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haniffalab
/
webatlas-pipeline
A data pipeline built in Nextflow to process spatial and single-cell experiment data for visualisation in WebAtlas
MIT License
46
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10
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Deps conflict with conda environment
#99
davehorsfall
closed
1 year ago
1
Error generating spatial label image
#98
davehorsfall
closed
1 year ago
1
Resolve Multimodal support for pipeline
#97
davehorsfall
closed
1 year ago
1
use dynamic resource allocation; disable timeline for now; added some…
#96
BioinfoTongLI
opened
1 year ago
2
used nextflow managed repo; simplified installation
#95
BioinfoTongLI
closed
1 year ago
1
update dev branch from main
#94
BioinfoTongLI
closed
1 year ago
1
added conda env as an option
#93
BioinfoTongLI
closed
1 year ago
1
add consolidate_metadata param to process_h5ad
#92
dannda
closed
1 year ago
1
add parameter to load raw count file from spaceranger output
#91
dannda
closed
1 year ago
1
Add support for Xenium 1.3 outputs
#90
prete
closed
1 year ago
2
Add license
#89
davehorsfall
closed
1 year ago
0
add license to close #87
#88
davehorsfall
closed
1 year ago
2
License decision
#87
davehorsfall
closed
1 year ago
1
Bump 0.3.1
#86
davehorsfall
closed
1 year ago
0
Upgrade build config
#85
dannda
closed
1 year ago
0
Prep version bump
#84
davehorsfall
closed
1 year ago
1
Update process_spaceranger.py
#83
davehorsfall
closed
1 year ago
1
add check for 'options' when adding files to view config
#82
dannda
closed
1 year ago
0
turn input path strings to file type
#81
dannda
closed
1 year ago
0
SeqFish demos
#80
davehorsfall
closed
1 year ago
6
Support spatial scale bar
#79
davehorsfall
opened
1 year ago
1
Support relative file path for data files in config yaml file
#78
davehorsfall
closed
1 year ago
1
Support xenium version 1.3
#77
davehorsfall
closed
1 year ago
0
Showing expression value in popover box
#76
davehorsfall
closed
1 year ago
1
Add visium tutorial
#75
davehorsfall
closed
1 year ago
1
load Xenium clustering into h5ad file
#74
BioinfoTongLI
closed
1 year ago
5
Manuscript prep
#73
davehorsfall
closed
1 year ago
0
Hyphon Daniela's last names
#72
davehorsfall
closed
1 year ago
0
codecov badge pointing to wrong location
#71
davehorsfall
closed
1 year ago
0
Preparation for WebAtlas manuscript
#70
davehorsfall
closed
1 year ago
1
Refactor to yaml input
#69
dannda
closed
1 year ago
1
Multimodal integration
#68
dannda
closed
1 year ago
0
limitation of multithread writing to shared file system
#67
BioinfoTongLI
closed
1 year ago
0
multimodal draft v1
#66
BioinfoTongLI
closed
1 year ago
0
Multimodal integration draft + Xenium conversion
#65
BioinfoTongLI
closed
1 year ago
2
Make build-docker-imgs.sh executable by default
#64
davehorsfall
closed
1 year ago
0
Move instructions for building the docker images into the "installation" section
#63
davehorsfall
closed
1 year ago
0
Show error if "-params-file" argument missing
#62
davehorsfall
closed
1 year ago
1
Feat/add technologies
#61
dannda
closed
1 year ago
2
bioformats2raw breaks with docker (24.0.2) in Nextflow
#60
BioinfoTongLI
closed
4 months ago
10
Review and clean all file headers, there are legacy headers containing license declarations that need removing
#59
davehorsfall
closed
1 year ago
2
Link to template directory in docs is not working
#58
davehorsfall
closed
1 year ago
0
Modify sphinx build action to deploy branches/PRs separately
#57
davehorsfall
closed
1 year ago
1
Refactor
#56
dannda
closed
1 year ago
1
Docs and citation
#55
davehorsfall
closed
1 year ago
1
Error: Unable to resolve action `JamesIves/github-pages-deploy-action@4.4.1`, unable to find version `4.4.1`
#54
davehorsfall
closed
1 year ago
0
WARNING: autodoc: failed to import module 'build_config'; the following exception was raised: No module named 'fire'
#53
davehorsfall
closed
1 year ago
0
Prep 0.1.0
#52
davehorsfall
closed
1 year ago
0
Codecov
#51
davehorsfall
closed
1 year ago
0
Automation workflows
#50
davehorsfall
closed
1 year ago
0
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