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Release notes for OpenScPCA-analysis

This document contains release notes for versioned releases of the OpenScPCA-analysis repository. We will also periodically release and tag dated snapshots of the repository, but these will not be reflected in this document.

v0.2.1

This release includes minor updates to the following modules:

  • cell-type-ewings
  • cell-type-consensus

In particular, the workflow for assigning consensus cell types has been created in cell-type-consensus module. This workflow is now present in OpenScPCA-nf, and results will be made available to all contributors.

New FAQs covering how to work with ScPCA data as Seurat objects and using gene symbols instead of Ensembl IDs have been added to the OpenScPCA documentation.

Rcpp package versions within modules were updated for compatibility.

v0.2.0

This release adds the first set of community-contributed analyses 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.

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