issues
search
nf-core
/
spatialvi
Pipeline for processing spatially-resolved gene counts with spatial coordinates and image data. Designed for 10x Genomics Visium transcriptomics.
https://nf-co.re/spatialvi
MIT License
49
stars
18
forks
source link
issues
Newest
Newest
Most commented
Recently updated
Oldest
Least commented
Least recently updated
Add quality control metrics as MultiQC custom content
#88
fasterius
opened
3 weeks ago
1
Report sample names
#87
fasterius
opened
3 weeks ago
1
Module updates
#86
fasterius
closed
4 weeks ago
1
Module updates
#85
fasterius
closed
1 month ago
1
MultiQC 1.21 doesn't support genomic_dna section
#84
Alan-pad
closed
1 month ago
1
Option to use the `--unknown-slide` parameter in `spaceranger count`
#83
pstorozenko
closed
1 month ago
1
Re-add empty line .nf-core.yml
#82
fasterius
closed
4 months ago
1
Fix CI issue
#81
fasterius
closed
4 months ago
1
Template merge
#80
fasterius
closed
4 months ago
1
Important! Template update for nf-core/tools v2.14.1
#79
nf-core-bot
closed
4 months ago
1
Important! Template update for nf-core/tools v2.14.0
#78
nf-core-bot
closed
4 months ago
1
Change name to `nf-core/spatialvi`
#77
fasterius
closed
5 months ago
2
Add Geary's C autocorrelation method for SVG report
#76
fasterius
closed
5 months ago
1
Use `to_legacy_anndata` function from `spatialdata_io` instead of custom code
#75
fasterius
opened
6 months ago
1
Missing SpatialDE package in Docker container for ST_SPATIAL_DE process
#74
lealiaxiong
closed
5 months ago
3
Fix schema validation for spaceranger reference
#73
grst
closed
5 months ago
2
Template updates
#72
fasterius
closed
7 months ago
3
Important! Template update for nf-core/tools v2.13.1
#71
nf-core-bot
closed
5 months ago
0
Add MultiQC support for Space Ranger
#70
fasterius
closed
7 months ago
3
Important! Template update for nf-core/tools v2.13
#69
nf-core-bot
closed
7 months ago
0
Quartonotebook
#68
fasterius
closed
7 months ago
2
Use spatialdata
#67
cavenel
closed
5 months ago
10
Important! Template update for nf-core/tools v2.12
#66
nf-core-bot
closed
8 months ago
2
Rename the pipeline
#65
fasterius
closed
5 months ago
1
Report updates
#64
fasterius
closed
8 months ago
1
Documentation
#63
fasterius
closed
9 months ago
1
Important! Template update for nf-core/tools v2.11.1
#62
nf-core-bot
closed
9 months ago
1
Allow tarballed inputs instead of only directories
#61
fasterius
closed
9 months ago
1
Important! Template update for nf-core/tools v2.11
#60
nf-core-bot
closed
9 months ago
0
Important! Template update for nf-core/tools v2.10
#59
nf-core-bot
closed
10 months ago
0
Important! Template update for nf-core/tools v2.9
#58
nf-core-bot
closed
1 year ago
0
Add MultiQC report
#57
grst
closed
1 year ago
1
Aggregate samples into single object
#56
grst
opened
1 year ago
4
Update DUMPSOFTWAREVERSIONS nf-core module
#55
fasterius
closed
1 year ago
1
Swap X and Y coords
#54
grst
closed
1 year ago
1
fix spatial de index error
#53
grst
closed
1 year ago
1
Update CHANGELOG with missing entries/description
#52
fasterius
closed
1 year ago
1
Version exporting of `leidenalg` and `SpatialDE` does not work
#51
fasterius
closed
1 year ago
0
Python module version export fixes
#50
fasterius
closed
1 year ago
5
Add non-ARM64 Conda profile for report modules
#49
fasterius
closed
1 year ago
1
Full-size test dataset
#48
grst
opened
1 year ago
0
Auto-detection of samplesheet type
#47
fasterius
closed
1 year ago
1
Add checks for QC filtering
#46
fasterius
closed
9 months ago
2
Switch to spaceranger module
#45
grst
closed
1 year ago
12
Cleanup custom download scripts
#44
grst
closed
1 year ago
2
Embed resources for quarto reports
#43
grst
closed
1 year ago
8
Add tests with nf-test
#42
grst
closed
1 year ago
2
Manual alignment in samplesheets
#41
fasterius
closed
1 year ago
2
Add MultiQC report
#40
grst
opened
1 year ago
13
Add SpatialData as output
#39
grst
closed
5 months ago
20
Next