Ecosyste.ms: Issues

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GitHub / ebi-gene-expression-group/atlas-anndata issues and pull requests

#45 - Update README.md to test CI

Pull Request - State: open - Opened by anilthanki 6 months ago

#44 - fix and optimise derive_metadata

Pull Request - State: closed - Opened by YalanBi over 1 year ago

#43 - create the idf template file at init_magetab step

Pull Request - State: closed - Opened by YalanBi over 1 year ago

#42 - Fixes to ensure SCXA loading compatibility

Pull Request - State: open - Opened by pmb59 over 1 year ago - 2 comments

#41 - bump version

Pull Request - State: closed - Opened by pmb59 over 1 year ago

#40 - issue with mamba

Issue - State: open - Opened by YalanBi over 1 year ago

#39 - Is There a Way to Do the Opposite Process (SCXA Bundle -> AnnData)?

Issue - State: closed - Opened by jeffquinn-msk over 2 years ago - 1 comment

#38 - Try to make sure altered object is readable

Pull Request - State: closed - Opened by pinin4fjords over 2 years ago

#37 - Make sure parameter is a string when adding to manifest

Pull Request - State: closed - Opened by pinin4fjords over 2 years ago

#36 - Fix unsupervised cluster renumbering

Pull Request - State: closed - Opened by pinin4fjords over 2 years ago

#35 - alternative sanitation

Pull Request - State: closed - Opened by pinin4fjords over 2 years ago

#33 - Remove single groups from marker detection

Pull Request - State: closed - Opened by pinin4fjords over 2 years ago

#31 - Fix a sample_field reference in non-droplet context

Pull Request - State: closed - Opened by pinin4fjords over 2 years ago - 1 comment

#30 - Unable to get sample annotations

Issue - State: closed - Opened by YalanBi over 2 years ago - 2 comments

#29 - Make sure stats for unsupervised clusterings are recorded correctly

Pull Request - State: closed - Opened by pinin4fjords over 2 years ago

#28 - More efficiency measures for marker stats table calc

Pull Request - State: closed - Opened by pinin4fjords over 2 years ago - 2 comments

#27 - Update README.md

Pull Request - State: closed - Opened by pinin4fjords over 2 years ago

#26 - Simplify setup to faciliate a conda wrapper

Pull Request - State: closed - Opened by pinin4fjords over 2 years ago

#25 - Make summary stats calculation for efficient

Pull Request - State: closed - Opened by pinin4fjords over 2 years ago - 2 comments

#24 - Write less matrices

Pull Request - State: closed - Opened by pinin4fjords over 2 years ago

#23 - Simplify workflow and allow operations based on curated metadata

Pull Request - State: closed - Opened by pinin4fjords over 2 years ago

#22 - Bump atlas-expeiriment-metadata version used in Snakemake workflow

Pull Request - State: closed - Opened by pinin4fjords over 2 years ago

#21 - clustering obs must be categorical

Pull Request - State: closed - Opened by pinin4fjords over 2 years ago

#20 - Feature/pyi upload

Pull Request - State: closed - Opened by pinin4fjords over 2 years ago

#19 - Feature/simplify first round

Pull Request - State: closed - Opened by pinin4fjords over 2 years ago

#18 - Incorporate curated metadata

Pull Request - State: closed - Opened by pinin4fjords over 2 years ago - 1 comment

#17 - Automatically reset the name used for SCXA DB matrix

Pull Request - State: closed - Opened by pinin4fjords over 2 years ago

#16 - write json parameters to manifest

Pull Request - State: closed - Opened by pinin4fjords over 2 years ago

#15 - Make sure we reverse any log transform for SCXA import

Pull Request - State: closed - Opened by pinin4fjords over 2 years ago

#14 - Revert "Relocate matrix scaling to anndata ops"

Pull Request - State: closed - Opened by pinin4fjords over 2 years ago

#13 - Relocate matrix scaling to anndata ops

Pull Request - State: closed - Opened by pinin4fjords over 2 years ago

#12 - Add a matrix scaling

Pull Request - State: closed - Opened by pinin4fjords over 2 years ago

#11 - Add cell/library mapping functionality

Pull Request - State: closed - Opened by pinin4fjords over 2 years ago

#10 - Feature/misc fixes

Pull Request - State: closed - Opened by pinin4fjords over 2 years ago

#9 - Compress MTX files directly

Pull Request - State: closed - Opened by pinin4fjords over 2 years ago - 1 comment

#8 - Feature/test with nonatlas

Pull Request - State: closed - Opened by pinin4fjords almost 3 years ago - 1 comment

#7 - Start to make bundles from validated config

Pull Request - State: closed - Opened by pinin4fjords almost 3 years ago - 1 comment

#6 - Add tests to actions

Pull Request - State: closed - Opened by pinin4fjords almost 3 years ago

#5 - Start to make bundles from validated config

Pull Request - State: closed - Opened by pinin4fjords almost 3 years ago - 1 comment

#4 - Add doctests to functions

Pull Request - State: closed - Opened by pinin4fjords almost 3 years ago

#3 - Organise as package

Pull Request - State: closed - Opened by pinin4fjords almost 3 years ago - 1 comment

#2 - Implement config yaml

Pull Request - State: closed - Opened by pinin4fjords almost 3 years ago - 2 comments

#1 - Initial commits to bundle creation from anndata

Pull Request - State: closed - Opened by pinin4fjords about 3 years ago - 1 comment