https://github.com/databio/bedboss - v0.7.3

Changes:

• Added filter for rerunning unprocessed bed files based on genome

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Published by khoroshevskyi about 1 year ago

https://github.com/databio/bedboss - v0.7.2

Changes:

• Updated path to the bigbed output folder
• Added update of metadata of the bed file
• Updated docker file
• Remove bedqc module

- Jupyter Notebook
Published by khoroshevskyi about 1 year ago

https://github.com/databio/bedboss - v0.7.1

Changes

• bug fix

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Published by khoroshevskyi about 1 year ago

https://github.com/databio/bedboss - v0.7.0

Changes:

• Added dockerfile
• Added R processing as separate service
• Refactored R code
• Added initial qc for GEO data (QC, without loading full data)
• Improved logging
• Fixed python3.12 warnings
• Improved bedmaker. (identifier, bigbed, qc)
• Removed bedqc module - moved it to handle everything by RegionSet object
• Improved bedclasifier #101
• Fixed #97
• Fixed #110
• Fixed #95
• Fixed #112
• Fixed multiple bugs in geo uploader
• Switched RegionSet from geniml to RegionSet from Gtars

- Jupyter Notebook
Published by khoroshevskyi about 1 year ago

https://github.com/databio/bedboss - v0.6.0

Big release 💥

Changes:

• Important speed improvements.
• Added open_chromatin plot back into processing.
• Added gtrs dependency, that calculates gc content.
• Added skipper that automatically skips samples in pep that were already processed.
• Added lite functionality to main functions that allows to run uploading without using any heavy processing.
• Added function that will reprocess files, if they were unprocessed in the bedbase.
• Added function that predicts genome if genome wasn't provided

- Jupyter Notebook
Published by khoroshevskyi over 1 year ago

https://github.com/databio/bedboss - v0.4.1

Added

• Standardization of peps using bedbase bedms schema
• Reference validator module

Fixed

• Pipeline failures (due to pipeline manager)
• Failure in cleaning temp files

- Jupyter Notebook
Published by khoroshevskyi over 1 year ago

https://github.com/databio/bedboss - v0.4.0

Changes:

• Added bbuploader

- Jupyter Notebook
Published by khoroshevskyi almost 2 years ago

https://github.com/databio/bedboss - v0.3.0

Changes:

• Added classifier
• Added create universe uploader
• Added tokenization and token uploader
• Updated efficiency of CLI help

- Jupyter Notebook
Published by khoroshevskyi almost 2 years ago

https://github.com/databio/bedboss - v0.2.1

added requirement check to cli and other small tweaks

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Published by khoroshevskyi about 2 years ago

https://github.com/databio/bedboss - v0.2.0

• Added indexing and deletion comands
• Moved uploading to bbconf
• Updated CLI

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Published by khoroshevskyi about 2 years ago

https://github.com/databio/bedboss - v0.1.0

First release

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Published by khoroshevskyi over 2 years ago

https://github.com/databio/bedboss - v0.1.0a3

- Jupyter Notebook
Published by khoroshevskyi over 2 years ago

https://github.com/databio/bedboss - v0.1.0a2

Fixed version importing error

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Published by khoroshevskyi almost 3 years ago

https://github.com/databio/bedboss - v0.1.0a1

First pre-release

- Jupyter Notebook
Published by khoroshevskyi almost 3 years ago