fls-bioinformatics-core/pegs issues and pull requests

#61 - Add CITATION.cff file

Pull Request - State: closed - Opened by pjbriggs 12 months ago
Labels: documentation

#60 - Update Github Python CI workflow to fix missing Python 3.6

Pull Request - State: closed - Opened by pjbriggs 12 months ago
Labels: bugfix, testing

#59 - Pin 'xlsxwriter' dependency version to 3.1.9

Pull Request - State: closed - Opened by pjbriggs 12 months ago
Labels: bugfix, dependencies

#58 - Pin 'xlsxwriter' dependency version to 3.9.1

Pull Request - State: closed - Opened by pjbriggs 12 months ago - 1 comment
Labels: bugfix, dependencies

#57 - Update configuration for building documentation on ReadTheDocs

Pull Request - State: closed - Opened by pjbriggs 12 months ago
Labels: documentation, bugfix

#56 - Update documentation to clarify input for 'mk_pegs_intervals'

Pull Request - State: closed - Opened by pjbriggs over 2 years ago
Labels: documentation, bugfix

#55 - mk_pegs_intervals: update to make agnostic to input format

Issue - State: open - Opened by pjbriggs over 2 years ago
Labels: enhancement

#54 - Always force use of non-interactive 'Agg' matplotlib backend for PEGS

Pull Request - State: closed - Opened by pjbriggs over 2 years ago
Labels: bugfix

#53 - Matplotlib backend is only set to non-interactive mode if 'DISPLAY' is unset

Issue - State: closed - Opened by pjbriggs over 2 years ago
Labels: bug

#52 - Documentation doesn't specify the input format for 'mk_pegs_interval'

Issue - State: closed - Opened by pjbriggs over 2 years ago
Labels: bug, documentation

#51 - Update citation information following final publication on F1000R

Pull Request - State: closed - Opened by pjbriggs about 3 years ago
Labels: update

#50 - Fix handling of input peaks and cluster files

Pull Request - State: closed - Opened by pjbriggs about 3 years ago
Labels: bugfix

#49 - Fix Conda installation instructions in README

Pull Request - State: closed - Opened by pjbriggs about 3 years ago
Labels: documentation, bugfix

#48 - PEGS must be installed into a new conda environment

Issue - State: closed - Opened by pjbriggs about 3 years ago
Labels: bug, documentation

#47 - PEGS crashes when input "files" are actually directories or distances

Issue - State: closed - Opened by pjbriggs about 3 years ago
Labels: bug

#46 - Update documentation to include installation via Conda

Pull Request - State: closed - Opened by pjbriggs about 3 years ago
Labels: documentation, enhancement

#45 - Fix usage examples for PEGS 0.6.0

Pull Request - State: closed - Opened by pjbriggs about 3 years ago
Labels: documentation, bugfix

#44 - Add citation information

Pull Request - State: closed - Opened by pjbriggs about 3 years ago
Labels: documentation, update

#43 - Enable peak and cluster files to be specified explicitly on PEGS command line

Pull Request - State: closed - Opened by pjbriggs about 3 years ago
Labels: enhancement, breaking change

#42 - Add options to customise the output heatmap

Pull Request - State: closed - Opened by pjbriggs about 3 years ago
Labels: enhancement

#41 - Fixes to handling input directories and files

Pull Request - State: closed - Opened by pjbriggs about 3 years ago
Labels: bugfix

#40 - Allow heatmap image format to be specified

Pull Request - State: closed - Opened by pjbriggs about 3 years ago
Labels: enhancement

#39 - Add PEGS to bioconda

Issue - State: closed - Opened by pjbriggs about 3 years ago - 2 comments
Labels: enhancement

#38 - Allow user to adjust heatmap colours and labels

Issue - State: closed - Opened by pjbriggs about 3 years ago - 1 comment
Labels: enhancement

#37 - Allow different formats for output heatmap (e.g. SVG, PDF)

Issue - State: closed - Opened by pjbriggs about 3 years ago - 1 comment
Labels: enhancement

#36 - Improve how peak sets and gene lists are supplied on command line

Issue - State: closed - Opened by pjbriggs about 3 years ago - 1 comment
Labels: enhancement

#35 - PEGS fails reading in data files if '.DS_Store' file is also present in the data directory

Issue - State: closed - Opened by pjbriggs over 3 years ago
Labels: bug

#34 - Add CHANGELOG to the documentation

Pull Request - State: closed - Opened by pjbriggs over 3 years ago
Labels: documentation, enhancement

#33 - Fix links in README to example data and outputs

Pull Request - State: closed - Opened by pjbriggs over 3 years ago
Labels: documentation, bugfix

#32 - Drop support for Python 2.7

Pull Request - State: closed - Opened by pjbriggs over 3 years ago

#31 - Add support for Python 3.9

Pull Request - State: closed - Opened by pjbriggs over 3 years ago
Labels: update

#30 - Update the required versions of Python package dependencies

Pull Request - State: closed - Opened by pjbriggs over 3 years ago
Labels: dependencies, update

#29 - Populate long description for package from README.rst

Pull Request - State: closed - Opened by pjbriggs over 3 years ago
Labels: documentation, enhancement

#28 - Fix bug in 'bedtools' auto-installation

Pull Request - State: closed - Opened by pjbriggs over 3 years ago
Labels: bugfix

#27 - Broken 'bedtools' auto-installation

Issue - State: closed - Opened by pjbriggs over 3 years ago
Labels: bug

#26 - Drop support for Python 2.7

Issue - State: closed - Opened by pjbriggs over 3 years ago

#25 - Update numpy and scipy dependencies

Issue - State: closed - Opened by pjbriggs over 3 years ago - 1 comment
Labels: dependencies

#24 - Add support for Python 3.9

Issue - State: closed - Opened by pjbriggs over 3 years ago
Labels: enhancement

#23 - Updates/fixes to PEGS for distribution via PyPI

Pull Request - State: closed - Opened by pjbriggs over 3 years ago
Labels: bugfix

#22 - Add continuous integration workflow with Github Actions

Pull Request - State: closed - Opened by pjbriggs over 3 years ago
Labels: enhancement, testing

#21 - Update unit tests to deal with missing bedtools

Pull Request - State: closed - Opened by pjbriggs over 3 years ago
Labels: enhancement, testing

#20 - Update to Pillow 8.1.1

Pull Request - State: closed - Opened by pjbriggs over 3 years ago
Labels: bugfix, dependencies

#19 - Add a worked example to the documentation

Pull Request - State: closed - Opened by pjbriggs over 3 years ago
Labels: documentation, enhancement

#18 - Improve error detection/reporting if TADs 'file' is a directory

Issue - State: closed - Opened by pjbriggs over 3 years ago
Labels: bug

#17 - Enable automated testing from Github

Issue - State: closed - Opened by pjbriggs over 3 years ago - 1 comment
Labels: enhancement, testing

#16 - Update README 'quick start' and 'licensing' section

Pull Request - State: closed - Opened by pjbriggs over 3 years ago
Labels: documentation, bugfix

#15 - Update required version of Pillow to 7.1.0

Pull Request - State: closed - Opened by pjbriggs over 3 years ago
Labels: bugfix, dependencies

#14 - Update "licensing" information in the README

Issue - State: closed - Opened by pjbriggs over 3 years ago
Labels: bug, documentation

#13 - Make "quick start" instructions in README consistent with the main documentation

Issue - State: closed - Opened by pjbriggs over 3 years ago
Labels: bug, documentation

#12 - Collect all files from cluster directory regardless of name

Pull Request - State: closed - Opened by pjbriggs over 4 years ago
Labels: enhancement

#11 - Document workaround for installing on Mac OS X when getting "Python not installed as framework" failure

Pull Request - State: closed - Opened by pjbriggs over 4 years ago
Labels: bug, documentation, mac osx

#10 - Collect and use all files in the 'clusters' directory

Issue - State: closed - Opened by pjbriggs over 4 years ago
Labels: enhancement

#9 - Add heatmap images to the 'outputs' documentation

Pull Request - State: closed - Opened by pjbriggs over 4 years ago
Labels: documentation, enhancement

#8 - Add CONTRIBUTING document and update setup.py metadata

Pull Request - State: closed - Opened by pjbriggs over 4 years ago
Labels: documentation

#7 - Add BSD 3-clause license

Pull Request - State: closed - Opened by pjbriggs over 4 years ago

#6 - outputs: explicitly set the matplotlib backend to 'TkAgg'.

Pull Request - State: closed - Opened by pjbriggs over 4 years ago - 1 comment
Labels: bug

#5 - RuntimeError running PEGS under Mac OSX

Issue - State: closed - Opened by pjbriggs over 4 years ago - 2 comments
Labels: bug, python 3.7, mac osx

#4 - Add heatmap example to the documentation

Issue - State: closed - Opened by pjbriggs over 4 years ago
Labels: documentation

#3 - Add citation information to the documentation and program

Issue - State: closed - Opened by pjbriggs over 4 years ago
Labels: documentation, enhancement

#2 - Add CONTRIBUTING document

Issue - State: closed - Opened by pjbriggs over 4 years ago

#1 - Add licence

Issue - State: closed - Opened by pjbriggs over 4 years ago

GitHub / fls-bioinformatics-core/pegs issues and pull requests