related-sciences gwas-analysis issues

related-sciences / gwas-analysis

GWAS data analysis experiments

Apache License 2.0

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Plink new xarray rep

#40 eric-czech opened 4 years ago
0
Remove dataset wrappers in prototype core.py

#39 eric-czech opened 4 years ago
0
Add bgen-reader backend

#38 tomwhite closed 4 years ago
8
Create pytest fixture to parameterize dask scheduler

#37 tomwhite opened 4 years ago
0
Read BGEN files

#36 tomwhite closed 4 years ago
2
PyData PC-Relate Integration

#35 eric-czech closed 3 years ago
1
Fix #33. Handle missing values in PackGeneticBits

#34 ravwojdyla closed 4 years ago
8
Zarr/packgeneticbits invalid missing values encoding

#33 ravwojdyla closed 4 years ago
1
PyData prototype package, repo, and directory structure

#32 hammer opened 4 years ago
1
PyData prototype simulation methods

#31 eric-czech opened 4 years ago
5
PyData prototype genetics method implementations

#30 eric-czech opened 4 years ago
0
Add rebalance info

#29 ravwojdyla closed 4 years ago
1
Use of pydantic for PyData prototype?

#28 hammer opened 4 years ago
3
Add single node dask cluster config notebook

#27 ravwojdyla closed 4 years ago
3
PyData prototype LD prune implementation

#26 eric-czech closed 4 years ago
13
Light cleanup

#25 ravwojdyla closed 4 years ago
3
PyData prototype backend dispatching

#24 eric-czech opened 4 years ago
3
PyData prototype IO

#23 eric-czech closed 3 years ago
7
Define Xarray data structures for PyData prototype

#22 eric-czech opened 4 years ago
0
PyData prototype testing

#21 eric-czech opened 4 years ago
0
Build PyData prototype for GWAS analysis

#20 eric-czech opened 4 years ago
3
Fix #18. Make almond kernel user independent

#19 ravwojdyla closed 4 years ago
1
Hard-coded path in almond kernel

#18 ravwojdyla closed 4 years ago
0
How can you statically type a duck array?

#17 eric-czech closed 4 years ago
0
Determine core operations necessary in general-purpose GWAS toolkits

#16 eric-czech closed 4 years ago
3
Define data structures that would accommodate general purpose genetic workflows

#15 eric-czech closed 4 years ago
11
Related work from TOPMed

#14 hammer closed 4 years ago
1
Try to quantify some assertions

#13 hammer opened 4 years ago
0
Enumerate cohort-specific QC

#12 hammer opened 4 years ago
0
Possibly include qctool in benchmarks

#11 hammer opened 4 years ago
0
Use asv for benchmarks of Dask/Ray prototype

#10 hammer opened 4 years ago
1
Try Ray as alternative to Dask in prototype

#9 hammer opened 4 years ago
0
Try sparse arrays in Dask prototypes

#8 eric-czech opened 4 years ago
1
Try Python accelerators on Dask prototype

#7 hammer opened 4 years ago
1
Try CuPy integration w/ Dask to see what, if any, operations benefit from GPU acceleration

#6 eric-czech opened 4 years ago
3
Explore Xarray as the basis for a genetic toolkit API

#5 eric-czech closed 4 years ago
2
Add small representative numpy vs breeze benchmarks

#4 eric-czech closed 4 years ago
4
Association tests for large cohorts

#3 hammer opened 4 years ago
0
Include WES and WGS QC workloads

#2 hammer opened 4 years ago
0
Determine why Hail population stratification results have minor, irritating differences from PLINK results

#1 eric-czech closed 4 years ago
1