v1.1.9

CAS Tools

CAS-Tools is a comprehensive utility package designed to facilitate the effective use and manipulation of the Cell Annotation Schema (CAS) in single-cell transcriptomics data analysis. CAS supports recording the rationale and evidence for single cell annotation, including gene expression evidence and details of automated annotation transfer. The standard can be saved as a separate JSON file with a resolvable link to a martix (AnnData) file containing annotated data, or embedded in the annotated AnnData file. Further details are available at https://cellannotation.github.io/cas-tools/.

Installation

You can install CAS-Tools pypi package using pip:

pip install cas-tools

Overview

CAS-Tools simplifies the use of CAS by offering a set of programmatically accessible operations including:

• Validate Annotations: Validate annotations against the CAS standard to ensure compliance and consistency.
• Validation of markers against linked AnnData file
• Merge to Anndata - updating annotations in the AnnData file and saving JSON to the AnnData header.
• Reporting: Generation of dataframe reports of CAS content from JSON.
• Export to CAP-Anndata format: Merges into AnnData file following a derived, flattened representation of CAS, used by the Cell Annotation Platform (CAP) (CAP-Anndata).
• Import from Allen Brain Cell Atlas (ABC) format DataFrames:

Getting Started

CAS-tools functionality can be accessed via imported object in python or via a command line tool. For CLI tool function details please see:

• Command line interface

v1.1.8

What's Changed

• Fix process_annotations fillna overwrite and improve documentation by @ubyndr in #168

Full Changelog: v1.1.7...v1.1.8

v1.1.7

Update pyproject.toml

v1.1.5

What's Changed

• 156 standardize list argument parsing across cli commands by @ubyndr in #159
• Make notebook tutorial for cas tools by @ubyndr in #146
• Auto generate accession ids on ingesting annotation tables by @hkir-dev in #160
• Use matrix strategy for Python version to avoid YAML float conversion by @ubyndr in #162

Full Changelog: v1.1.4...v1.1.5

v1.1.4

Update version to 1.1.4

v1.1.3

What's Changed

• 149 refine checks on populate cell ids by @ubyndr in #150
• Split cas neurotransmitter accession support by @ubyndr in #155

Full Changelog: v1.1.2...v1.1.3

v1.1.2

Refactor validate_labelset_values method

v1.1.1

Update spreadsheet_to_cas_test.py

v1.1.0

Merge branch 'main' into 143-make-notebook-tutorial-for-cas-tools

v1.0.20

Allen-style spreadsheet ingestions now has option to generate accession ids incrementally

Full Changelog: v1.0.18...v1.0.20