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Use All Cores by Default in Scanpy-Scripts

Status: Open.

#137 In ebi-gene-expression-group/scanpy-scripts;

· anilthanki opened on Jan 14, 2025

Scrublet failing on certain dataset

Status: Open.

#134 In ebi-gene-expression-group/scanpy-scripts;

· anilthanki opened on May 31, 2024

Highly variable genes calculations should allow to blacklist or white list specific subset of genes

Status: Open.

#129 In ebi-gene-expression-group/scanpy-scripts;

· pcm32 opened on Feb 12, 2024

Scrublet double prediction fails with cells with under 5 expressed genes

Status: Open.

#125 In ebi-gene-expression-group/scanpy-scripts;

· pcm32 opened on Jan 23, 2024

Scrubblet module fails when running with less than 30 cells

Status: Open.

#124 In ebi-gene-expression-group/scanpy-scripts;

· pcm32 opened on Oct 30, 2023

Using a single group in find marker genes fails

Status: Open.

#123 In ebi-gene-expression-group/scanpy-scripts;

· pcm32 opened on Apr 20, 2023

Add filtering by quantiles

Status: Open.

#122 In ebi-gene-expression-group/scanpy-scripts;

· pcm32 opened on Mar 27, 2023

PlotEmbedd could give more user friendly errors to allow users to recover

Status: Open.

#121 In ebi-gene-expression-group/scanpy-scripts;

· pcm32 opened on Mar 10, 2023

Should we add ability to mark ribosomal genes?

Status: Open.

#119 In ebi-gene-expression-group/scanpy-scripts;

· pcm32 opened on Nov 18, 2022

How can I use scanpy_scripts?

Status: Open.

#118 In ebi-gene-expression-group/scanpy-scripts;

· cooperist opened on Oct 9, 2022

Calculations of mito directly generate columns with dtypes that break qc calculations on subsequent filtering

Status: Open.

#116 In ebi-gene-expression-group/scanpy-scripts;

· pcm32 opened on Sep 21, 2022

Problems with Python 3.9.* - umap-learn<0.4.0 needed?

Status: Open.

#102 In ebi-gene-expression-group/scanpy-scripts;

· LustigePerson opened on Jul 12, 2021