https://github.com/andim/pyrepseq - v1.5.1 Release

Object-oriented fast lookup implementations for speeding up repeated computations.

- Python
Published by andim almost 2 years ago

https://github.com/andim/pyrepseq - v1.5

What's Changed

• New information theory functions by @jhenderson0 in https://github.com/andim/pyrepseq/pull/45
• Symdel progress bar by @MVCowley in https://github.com/andim/pyrepseq/pull/46

New Contributors

• @MVCowley made their first contribution in https://github.com/andim/pyrepseq/pull/46

Full Changelog: https://github.com/andim/pyrepseq/compare/v1.4.3...v1.5

- Python
Published by andim almost 2 years ago

https://github.com/andim/pyrepseq - v1.4.3

What's Changed

• Improve pc tests by @yutanagano in https://github.com/andim/pyrepseq/pull/31
• Catch import errors for optional dependencies by @andim in https://github.com/andim/pyrepseq/pull/35
• Fix bug in pcDelta when setting maxseqs by @yutanagano in https://github.com/andim/pyrepseq/pull/38
• Update README.md by @yutanagano in https://github.com/andim/pyrepseq/pull/40
• Improve cdr levenshtein by @yutanagano in https://github.com/andim/pyrepseq/pull/39
• Update tcrdist names to capitalised form (TCRdist) by @yutanagano in https://github.com/andim/pyrepseq/pull/43
• Bump patch to v1.4.3 by @yutanagano in https://github.com/andim/pyrepseq/pull/44

Full Changelog: https://github.com/andim/pyrepseq/compare/v1.4.2...v1.4.3

- Python
Published by yutanagano about 2 years ago

https://github.com/andim/pyrepseq - Release 1.4.2

What's Changed

• Fix function call discrepancies between TcrMetric and Tcrdist variants
• Nearest-neighbor fix to TCRdist weighting of indels vs substitutions, renamed internal function 'symspell' -> 'symdel' for clarity

- Python
Published by andim over 2 years ago

https://github.com/andim/pyrepseq - Release 1.4.1

• Bug fix for Cdr3Levenshtein metric and relatives: now no longer requires V gene data to function
• Bug fix for pyrepseq.pc: now properly handles coincidence calculations accross multiple features

- Python
Published by yutanagano over 2 years ago

https://github.com/andim/pyrepseq - Release 1.4

New functionality:

• Full integration of flexible metric module throughout downstream functions (pcDelta, plotting etc.)
• added seqs to regex converter

Fixes:

• nn fixes for cross-set searches

New Contributors

• @rsaxena20 made their first contribution in https://github.com/andim/pyrepseq/pull/17

Full Changelog: https://github.com/andim/pyrepseq/compare/v1.3...v1.4

- Python
Published by andim over 2 years ago

https://github.com/andim/pyrepseq - Release 1.3

New functionality: - fast symspell-based nearest neighbor finding - adjacency graph community detection for TCR clustering

Breaking changes: - renames submodule nearest_neighbor -> nn

- Python
Published by andim over 2 years ago

https://github.com/andim/pyrepseq - Release 1.2.1

Updated pypi description and version bump

- Python
Published by andim over 2 years ago

https://github.com/andim/pyrepseq - Release 1.2

Major updates: - Scatter plots with density shading - Fast near neighbor finding

- Python
Published by andim over 2 years ago

https://github.com/andim/pyrepseq - Release 1.1

Major updates: - Added gene name standardization using @yutanagano's tidytcell package: https://github.com/yutanagano/tidytcells - Added unbiased estimator for the variance of Simpson's index (paper forthcoming!)

- Python
Published by andim about 3 years ago

https://github.com/andim/pyrepseq - Release 1.0

First major release with code to support analyses in the paper "Measures of epitope binding degeneracy from T cell receptor repertoires".

- Python
Published by andim over 3 years ago

https://github.com/andim/pyrepseq - Extended release v0.1.3

Main novelty: added default pcDelta background from blood sample

- Python
Published by andim over 3 years ago

https://github.com/andim/pyrepseq - Extended release v0.1.2

Main novelty: added plotting routines for sequence logos

- Python
Published by andim over 3 years ago

https://github.com/andim/pyrepseq - Extended release v0.1.1

Major change: added plotting functionality

- Python
Published by andim over 3 years ago

https://github.com/andim/pyrepseq - Initial release v0.1

Initial public release of pyrepseq

- Python
Published by andim almost 4 years ago