mapseq - v0.2.1-alpha

What's Changed

• Update TCR data path and enhance VDJdb exploration output by @willisbillis in https://github.com/willisbillis/MAPseq/pull/87
• Refactor binding column cleanup and update ATAC analysis parameters by @willisbillis in https://github.com/willisbillis/MAPseq/pull/90

Full Changelog: https://github.com/willisbillis/MAPseq/compare/v0.2.0-alpha...v0.2.1-alpha

- R
Published by willisbillis 8 months ago

mapseq - v0.2.0-alpha

What's Changed

Merge development updates into the main branch, including enhancements to the pipeline with new algorithms and tools, removal of outdated steps, and improvements to documentation. Introduce automated cell type annotation and optional batch correction, while updating the demux algorithm and simplifying the mapping process of ASAPseq reads with kb-python. Address compatibility issues by removing the CellBender step.

New Features: - Introduce automated cell type annotation using Azimuth in the pipeline. - Add optional batch correction section to the pipeline.

Bug Fixes: - Fix issues in the pipeline scripts related to sample name extraction and processing.

Enhancements: - Update the demux algorithm to use MULTIseqDEMUX for improved performance. - Improve the kallisto-bustools step by integrating the kb-python package for simplified mapping. - Remove the CellBender Ambient RNA preprocessing step due to compatibility issues with Python 3.9 and GPU requirements.

Documentation: - Revise README.md to improve clarity and update installation instructions.

Disclaimer: As this repository is currently still in its alpha phase and there has not been extensive edge case, stress, and other testing, this release is intended for INTERNAL USE ONLY.

Full Changelog: https://github.com/willisbillis/MAPseq/compare/v0.1.0-alpha...v0.2.0-alpha

- R
Published by willisbillis over 1 year ago

mapseq - v0.1.0-alpha

What's Changed

• This is the initial release of the MAPseq processing and analysis code. As it is currently still in its alpha phase and there has not been extensive edge case, stress, and other testing, this release is intended for INTERNAL USE ONLY.

New Contributors

• @willisbillis made their first contribution in https://github.com/willisbillis/MAPseq/pull/26

Full Changelog: https://github.com/willisbillis/MAPseq/commits/v0.1.0-alpha

- R
Published by willisbillis almost 2 years ago