airr - AIRR Standards v1.6.0

What's Changed

• exclude deprecated by @schristley in https://github.com/airr-community/airr-standards/pull/791
• curie resolve, handle undefined, fix deprecate bug by @schristley in https://github.com/airr-community/airr-standards/pull/792
• minimums for physical quantities by @schristley in https://github.com/airr-community/airr-standards/pull/799
• sync with 2.0 code by @schristley in https://github.com/airr-community/airr-standards/pull/807
• AKC updates for v1.6 by @schristley in https://github.com/airr-community/airr-standards/pull/814

Full Changelog: https://github.com/airr-community/airr-standards/compare/v1.5.1...v1.6.0

- Python
Published by schristley 8 months ago

airr - AIRR Standards v1.5.1

Version 1.5.1 of the AIRR Schema

Minor Schema Changes:

• Corrected schema version number in the Info object.

Minor Python Library Changes:

• Updated versioneer to v0.29.

JavaScript Library

• Initial release.

Full Release Notes:

• Schema release notes

- Python
Published by javh over 1 year ago

airr - AIRR Standards v1.5.0

Version 1.5 of the AIRR Schema

Major Schema Changes:

• Major cleanup, definition clarification, and attribute fixes in the Germline and Genotype schema.
• Set the default for x-airr.miarr attributes to defined.
• Added “IGI” as a valid value to the locus enum fields in multiple schema.
• Added a property type field to the CellExpression object.
• Updated all enum values to snake_case and added allowance for null enum values when appropriate.

Major R and Python Library Changes:

• Officially dropped support for Python 2.
• Updated enum validation and template handling in the python library.

Full Release Notes:

• Schema release notes
• Python library release notes
• R library release notes

- Python
Published by javh over 2 years ago

airr - AIRR Standards v1.4.1

Version 1.4 of the AIRR Schema

Major Schema Changes:

• Updated quantification fields in the Rearrangement and Clone schemas for better compatibility with single-cell and emerging technologies. Changes include new optional fields and modifications to the semantics of existing *_count fields.
• Various new optional fields in the Study, Subject and Rearrangement schemas.
• Modified how time points and template concentrations are stored in Sample and NucleicAcidProcessing Schemas.

New Experimental Schema:

• Experimental releases of new single-cell associated schemas.
• Experimental releases of germline reference and genotype schemas.
• Experimental release of data aggregation schemas, including collections of repertoires and JSON/YAML files bundling multiple AIRR Data Model objects.

Major R and Python Library Changes:

• Added support for generalized AIRR Data Model files and objects that bundle multiple data classes.
• Deprecated support for files storing only Repertoire objects in favor of a general AIRR Data Model, which is backwards compatible with Repertoire metadata files.

Full Release Notes:

• Schema release notes
• Python library release notes
• R library release notes

- Python
Published by javh over 3 years ago

airr - Documentation Updates

Overview

• Improvements to the organization and wording of various documentation pages.
• Added missing deprecation tags for rearrangement_id in the Alignment schema.
• Modified merge_rearrangement in the airr python library so that it can handle a large number of files.
• Improved validation error handling in the airr python library.

Full Release Notes:

• Schema release notes
• Python library release notes

- Python
Published by javh over 5 years ago

airr - AIRR Schema v1.3

Version 1.3 of the AIRR Schema

Major changes:

• First official release of the Repertoire metadata schema.
• First official release of the AIRR Data Commons API specification.
• Expansion of schema field annotations.
• Extensions to the Rearrangement schema for multiple D regions.
• New experimental schema for clones, lineage trees, and cells.

Full Release Notes:

• Schema release notes
• Python library release notes
• R library release notes

- Python
Published by schristley over 5 years ago

airr - Python reference library fix

Fixed a bug in the python reference library causing start coordinate values to be empty in some cases when writing data.

Python library release notes.

- Python
Published by javh over 7 years ago

airr - Rearrangement schema v1.2

Schema Release Notes

Definition change for the coordinate fields of the Rearrangement and Alignment schema. Coordinates are now defined as 1-based closed intervals, instead of 0-based half-open intervals (as previously defined in v1.1 of the schema).

Reference Library Release Notes

Several changes to the python and R reference library to support the new schema coordinate definition and improve validation. See the package release notes for details:

• Python library release notes
• R library release notes

- Python
Published by javh over 7 years ago

airr - Data Representation standards and reference libraries

Initial official release of the AIRR Data Representation standards and associated python and R reference libraries.

- Python
Published by javh almost 8 years ago

airr - Early revision of AIRR definitions

An early revision of the AIRR definitions with corresponding reference library.

- Python
Published by schristley almost 8 years ago

airr - MiAIRR V1

This is the V1 release of the Standard for the Minimum information about an Adaptive Immune Receptor Repertoire Sequencing Experiment (MiAIRR V1).

Description of MiAIRR V1 can be found in this article:

• Rubelt, F. et al. Adaptive Immune Receptor Repertoire Community recommendations for sharing immune-repertoire sequencing data. Nat Immunol 18:1274-1278 (2017) [PMID:29144493]

Description of the Adaptive Immune Receptor Repertoire (AIRR) Community can be found in this article:

• Breden, F. et al. Reproducibility and Reuse of Adaptive Immune Receptor Repertoire Data. Frontiers Immunol 8:1418 (2017) [PMID:29163494]

The V1 release defines the primary data elements as the minimum information to be archived with an adaptive immune receptor repertoire sequencing experiment. The computational specifications, data file formats, and reference libraries are still being finalized and will be released in a later version.

- Python
Published by schristley about 8 years ago

airr - release candidate

- Python
Published by schristley over 8 years ago