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szhan
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onekg_analysis
Evaluation of genotype imputation methods using the unified genealogy dataset
MIT License
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Correct input VCF file name
#27
szhan
closed
1 year ago
0
Compare results of tskit.lshmm and BEAGLE using correct BEAGLE VCF file
#26
szhan
closed
1 year ago
0
Analysis comparing output of `tskit.lshmm` and Duncan's lshmm
#25
szhan
closed
1 year ago
0
Run `tskit.lshmm` using BEAGLE like HMM parameters
#24
szhan
closed
1 year ago
2
Compare sample paths obtained using `_tskit.lshmm` and Duncan's 'lshmm'
#23
szhan
closed
1 year ago
0
Update notebooks running lshmm with mu set to 1e-04
#22
szhan
closed
1 year ago
0
Looking into the source code of BEAGLE
#21
szhan
closed
1 year ago
6
Explore switch paths obtained under different parameters
#20
szhan
closed
1 year ago
1
Explore patterns of switches in HMM copying paths
#19
szhan
closed
1 year ago
8
Check switch site positions in HMM copying paths
#18
szhan
closed
1 year ago
2
Update notebook with sample path visualization
#17
szhan
closed
1 year ago
0
Update notebooks after packaging some code
#16
szhan
closed
1 year ago
0
Call `bgzip` and `bcftools` from Python
#15
szhan
opened
1 year ago
0
Convert `run_lshmm.ipynb` into pipeline
#14
szhan
opened
1 year ago
0
Clear cell output
#13
szhan
closed
1 year ago
0
Add notebook running lshmm on chip-like data under different parameters
#12
szhan
closed
1 year ago
1
Investigate differences in imputation results between `tskit.lshmm` and BEAGLE
#11
szhan
closed
1 year ago
2
Choice of genotype array to generate pseudo-chip data
#10
szhan
opened
1 year ago
0
Polish Jupyter notebooks
#9
szhan
closed
1 year ago
0
Rerun after `tsimpute` enhancements, refactoring, and bug fixes
#8
szhan
closed
1 year ago
0
Rerun after debugging
#7
szhan
closed
1 year ago
0
Initial analysis
#6
szhan
closed
1 year ago
1
Test sensitivity of sample matching to exact values of mismatch probabilities and switch probabilities
#5
szhan
closed
1 year ago
1
Split `prepare_dataset.ipynb` into separate notebooks
#4
szhan
closed
1 year ago
4
Use Dask to distribute runs of `tskit.lshmm`
#3
szhan
closed
1 year ago
1
Replace use of `tsinfer.SampleData` with `sgkit`
#2
szhan
closed
1 year ago
3
Compare imputation performance using tskit.lshmm and BEAGLE
#1
szhan
closed
1 year ago
3