Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / SBRG/pymodulon issues and pull requests

#121 - Update .pre-commit-config.yaml - remove-pre-commit checks

Pull Request - State: closed - Opened by jtburrows 3 months ago

#119 - Update files for pre-commit testing

Pull Request - State: closed - Opened by jtburrows 3 months ago

#118 - Update to master version

Pull Request - State: closed - Opened by jtburrows 3 months ago

#117 - Experimental branch - Update Eukaryotic functions and testing for python 3.8

Pull Request - State: closed - Opened by jtburrows 3 months ago - 1 comment

#115 - Add additional arguments to ensure functionality in python 3.8

Pull Request - State: closed - Opened by jtburrows 3 months ago

#111 - DIMA with more than 2 replicates

Issue - State: open - Opened by meono about 1 year ago

#110 - fix: allow for plotting to use sets as indexers

Pull Request - State: open - Opened by siddC over 1 year ago

#109 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: open - Opened by pre-commit-ci[bot] over 2 years ago

#108 - fix: update COG category mapping

Pull Request - State: open - Opened by siddC over 2 years ago - 1 comment

#107 - Update core.py

Pull Request - State: closed - Opened by avsastry over 2 years ago

#106 - Need to change "precision/recall" in `compute_{var}_enrichment` functions

Issue - State: open - Opened by siddC about 3 years ago
Labels: good first issue

#105 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] about 3 years ago

#104 - Added old locus tags for S. acidocaldarius to imodulondb.py

Pull Request - State: closed - Opened by kevin-rychel about 3 years ago - 1 comment

#103 - Add seaborn pairplot

Issue - State: open - Opened by sapoudel over 3 years ago
Labels: enhancement, good first issue

#102 - Changing imodulon names throws KeyError

Issue - State: closed - Opened by sapoudel over 3 years ago - 1 comment
Labels: bug

#101 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] over 3 years ago - 1 comment

#100 - Updates to documentation

Pull Request - State: closed - Opened by avsastry over 3 years ago - 1 comment

#99 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] over 3 years ago - 1 comment

#98 - Minor iMdb changes

Pull Request - State: closed - Opened by kevin-rychel over 3 years ago - 1 comment

#97 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] over 3 years ago

#96 - ci: gh-actions for pypi and docker only occur on tags

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

#95 - fixed typo with bulleted lists in iMdb docs; added section links.

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

#94 - Remove savefig

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

#93 - Testing pre-commit.ci

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

#92 - Updated github actions

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

#91 - Updated iModulonDB code & docs

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

#90 - Files oddly missing from imdb_june21, merging master in

Pull Request - State: closed - Opened by kevin-rychel over 3 years ago - 1 comment

#89 - iModulonDB case insensitivity and created imodulondb_table variable

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

#88 - Test gh-actions

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

#87 - New version of iModulonDB code

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

#86 - Fix legend to compare_imodulons_vs_regulons

Issue - State: open - Opened by avsastry over 3 years ago
Labels: enhancement

#85 - Imodulon vs regulon

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

#84 - Various plotting updates

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

#83 - create precision/recall overview plot function

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

#82 - metadata box plot: choosing which box/condition to display

Issue - State: closed - Opened by AnnieYuan21 over 3 years ago - 1 comment

#81 - Fixes #46 and #80

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

#80 - Saving and reloading model from json converts small numbers to 0

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

#79 - create regulon_venn function

Issue - State: open - Opened by avsastry over 3 years ago
Labels: enhancement

#78 - Add prefix to data in dot plot

Issue - State: open - Opened by avsastry over 3 years ago
Labels: enhancement

#77 - Added test function and new logic for deciding thresholds

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

#76 - Return an error when creating ica_data object without optimization

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

#75 - fix: replace plt.gcf() with ax.figure

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

#74 - IcaData iModulon Table is not properly set

Issue - State: closed - Opened by siddC over 3 years ago - 1 comment
Labels: bug

#73 - feat: add savefig option to barplot, scatterplot

Pull Request - State: closed - Opened by siddC over 3 years ago - 2 comments

#72 - Sp dev

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

#71 - Sp dev

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

#70 - make_prots_db now handles multiple fasta files. Tests updated to cove…

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

#69 - Test functions for enrichments.py

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

#68 - Allow users to enter multiple fasta files to make_prots_db

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

#67 - Make_prots_db doesn't work with NCBI files

Issue - State: closed - Opened by sapoudel over 3 years ago - 1 comment
Labels: bug

#66 - Create .readthedocs.yaml

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

#64 - Changed Docstrings of compare, core, and io

Pull Request - State: closed - Opened by Reosu over 3 years ago - 1 comment

#63 - Update make_prots and BBH functions to play nice with NCBI

Issue - State: closed - Opened by avsastry over 3 years ago - 1 comment
Labels: enhancement

#62 - Add fit_metric=None in plotting.scatterplot

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

#61 - Make a __repr__ function for the IcaData object

Issue - State: open - Opened by avsastry over 3 years ago - 1 comment
Labels: enhancement

#60 - Update docstrings and remove typing

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

#59 - explained_variance improvements

Issue - State: closed - Opened by avsastry almost 4 years ago - 2 comments
Labels: documentation, enhancement

#58 - Italicize gene names in plot_gene_weights

Issue - State: closed - Opened by avsastry almost 4 years ago

#57 - Dima fix

Pull Request - State: closed - Opened by Reosu almost 4 years ago

#56 - Fixed bug in plot_dima associated with labeling

Pull Request - State: closed - Opened by Reosu almost 4 years ago

#55 - Add evidence levels for regulon enrichments

Issue - State: closed - Opened by avsastry almost 4 years ago - 1 comment

#53 - Update imodulondb to match master

Pull Request - State: closed - Opened by kevin-rychel almost 4 years ago

#52 - Fixed a COG color error if the gene table is unexpectedly updated

Pull Request - State: closed - Opened by kevin-rychel almost 4 years ago

#51 - Implement automated activity classification from experimental metadata

Issue - State: closed - Opened by avsastry almost 4 years ago - 1 comment

#50 - Move plasmid gene locations to end of iModulon gene scatter

Issue - State: open - Opened by avsastry almost 4 years ago
Labels: enhancement

#49 - Fixed minor errors in iModulonDB_setup.py

Pull Request - State: closed - Opened by kevin-rychel almost 4 years ago

#48 - Minor bug fixes

Pull Request - State: closed - Opened by kevin-rychel almost 4 years ago

#47 - Change certain warnings to log.warning

Issue - State: closed - Opened by avsastry almost 4 years ago - 2 comments
Labels: experimental

#46 - Add option in get_prots function to use 'old_locus_tags'

Issue - State: closed - Opened by sapoudel almost 4 years ago
Labels: enhancement

#45 - Added iModulonDB Compatibility

Pull Request - State: closed - Opened by kevin-rychel almost 4 years ago

#44 - Incorrect/bad dimensionality recommendation

Issue - State: closed - Opened by sapoudel almost 4 years ago - 1 comment
Labels: bug

#43 - Highlighting Differential Genes in the DIMA plots

Issue - State: closed - Opened by Reosu almost 4 years ago

#42 - Setter for iModulon names

Issue - State: closed - Opened by sapoudel almost 4 years ago - 1 comment
Labels: enhancement, good first issue

#41 - Add pre-commit

Issue - State: closed - Opened by avsastry almost 4 years ago

#40 - For barplot base figure, automatically highlight project if it's the only project selected

Issue - State: closed - Opened by avsastry almost 4 years ago - 1 comment
Labels: enhancement

#39 - Add error message if threshold method is not 'kmeans' or 'dagostino'

Issue - State: closed - Opened by avsastry almost 4 years ago - 1 comment

#38 - Add ica_data objects for published datasets

Issue - State: closed - Opened by avsastry about 4 years ago - 7 comments
Labels: enhancement

#37 - Use iModulons to interpret new data

Issue - State: closed - Opened by avsastry about 4 years ago - 1 comment
Labels: enhancement

#36 - Update IO to use gzip

Pull Request - State: closed - Opened by camlam about 4 years ago

#35 - ZIP handling for IO functions

Pull Request - State: closed - Opened by camlam about 4 years ago - 1 comment

#34 - Clustering/DIMCA

Pull Request - State: closed - Opened by camlam about 4 years ago

#33 - Add MEME integration

Issue - State: closed - Opened by avsastry about 4 years ago
Labels: enhancement

#32 - Recovered variance

Issue - State: closed - Opened by avsastry about 4 years ago - 1 comment
Labels: enhancement

#31 - Timeseries visualizations

Issue - State: closed - Opened by avsastry about 4 years ago
Labels: enhancement

#30 - Previous code identifies different optimal thresholds

Issue - State: closed - Opened by avsastry about 4 years ago - 2 comments
Labels: bug

#29 - plot_gene_weights() Not working

Issue - State: closed - Opened by kevin-rychel about 4 years ago - 2 comments

#28 - Org compare

Pull Request - State: closed - Opened by Reosu about 4 years ago

#27 - Org compare

Pull Request - State: closed - Opened by Reosu about 4 years ago

#26 - IO Error in pymodulon

Issue - State: closed - Opened by avsastry about 4 years ago - 2 comments
Labels: bug

#25 - compute_trn_enrichment() does not allow for unnamed iModulons

Issue - State: closed - Opened by siddC about 4 years ago - 4 comments
Labels: bug

#24 - Keep parity with master

Pull Request - State: closed - Opened by siddC about 4 years ago

#23 - Gene weight x axis

Pull Request - State: closed - Opened by siddC about 4 years ago

#22 - Cross-species Gene Weight Comparison

Issue - State: closed - Opened by siddC about 4 years ago - 1 comment
Labels: enhancement