Releases · AlexsLemonade/scpca-docs

Consensus cell types have been updated to fix a minor bug in assigning labels.
- Previously, if two out of three methods (SingleR, CellAssign, and SCimilarity) agreed but the third method was unable to classify a cell, the consensus cell type was incorrectly classified as Unknown. The consensus cell types have been updated so that if two out of three methods agree the consensus cell type is assigned with the appropriate label using an ontology-based approach, regardless of whether or not the third method is able to classify the cell.
The infercnv_success status previously reported in the metadata of SingleCellExperiment objects and uns of AnnData objects has been renamed as infercnv_status and now contains a string instead of boolean value.

Full Changelog: 2026.01.08...2026.02.09

Assets 2

08 Jan 15:13

allyhawkins

2026.01.08

What's Changed

Data on the Portal can now be downloaded in three different ways:
- By selecting a single project to download.
- By creating a custom dataset with a selection of projects and/or samples.
  Custom datasets are referred to as My Dataset on the Portal.
- By choosing one of the Portal-wide download options.
Although the content of the data included in each download has not changed, the download file structures have changed.
See the Downloadable Files page for more information.
A new section of the documentation describing possible download options has been added.
The previously named single_cell_metadata.tsv files that are included with each download have been renamed to single-cell_metadata.tsv.

Full Changelog: 2025.12.17...2026.01.08

Assets 2

17 Dec 17:56

sjspielman

2025.12.17

This release fixes some minor typos and broken links in the documentation.

Full Changelog: 2025.12.04...2025.12.17

Assets 2

05 Dec 16:27

allyhawkins

2025.12.04

Updated documentation to reflect the new features added for all data on the Portal.

Doublet detection was run on all samples using scDblFinder.
No doublets were filtered, but the results from scDblFinder are present in the filtered and processed objects.
Updated cell type annotations
- All samples include cell type annotations obtained from SCimilarity, in addition to the existing cell type annotations from SingleR and CellAssign.
- Consensus cell types have been updated to incorporate SCimilarity results.
  If two of the three automated methods agree using an ontology-based approach, a consensus cell type is assigned.
Cell types were annotated as part of the ongoing OpenScPCA project for SCPCP000004 (Neuroblastoma) and SCPCP000015 (Ewing sarcoma).
These cell types are now included in all objects for those samples.
CNV inference was performed using InferCNV on all samples with at least 100 non-malignant reference cells, as identified by the consensus cell types.