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vib-singlecell-nf
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scanpy
A repository for the scanpy module of the vib-singlecell-nf pipeline
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Develop
#49
dweemx
closed
3 years ago
0
[SUGGESTION] Scanpy find markers step can fail when only one cluster found from clustering algorithm
#48
dweemx
closed
3 years ago
0
Add strategy filter based on adaptive thresholds (e.g.: MAD)
#47
dweemx
closed
3 years ago
0
Develop
#46
dweemx
closed
4 years ago
0
Bump bleach from 3.1.0 to 3.1.4
#45
dependabot[bot]
closed
4 years ago
0
Develop
#44
dweemx
closed
4 years ago
0
highly_variable_genes not working for normalized values from edgeR::cpm
#43
dweemx
closed
4 years ago
0
Develop
#42
dweemx
closed
4 years ago
0
Parameter exploration for clustering fails for some resolutions
#41
cflerin
closed
4 years ago
1
Bump bleach from 3.1.2 to 3.1.4
#40
dependabot[bot]
closed
4 years ago
0
Develop
#39
dweemx
closed
4 years ago
0
Dependabot/pip/bleach 3.1.2
#38
dweemx
closed
4 years ago
0
Bump bleach from 3.1.1 to 3.1.2
#37
dependabot[bot]
closed
4 years ago
0
Fix bug sample_id not added to annotations_to_plot because not using unique values
#36
dweemx
closed
4 years ago
0
Fix bug when sample_id not generated by VSN and values are cell ids for instance
#35
dweemx
closed
4 years ago
0
Develop
#34
dweemx
closed
4 years ago
0
Genes filter is applied at the wrong step
#33
cflerin
closed
4 years ago
0
annotations_plot not passed to clustering report when using parameter exploration mode
#32
dweemx
closed
4 years ago
0
Develop
#31
dweemx
closed
4 years ago
0
Feature/vsn pipelines/149 allow skip filter norm steps
#30
dweemx
closed
4 years ago
0
Develop
#26
dweemx
closed
4 years ago
0
Fix bug missing space for k argument in batch_effect_correct
#25
dweemx
closed
4 years ago
0
Develop
#24
dweemx
closed
4 years ago
0
Bump bleach from 3.1.0 to 3.1.1
#23
dependabot[bot]
closed
4 years ago
0
mnnCorrect does not run properly
#22
dweemx
closed
4 years ago
1
Develop
#21
dweemx
closed
4 years ago
0
Explicitly subset the variable features
#20
dweemx
closed
4 years ago
3
Fix bug BEC_MNNCORRECT module should return the marker genes channel
#19
dweemx
closed
4 years ago
0
Develop
#18
dweemx
closed
4 years ago
0
Develop
#17
dweemx
closed
4 years ago
0
Develop
#16
dweemx
closed
4 years ago
0
Feature/43 set seed
#15
dweemx
closed
4 years ago
0
Develop
#14
dweemx
closed
4 years ago
0
Improve benchmarking strategy to handle empty params
#13
dweemx
closed
4 years ago
0
Develop
#12
dweemx
closed
4 years ago
0
Feature/115 benchmark clustering
#11
dweemx
closed
4 years ago
0
Develop
#10
dweemx
closed
4 years ago
0
Add leiden algorithm #8
#9
dweemx
closed
4 years ago
0
Add Leiden algorithm
#8
dweemx
closed
4 years ago
0
Use condition expression operation
#6
dweemx
closed
4 years ago
0
Develop
#5
dweemx
closed
4 years ago
0
Implement Scrublet
#4
dweemx
closed
4 years ago
1
nComps config parameter has no effect when computing UMAP
#3
dweemx
closed
4 years ago
1
Allow to set the n_pcs when computing t-SNE with sc.tl.tsne
#2
dweemx
closed
4 years ago
1