peka - v1.0.2

What's Changed

• Fixed future warning in pandas concat, and cleaned up defaults for percentile parameter within functions. by @kkuret in https://github.com/ulelab/peka/pull/27

Full Changelog: https://github.com/ulelab/peka/compare/v1.0.1...v1.0.2

- Python
Published by kkuret almost 2 years ago

peka - v1.0.1

What's Changed

• Fix - script exits when regions file lacks any of the expected regions; minor fixes by @kkuret in https://github.com/ulelab/peka/pull/18
• Update dependencies by @kkuret in https://github.com/ulelab/peka/pull/21 - code was changed to wirk with newer version of pandas and nupmy
• Update setup.py by @kkuret in https://github.com/ulelab/peka/pull/25

Full Changelog: https://github.com/ulelab/peka/compare/v1.0.0...v1.0.1

- Python
Published by kkuret almost 2 years ago

peka - v1.0.0-zenodo

Get the repo picked up by zenodo.

- Python
Published by kkuret over 2 years ago

peka - v1.0.0

A stable version - additional checks to catch potential errors.

What's Changed

• Minor fixes072022 by @kkuret in https://github.com/ulelab/peka/pull/15

Full Changelog: https://github.com/ulelab/peka/compare/v0.1.6...v1.0.0

- Python
Published by kkuret over 3 years ago

peka - v0.1.6

What's Changed

• If percentile is set to 0, set all crosslinks within peaks as tXn. by @kkuret in https://github.com/ulelab/peka/pull/11
• Determination of relevant positions, Bugfixes for working with soft-masked genome, other minor fixes by @kkuret in https://github.com/ulelab/peka/pull/14
  • bugfixes for working with soft-masked genomes: 49198591ca34b9d727b8c6774f3f74c0e6304b44, dd892efb2d6766459d9eb1b25b2b4a09457e4c78
  • calculation of threshold for relevant positions based on kmer length and number of thresholded crosslinks in analyzed region. Allowing more control over relevant positions threshold trough cli arguments: 588e273e19bafe828fd8d9f1fccfb03d31eb6dde, 9b690eba28fc1d0902b2a02dbde5ecdb7dcc4085
  • changed handling of ZeroDivisionError to divide by smallest non-zero value instead of arbitrary small value
• Added script to produce a heatmap of relative occurrences for top k-mers from PEKA results a17d58bfc3782eb4b77d000f1d5ff117eeb73290
• Improved descriptions of arguments, formatting in https://github.com/ulelab/peka/pull/14

Full Changelog: https://github.com/ulelab/peka/compare/v0.1.5...v0.1.6

- Python
Published by kkuret almost 4 years ago

peka - Fixed compatibility with Ensembl naming conventions / Reproducible results

What's Changed

• Fixed Ensembl compatibility: remove_chr function now removes entries annotated either "chrM" or "MT"
• Reproducibility of results: added --setseeds flag enables reproducible random sampling of background sequences. When --setseeds is set to True, re-running the analysis on the same data will produce the same results.

by @kkuret in https://github.com/ulelab/peka/pull/10

Full Changelog: https://github.com/ulelab/peka/compare/v0.1.4...v0.1.5

- Python
Published by kkuret about 4 years ago

peka - v0.1.4

What's new:

v0.1.2 - v0.1.3

1. Important fixes - CLI and clustering of top k-mers:

   • resolved a bug affecting clustering optimization that caused the script to ignore the maximal number of clusters set by the user (1a522d7c24e36af4fbb680fe8bba2d7c9a4a9868)
   • CLI parsing of boolean arguments now works as expected. In prior version, the input "False", was interpreted as boolean True by argparse. (0b666ceeabeaf220e5bf16fbc7315f6bbaf84430)

2. Reduced runtime by reduction of covered parameter space for clustering optimization. (2420df06443788e6e75afcd8f3304d5c54217bf1)

3. Example run script, input files and example results. This enables users to easily test if their PEKA setup works.

4. Cleaner syntax - removal of unused variables.

v0.1.3 - v0.1.4

1. Updated setup.py to be compatible with peka.py for bioconda implementation. (42c8d9ec179d8bdec707d9133ba88f2d822efa30)

- Python
Published by kkuret about 4 years ago