ebi-gene-expression-group scanpy-scripts issues

ebi-gene-expression-group / scanpy-scripts

Scripts for using scanpy

Apache License 2.0

28 stars 13 forks source link

issues

Newest

Newest Most commented Recently updated Oldest Least commented Least recently updated

Updating_bats_test

#136 anilthanki opened 4 days ago
0
Fixing Scanpy 1.9.3 error for mixed datatype column

#135 anilthanki opened 3 weeks ago
0
Scrublet failing on certain dataset

#134 anilthanki opened 1 month ago
0
Move to scanpy 1.9.8

#133 pcm32 opened 4 months ago
0
Release/v1.9.301 to develop

#132 pcm32 closed 4 months ago
5
Release/v1.9.301

#131 pcm32 closed 4 months ago
0
HVG genes setting through files

#130 pcm32 closed 4 months ago
1
Highly variable genes calculations should allow to blacklist or white list specific subset of genes

#129 pcm32 opened 4 months ago
0
Change deprecated sc.read() usages for read_h5ad call

#128 pcm32 closed 4 months ago
0
Explain how to update all the way to the Galaxy tools

#127 pcm32 opened 4 months ago
0
Remove extra pinning for mmnpy

#126 pcm32 closed 5 months ago
1
Scrublet double prediction fails with cells with under 5 expressed genes

#125 pcm32 opened 5 months ago
0
Scrubblet module fails when running with less than 30 cells

#124 pcm32 opened 8 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 5 months ago
8
Calculations of mito directly generate columns with dtypes that break qc calculations on subsequent filtering

#116 pcm32 opened 1 year 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 2 years ago
3
Fix boolean columns during merges of extra info at read time

#109 pinin4fjords closed 2 years ago
3
Adding fa2 to install so that trajectory tools can use it for setting up the plots

#108 nomadscientist closed 2 years ago
1
Remove batch handling in favour of scanpy-located code

#107 pinin4fjords closed 2 years ago
1
Fix mito calculations

#106 pinin4fjords closed 2 years ago
1
Batch aware Scrublet

#105 pinin4fjords closed 2 years ago
0
Always generate mito stats, even if not filtering by mito stats

#104 pinin4fjords closed 2 years ago
4
Try unpinning umap-learn

#103 pinin4fjords closed 2 years ago
4
Problems with Python 3.9.* - umap-learn<0.4.0 needed?

#102 LustigePerson opened 2 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 4 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 3 years ago
2