiro in #869
• Wilms-06 update CNV methods: copykat (1/3) by @sjspielman in #872
• Wilms-06 update CNV methods: infercnv (2/3) by @sjspielman in #873
• Update calculate_stability usage by @sjspielman in #871
• Update simulate-sce to keep all metadata columns by @jashapiro in #879
• Account for multiplexed samples in metadata permutation by @jashapiro in #880
• Wilms-06 update CNV methods (3/3), and run module in CI by @sjspielman in #876
• Add rOpenScPCA to renv/docker in ewing module by @allyhawkins in #881
• Fix wilms-06 typos by @sjspielman in #885
• Add zellkonverter to wilms-06 environment by @sjspielman in #890
• Merge main into feature/wilms-tumor-06-azimuth by @sjspielman in #891
• Merge wilms-tumor-06-azimuth into main by @sjspielman in #893
• Remove zero cells in simulations by @jashapiro in #898
• only warn if there are too many labels in simulations by @jashapiro in #901
• Initiate module for consensus cell typing by @allyhawkins in #903
• Update creating-vcs.md to no longer reference selecting an Availability Zone by @jaclyn-taroni in #904
• Use h5ad reference in cell-type-wilms-tumor-06 by @sjspielman in #902
• Update clustering report to include leiden clustering by @allyhawkins in #895
• Shrink and fix simulated SCEs by @jashapiro in #907
• Fix spelling errors by @sjspielman in #911
• Add workflow for evaluating clustering to Ewing's module by @allyhawkins in #908
• Initial assignment of cell ontology IDs to panglao cell types by @allyhawkins in #909
• Regenerate wilms notebooks: Code updates by @sjspielman in #913
• Regenerate wilms-tumor-06 notebooks 2/N by @sjspielman in #916
• Wilms tumor notebooks: next batch by @sjspielman in #918
• Make sure cluster assignments are factors by @allyhawkins in #919
• Next batch of SCPCP000006 notebooks by @sjspielman in #921
• Penultimate batch of SCPCP000006 notebooks by @sjspielman in #922
• Last batch of SCPCP000006 notebooks by @sjspielman in #923
• Second group of manual cell type ontology assignments by @allyhawkins in #917
• Add first set of manual cell ontology assignments by @allyhawkins in #914
• Specify number of threads used when calculating cluster stability by @allyhawkins in #925

Full Changelog: 2024-11-07...2024-12-03

2024-11-07

What's Changed

• Initiate hello-clusters by @sjspielman in #805
• Add biocViews to rOpenScPCA by @sjspielman in #807
• Scripts to run copykat and infercnv for a subselection of Wilms tumor from SCPCP000006 by @maud-p in #801
• Switch to using precommit action locally by @jashapiro in #820
• SCPCP000006_05_explore_COPYKAT by @maud-p in #813
• cell type/tumor annotation for ETP T-ALL (SCPCP000003) by @UTSouthwesternDSSR in #826
• Add fetusref.SeuratData to renv by @jashapiro in #831
• Add rOpenScPCA install instructions by @sjspielman in #833
• Exploratory CNV notebook for Wilms tumor annotation (SCPCP000014) by @JingxuanChen7 in #825
• Attempt to identify tumor cells in those non-ETP samples without B cells (SCPCP000003) by @UTSouthwesternDSSR in #815
• Included initial exploratory analysis notebook by @danhtruong in #794
• Add docker image for cell-type-wilms-tumor-14 by @jashapiro in #841
• 04- Explore the mapping scores for Wilms tumor -06 by @maud-p in #835
• 06 explore infercnv for Wilms tumor -06 by @maud-p in #828
• Adding SCTransform as an alternative to anchor transfer-Wilms tumor annotation (SCPCP000014) by @JingxuanChen7 in #836
• Add words to dictionary by @sjspielman in #845
• Add rough tumor classification into the result table-Wilms tumor annotation (SCPCP000014) by @JingxuanChen7 in #846
• Update hello-python docker image by @jashapiro in #850
• Draft annotation by @maud-p in #844
• Exploratory results for inferCNV on non-ETP samples (SCPCP000003) by @UTSouthwesternDSSR in #838
• Submission table for cell type and tumor classification of ETP T-ALL (SCPCP000003) by @UTSouthwesternDSSR in #847
• Remove rOpenScPCA from this repo by @sjspielman in #861

Full Changelog: 2024-10-09...2024-11-07

2024-10-09

What's Changed

• Initiate ropenspca package by @sjspielman in #735
• Merge main into ropenscpca by @jashapiro in #753
• Add function to perform graph-based clustering by @sjspielman in #749
• Add function to extract PC matrix (1/2) by @sjspielman in #758
• Add download option to sync script by @jashapiro in #751
• Update sync-results.py printing by @sjspielman in #763
• Extract PC matrix within clustering function (2/2) by @sjspielman in #759
• Start an analysis for Wilms tumor annotation (SCPCP000014) by @JingxuanChen7 in #764
• Add function to sweep clustering parameters by @sjspielman in #765
• Wilms tumor 06- clustering exploration by @maud-p in #750
• Merge main into feature/ropenscpca by @sjspielman in #769
• Update rOpenScPCA gha by @sjspielman in #770
• initial commit by @danhtruong in #766
• Add silhouette and purity functions by @sjspielman in #777
• Do not print messages about syncs completing when using --dryrun by @jaclyn-taroni in #780
• Add function for cluster stability by @sjspielman in #779
• Celltype annotation for non-ETP T-ALL (SCPCP000003) by @UTSouthwesternDSSR in #767
• 04_annotation_Across_Samples_exploration by @maud-p in #776
• Initiation of new Glioblastoma analysis module by @georginaalbadri in #783
• Anchor transfer (with Seurat) for Wilms tumor annotation (SCPCP000014) by @JingxuanChen7 in #784
• Add PNGs to large file exclusion by @jaclyn-taroni in #792
• Merge rOpenScPCA into main by @sjspielman in #795
• celltype/tumor annotation for non-ETP T-ALL (SCPCP000003) by @UTSouthwesternDSSR in #789
• Add remaining modules with PR triggers to the run all workflow by @sjspielman in #798

New Contributors

• @JingxuanChen7 made their first contribution in #764
• @danhtruong made their first contribution in #766
• @UTSouthwesternDSSR made their first contribution in #767
• @georginaalbadri made their first contribution in #783

Full Changelog: 2024-09-04...2024-10-09

2024-09-04

What's Changed

• Update periodic release issue template to minimize steps by @jaclyn-taroni in #707
• Remove defaults channel from all modules and templates by @jashapiro in #714
• Don't have spellcheck action fail by @jashapiro in #720
• revert cell-type-ewings conda-lock by @jashapiro in #718
• Add some words to dictionary by @sjspielman in #721
• 724 Update simulation scripts to handle new data formats by @jashapiro in #725
• Custom function in ipynb should talk about AnnData by @jaclyn-taroni in #715
• Fix linking to use relative links by @jashapiro in #736
• Run Docker build and push on a larger runner by @jaclyn-taroni in #734
• Update code styling workflow by @sjspielman in #728
• Add README for github workflows directory by @sjspielman in #739
• Update docker images and GHA to use miniforge by @jashapiro in #740
• 02 run azimuth before kweight by @maud-p in #737
• Test fix for docker actions failing after miniforge by @jashapiro in #744
• Propagate miniforge Docker changes by @jashapiro in #746
• Update documentation to remove defaults channel and suggest miniforge by @jashapiro in #747
• Make GHA trigger & Dockerfiles consistent by @jashapiro in #748

Full Changelog: 2024-08-08...2024-09-04

2024-08-08

What's Changed

• Fix docker action repository naming by @jashapiro in #657
• Add ensembldb to lock file and Docker by @allyhawkins in #660
• Fix failed GHA for building and pushing docker images by @allyhawkins in #661
• One more bug in the docker GHA by @allyhawkins in #662
• Remove prettier from precommit recommendations by @sjspielman in #665
• Make sure renv is up to date by @allyhawkins in #667
• 610 Add script to apply SEACells to AnnData objects by @jashapiro in #658
• Add running SingleR to annotation workflow by @allyhawkins in #659
• Add module results FAQ by @sjspielman in #664
• Add metacells to GHA and handle small data by @jashapiro in #670
• Update CODEOWNERS by @jaclyn-taroni in #673
• Update CODEOWNERS by @jaclyn-taroni in #674
• Add zellkonverter step to doublets Dockerfile by @sjspielman in #675
• Assign clusters to SCPCL000822 and SCPCL000824 by @allyhawkins in #683
• Start wilms analysis by @maud-p in #681
• Add push trigger to Wilms tumor cell typing Docker build/push workflow & proposed change to template by @jaclyn-taroni in #688
• Test for building Ewing Docker image by @allyhawkins in #690
• Work around disk space limits for building Docker images by @allyhawkins in #692
• Disable second docker build summary by @allyhawkins in #695
• Add Rosetta to Docker installation instructions by @sjspielman in #694
• Add template to evaluate clustering to Ewing cell typing by @allyhawkins in #693
• Fix some bullet spacing by @sjspielman in #702

New Contributors

• @maud-p made their first contribution in #681

Full Changelog: v0.1.0...2024-08-08

v0.1.0

This is the initial versioned release of the OpenScPCA-analysis repository.
The repository at this stage should be generally complete with respect to infrastructure, but the analysis is still only in the early stages.

With respect to infrastructure, the repository contains the following components:

• detailed documentation in the docs directory explaining how to interact with the OpenScPCA project and how to set up and run analyses (published at https://openscpca.readthedocs.io/)
• a create-analysis-module.py script for setting up new analysis modules
• download-data.py and download-results.py scripts to download data and results from the OpenScPCA project
• template notebooks, scripts, environment files, and Docker images for analysis modules

The repository contains the following analysis modules that are now in a relatively mature state:

• hello-R
• hello-python
• simulate-sce
• doublet-detection

The following additional modules are in active development:

• cell-type-ewings
• metacells