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task_batch_integration devel

New functionality

  • Added metrics/kbet_pg and metrics/kbet_pg_label components (PR #52).

  • Added methods/stacas new method (PR #58).

    • Add non-supervised version of STACAS tool for integration of single-cell transcriptomics data. This functionality enables correction of batch effects while preserving biological variability without requiring prior cell type annotations.

  • Added method/drvi component (PR #61).

  • Added ARI_batch and NMI_batch to metrics/clustering_overlap (PR #68).

  • Added metrics/cilisi new metric component (PR #57).

    • ciLISI measures batch mixing in a cell type-aware manner by computing iLISI within each cell type and normalizing the scores between 0 and 1. Unlike iLISI, ciLISI preserves sensitivity to biological variance and avoids favoring overcorrected datasets with removed cell type signals. We propose adding this metric to substitute iLISI.

Minor changes

  • Un-pin the scPRINT version and update parameters (PR #51)
  • Update scPRINT to better handle large datasets, including a new default model (PR #54)

Bug fixes

  • Update scPRINT to use latest stable version (PR #70)
  • Fix kbet dependencies to numpy<2 and scipy<=1.13 (PR #78).

task_batch_integration 2.0.0

A major update to the OpenProblems framework, switching from a Python-based framework to a Viash + Nextflow-based framework. This update features the same concepts as the previous version, but with a new implementation that is more flexible, scalable, and maintainable.

Migration

  • Added expected input/output interfaces in src/api and document them in README.md.

  • Store common resources used across tasks in a git submodule common.

  • Methods, metrics, workflows and other components are implemented as Viash components with a per-component Docker image.

New functionality

  • Switched to larger datasets derived from CELLxGENE.

  • Added SCimilarity (PR #3).

  • Added Geneformer (PR #6).

  • Added UCE method (PR #7).

  • Added scGPT zero shot (PR #8, #16).

  • Added scPRINT (PR #13).

  • Added scGPT fine-tuned (PR #17).

Major changes

  • Prefilter batches in HVG overlap metric (PR #9).

  • Precompute clustering for some metrics (PR #18).

Minor changes

  • Add arguments for filtering methods in benchmarking workflow (PR #4).

  • Update compute environment (PR #5).

  • Adjust resources (PR #10).

  • Update dependency components (PR #10).

  • Update API formats (PR #21, #28, #31).

  • Add support for zebrafish and C. elegans (PR #22).

  • Bump scIB to v1.1.7 (PR #30).

  • Update common submodule (PR #29).

Bug fixes

  • Multiple fixes prior to release (PR #24, #25, #26, #27, #32, #34, #36, #37, #39, #41, #42, #43, #44).

Documentation

  • Update documentation (PR #45).

task_batch_integration 1.0.0

This version can be found here.