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ebi-gene-expression-group
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scanpy-scripts
Scripts for using scanpy
Apache License 2.0
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Updating_bats_test
#136
anilthanki
opened
3 months ago
0
Fixing Scanpy 1.9.3 error for mixed datatype column
#135
anilthanki
opened
3 months ago
2
Scrublet failing on certain dataset
#134
anilthanki
opened
4 months ago
0
Move to scanpy 1.9.8
#133
pcm32
opened
7 months ago
0
Release/v1.9.301 to develop
#132
pcm32
closed
7 months ago
5
Release/v1.9.301
#131
pcm32
closed
7 months ago
0
HVG genes setting through files
#130
pcm32
closed
7 months ago
1
Highly variable genes calculations should allow to blacklist or white list specific subset of genes
#129
pcm32
opened
7 months ago
0
Change deprecated sc.read() usages for read_h5ad call
#128
pcm32
closed
7 months ago
0
Explain how to update all the way to the Galaxy tools
#127
pcm32
opened
7 months ago
0
Remove extra pinning for mmnpy
#126
pcm32
closed
8 months ago
1
Scrublet double prediction fails with cells with under 5 expressed genes
#125
pcm32
opened
8 months ago
0
Scrubblet module fails when running with less than 30 cells
#124
pcm32
opened
11 months ago
0
Using a single group in find marker genes fails
#123
pcm32
opened
1 year ago
0
Add filtering by quantiles
#122
pcm32
opened
1 year ago
0
PlotEmbedd could give more user friendly errors to allow users to recover
#121
pcm32
opened
1 year ago
0
What is scanpy-run-umap default for --maxiter INTEGER
#120
swbioinf
closed
1 year ago
4
Should we add ability to mark ribosomal genes?
#119
pcm32
opened
1 year ago
0
How can I use scanpy_scripts?
#118
cooperist
opened
1 year ago
3
Move to scanpy 1.9.3 and other improvements
#117
pcm32
closed
8 months ago
8
Calculations of mito directly generate columns with dtypes that break qc calculations on subsequent filtering
#116
pcm32
opened
2 years ago
3
Update setup.py to remove t-SNE dependency
#115
pinin4fjords
closed
2 years ago
1
Add compression option to export
#114
pinin4fjords
closed
2 years ago
0
Add Black format checking
#113
pinin4fjords
closed
2 years ago
1
Feature/gzip mtx output
#112
pinin4fjords
closed
2 years ago
2
Feature/unit tests
#111
irisdianauy
closed
2 years ago
0
Add fix for exporting mtx from .raw.X
#110
pinin4fjords
closed
3 years ago
3
Fix boolean columns during merges of extra info at read time
#109
pinin4fjords
closed
3 years ago
3
Adding fa2 to install so that trajectory tools can use it for setting up the plots
#108
nomadscientist
closed
3 years ago
1
Remove batch handling in favour of scanpy-located code
#107
pinin4fjords
closed
3 years ago
1
Fix mito calculations
#106
pinin4fjords
closed
3 years ago
1
Batch aware Scrublet
#105
pinin4fjords
closed
3 years ago
0
Always generate mito stats, even if not filtering by mito stats
#104
pinin4fjords
closed
3 years ago
4
Try unpinning umap-learn
#103
pinin4fjords
closed
3 years ago
4
Problems with Python 3.9.* - umap-learn<0.4.0 needed?
#102
LustigePerson
opened
3 years ago
3
Is make_plot_function passing the color argument correctly for plot embed?
#101
pcm32
closed
3 years ago
2
Make sure that paga without basis uses color if given
#100
pcm32
closed
3 years ago
3
Unpin loompy
#99
pinin4fjords
closed
3 years ago
1
loompy version problem
#98
kaji331
closed
3 years ago
1
Move to self-hosted runner
#97
pinin4fjords
closed
7 months ago
0
Store matrix variants
#96
pinin4fjords
closed
3 years ago
6
Allow annData output from plotting functions.
#95
pinin4fjords
closed
3 years ago
3
FDG and paga
#94
pinin4fjords
closed
3 years ago
1
Add first basic scrublet integration
#93
pinin4fjords
closed
3 years ago
2
n_genes in the var table
#92
ksenia007
closed
3 years ago
1
Add pushes to CI, limited to tags starting with 'v', for releasing
#91
pinin4fjords
closed
3 years ago
2
Feature/ci to GitHub
#90
pinin4fjords
closed
3 years ago
2
Remove CLI-level n_pcs hack and allow fallback to Scanpy's
#89
pinin4fjords
closed
3 years ago
6
Hide singlet cell groups before marker detection
#88
pinin4fjords
closed
3 years ago
13
1.6.0 bugfixes
#87
pinin4fjords
closed
4 years ago
2
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