TheJacksonLaboratory scanpy_recipes issues

TheJacksonLaboratory / scanpy_recipes

Generalized and aggregated analysis functions for working with Anndata and Scanpy

BSD 3-Clause "New" or "Revised" License

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issues

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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