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becavin-lab
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checkatlas
One liner tool to check the quality of your single-cell atlases.
https://checkatlas.readthedocs.io/en/latest/
BSD 3-Clause "New" or "Revised" License
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Create github with all metrics
#43
drbecavin
opened
5 months ago
0
Add multiomic singlce cell mangamenet
#42
drbecavin
opened
5 months ago
0
Add test datasets for spatial transcriptomics
#47
drbecavin
opened
5 months ago
0
Spatial Image QC
#46
drbecavin
opened
5 months ago
0
Add SpatialData management
#41
drbecavin
opened
5 months ago
0
Dimensionality reduction metrics
#40
drbecavin
opened
5 months ago
0
Implement metrics from Malte Luecken's integration benchmark
#39
drbecavin
opened
5 months ago
0
Implement metrics from Antoine Collin master thesis
#48
drbecavin
opened
5 months ago
0
Tutorial for adding metrics in checklatlas
#45
drbecavin
opened
5 months ago
0
Add test datasets
#44
drbecavin
opened
5 months ago
0
Nf core
#38
drbecavin
closed
1 year ago
0
Multiqc
#37
drbecavin
closed
1 year ago
0
Improve Mito and ribo QC calculation
#36
drbecavin
opened
1 year ago
0
Integration to scVerse
#35
drbecavin
opened
1 year ago
0
Integration with nf-core pipelines
#34
grst
opened
1 year ago
5
Workflow
#33
drbecavin
closed
1 year ago
0
Metrics
#32
drbecavin
closed
1 year ago
1
Metrics
#31
drbecavin
closed
1 year ago
0
Metrics
#30
drbecavin
closed
1 year ago
0
Metrics
#29
drbecavin
closed
1 year ago
1
Switch to poetry
#28
drbecavin
closed
1 year ago
0
Dim reduction metric management for seurat object
#27
drbecavin
opened
2 years ago
0
Rpy2
#26
drbecavin
closed
2 years ago
1
Checkatlas conda, docker, singularity definition file
#25
drbecavin
closed
1 year ago
2
Seurat import
#24
drbecavin
opened
2 years ago
1
Rpy2
#23
drbecavin
closed
2 years ago
0
Add Muon object
#22
drbecavin
opened
2 years ago
0
Add knee plots
#21
grst
closed
1 year ago
5
Parse additional cellranger outputs
#20
chris-rands
closed
2 years ago
3
QC figures does not display parameters for Seurat object
#19
drbecavin
closed
1 year ago
0
Checkatlas .tsv tables in a separate folder
#18
drbecavin
closed
2 years ago
1
Add management of information from integrated Atlas
#16
drbecavin
closed
1 year ago
0
Write wiki/tutorial
#15
drbecavin
closed
1 year ago
1
Problem of CPUs and ram utilization in multithread mode
#14
drbecavin
closed
1 year ago
0
Automatic/Semi-automatic search of celltype key
#13
drbecavin
closed
1 year ago
0
QC figures too big
#12
drbecavin
closed
1 year ago
0
Fix parameters for checkatlas tools
#11
drbecavin
closed
2 years ago
1
Umap with seurat_cluster does not display cluster
#10
drbecavin
closed
2 years ago
1
Add Kruskal stress calculation
#9
drbecavin
closed
1 year ago
0
Multiome seurat object bad conversion
#8
drbecavin
closed
1 year ago
0
Create summary html with multiqc
#7
drbecavin
closed
2 years ago
1
Save table metrics
#6
drbecavin
closed
2 years ago
0
Implement all metrics
#5
drbecavin
closed
2 years ago
0
Implement metrics object
#4
drbecavin
closed
2 years ago
0
Parse all features of an atlas
#3
drbecavin
closed
2 years ago
0
Load Scanpy object
#2
drbecavin
closed
2 years ago
0
Load and Convert Seurat atlas
#1
drbecavin
closed
2 years ago
0