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TheJacksonLaboratory
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scanpy_recipes
Generalized and aggregated analysis functions for working with Anndata and Scanpy
BSD 3-Clause "New" or "Revised" License
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Create hemoglobin_genes.BDGP6.csv
#69
mjseignon
closed
3 years ago
0
Create mito_genes.BDGP6.csv
#68
mjseignon
closed
3 years ago
0
added gene lists for more than mm10/grch38
#67
wflynny
closed
4 years ago
0
Update setup.py to add brackets to key:value pair at line 31
#66
mjseignon
closed
4 years ago
0
Update read_write.py to fix typo in get_rds_embedding() function
#65
mjseignon
closed
4 years ago
0
Make cluster reordering via hierarchical clustering
#64
wflynny
opened
4 years ago
0
Change report to show final metrics, not 10X's unfiltered metrics.
#63
wflynny
opened
4 years ago
0
Mjseignon patch 1
#62
mjseignon
opened
5 years ago
1
Add per cluster violin plot metrics to report
#61
wflynny
opened
5 years ago
0
Clean up `.var` during aggregation
#60
wflynny
opened
5 years ago
0
Rds 2d embedding broken
#59
wflynny
opened
5 years ago
0
Incorporate gene sets and convenience function to remove them from highly_variable genes
#58
wflynny
opened
5 years ago
0
quick report changes
#57
wflynny
closed
5 years ago
0
Fix reporting qc kwds
#56
wflynny
closed
5 years ago
0
Report improvements
#55
wflynny
opened
5 years ago
0
Notebooks updates
#54
mjseignon
opened
5 years ago
0
Aggr notebook QC axis label
#53
mjseignon
closed
5 years ago
1
Hotfixes for last PR
#52
wflynny
closed
5 years ago
0
Modernize highly variable genes and qc_filtering
#51
wflynny
closed
5 years ago
0
Hotfix bandaids
#50
wflynny
closed
5 years ago
0
Decouple data reading and metadata annotation.
#49
wflynny
opened
5 years ago
0
HTML report QC procedure Table, Field shift
#48
mjseignon
closed
5 years ago
1
Feat/add tests
#47
wflynny
closed
5 years ago
0
Fix/cherrypick ms docs
#46
wflynny
closed
5 years ago
0
Incorporate `harmony` for batch correction
#45
wflynny
opened
5 years ago
0
fixed violin scale issue
#44
wflynny
closed
5 years ago
0
Fixed scanpy version in report and cleaned fig adding
#43
wflynny
closed
5 years ago
0
sample labels on scatter plots for aggregated sample analysis.
#42
mjseignon
closed
5 years ago
1
Fix for weird RDS creation bugs
#41
wflynny
closed
5 years ago
0
Fix 39
#40
wflynny
closed
5 years ago
0
Rds file submission script length and generality
#39
wflynny
closed
5 years ago
1
Add HTO/ADT demuxing function
#38
wflynny
opened
5 years ago
0
Fixes for #34
#37
wflynny
closed
5 years ago
0
Set Scale lower limit for vertical axis of Hemoglobin violin plots
#36
mjseignon
closed
5 years ago
1
small fixes to reporting
#35
wflynny
closed
5 years ago
0
Capture scanpy version, real reference version, cellranger version in report
#34
wflynny
closed
5 years ago
1
Fix aggregation/report aggregation
#33
wflynny
closed
5 years ago
0
Finally a fix for #11
#32
wflynny
closed
5 years ago
0
fixed config validation with new sample_info section
#31
wflynny
closed
5 years ago
0
Fix #27
#30
wflynny
closed
5 years ago
0
Short blurbs on how to use Cellview
#29
mjseignon
closed
5 years ago
1
Issue #3
#28
mjseignon
closed
5 years ago
1
Support for v3
#27
wflynny
closed
4 years ago
1
Rank plots for aggregation notebook
#26
mjseignon
opened
5 years ago
0
Get tests
#25
wflynny
opened
5 years ago
3
Analysis-template-aggregation QC plots naming
#24
mjseignon
closed
5 years ago
1
Analysis-Template_aggregation notebook
#23
mjseignon
opened
5 years ago
1
Use pathlib to manage paths.
#22
wflynny
opened
5 years ago
0
Add fake doublets code
#21
wflynny
opened
5 years ago
0
Incorporate edgepy
#20
wflynny
opened
5 years ago
1
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