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denoising devel

NEW FUNCTIONALITY

  • Add new method: CellMapper (PR #31)

MINOR CHANGES

  • Update the Viash version to 0.9.4 (PR #32)

  • Dependencies were moved to main openproblems repository (PR #32)

BUG FIXES

  • Update scPRINT, including a new default model (PR #26)

denoising v1.0.0

BREAKING CHANGES

  • Update to viash 0.9.0 RC6

  • Directory structure has been updated.

  • Update to viash 0.9.0 (PR #13).

NEW FUNCTIONALITY

  • Add CHANGELOG.md (PR #7).

  • Update process_dataset component to subsample large datasets (PR #14).

  • Add the scPRINT method (PR #25)

MAJOR CHANGES

  • Revamp scripts directory (PR #13).

  • Relocated process_datasets to data_processors/process_datasets (PR #13).

MINOR CHANGES

  • Remove dtype parameter in .Anndata() (PR #6).

  • Fix target_sum deprecation warning in mse mmetric (PR #8).

  • Update task_name variable to denoising in component scripts (PR #9).

  • Update docker containers used in components (PR #12).

  • Set numpy<2 for some failing methods (PR #13).

  • Small changes to api file names (PR #13).

  • Update test_resources path in components (PR #18).

  • Update workflows to use core repository dependency (PR #20).

  • Update the common submodule (PR #24)

  • Use the common checkItemAllowed() for the method check in the benchmark workflow (PR #24)

  • Use the cxg_immune_cell_atlas dataset instead of the cxg_mouse_pancreas_atlas for testing (PR #24)

  • Update README (PR #24)

  • Add a base method API schema (PR #24)

  • Add dataset_organism to training input files (PR #24)

  • Remove n_obs_limit default setting.

BUG FIXES

  • Update the nextflow workflow dependencies (PR #17).

  • Fix paths in scripts (PR #18).

  • Subsample datasets by batch if batch is defined (PR #22).

transfer from openproblems-v2 repository

NEW FUNCTIONALITY

  • api/file_*: Created a file format specifications for the h5ad files throughout the pipeline.

  • api/comp_*: Created an api definition for the split, method and metric components.

  • process_dataset: Added a component for processing common datasets into task-ready dataset objects.

  • resources_test/denoising/pancreas with src/tasks/denoising/resources_test_scripts/pancreas.sh.

  • workflows/run: Added nf-tower test script. (PR #205)

V1 MIGRATION

  • control_methods/no_denoising: Migrated from v1. Extracted from baseline method

  • control_methods/perfect_denoising: Migrated from v1.Extracted from baseline method

  • methods/alra: Migrated from v1. Changed from python to R and uses lg_cpm normalised data instead of L1 sqrt

  • methods/dca: Migrated and adapted from v1.

  • methods/knn_smoothing: Migrated and adapted from v1.

  • methods/magic: Migrated from v1.

  • metrics/mse: Migrated from v1.

  • metrics/poisson: Migrated from v1.

Changes from V1

  • Anndata layers are used to store data instead of obsm

  • extended the use of sparse data in methods unless it was not possible

  • process_dataset also removes unnecessary data from train and test datasets not needed by the methods and metrics.