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szhan
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tsimpute
Genome-wide genotype imputation using tree sequences.
MIT License
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Mention PR 2815 in tskit
#194
szhan
closed
5 months ago
0
Function to convert variants in xarray.Dataset to SampleData format
#193
szhan
closed
7 months ago
0
Fix bug introduced when refactoring
#192
szhan
closed
7 months ago
0
Explain parameters
#191
szhan
closed
7 months ago
0
Compute R-squared between allele dosages of two sets of genotypes
#190
szhan
opened
7 months ago
1
Minor refactor
#189
szhan
closed
7 months ago
0
Refactor so that data compatbility functions are separated
#188
szhan
closed
7 months ago
0
Default should be passing None to metadata when calling add_sites
#187
szhan
closed
8 months ago
0
Improve docs and comments
#186
szhan
closed
8 months ago
0
Remove its use as a script
#185
szhan
closed
8 months ago
0
Refactor util.py
#184
szhan
closed
8 months ago
0
Add init file and modify import statements
#183
szhan
closed
9 months ago
0
Remove reference to self
#182
szhan
closed
9 months ago
0
Enrich filtered ref. trees
#181
szhan
closed
9 months ago
0
Update nb to enrich trees with ancestors (hack)
#180
szhan
closed
9 months ago
0
Update example setting recombination rate
#179
szhan
closed
9 months ago
0
Add arguments recombination_rate and mutation_rate
#178
szhan
closed
9 months ago
0
Site positions rather than indices should be used
#177
szhan
closed
9 months ago
0
Refactor demo nb
#176
szhan
closed
9 months ago
0
Rename file
#175
szhan
closed
9 months ago
0
Remove deprecated functions
#174
szhan
closed
9 months ago
0
Rework print_tsdata_to_vcf
#173
szhan
closed
9 months ago
0
Refactor and assume diploids only
#172
szhan
closed
9 months ago
1
Temporary fix
#171
szhan
closed
9 months ago
0
Update after getting imputation results using tsinferred trees
#170
szhan
closed
9 months ago
0
Ignore simulated_data dir
#169
szhan
closed
9 months ago
0
Parallelise sample matching
#168
szhan
closed
9 months ago
0
Keep bash scripts in case they are useful
#167
szhan
closed
9 months ago
0
Rename notebooks
#166
szhan
closed
9 months ago
0
Show example performing imputation a la BEAGLE using ts
#165
szhan
closed
9 months ago
0
Edit docstring
#164
szhan
closed
9 months ago
0
Dump reference ts to samples for tsinfer
#163
szhan
closed
9 months ago
0
Change impute_samples to output sequences in ACGT encoding
#162
szhan
closed
9 months ago
0
Wrong variable names
#161
szhan
closed
9 months ago
0
Add warning about ACGT-encoded query haplotypes
#160
szhan
closed
9 months ago
0
Simulate reference panel and query haplotypes
#159
szhan
closed
10 months ago
0
Move num_ref_inds, num_query_inds, and sequence_length as arguments
#158
szhan
closed
10 months ago
0
Add option to specify demes YAML directory
#157
szhan
closed
10 months ago
0
Refactor
#156
szhan
closed
10 months ago
0
Remove copying contig length from ds
#155
szhan
closed
1 year ago
0
Do not require copying contig length from ds to remapped ds
#154
szhan
closed
1 year ago
0
Add functions to set HMM parameters
#153
szhan
closed
1 year ago
0
Add argument to show chip sites or all sites to `create_sample_path_vis_app`
#152
szhan
opened
1 year ago
0
Update `example_add_individual_to_ts` notebook
#151
szhan
closed
1 year ago
0
Tracks above sample path encodes nucleotide bases and presence/absence
#150
szhan
closed
1 year ago
0
Add arguments to set bounds on site ids when visualising sample paths
#149
szhan
opened
1 year ago
0
Set ranges when visualising sample paths
#148
szhan
closed
1 year ago
0
Add arguments to set bounds when visualising sample paths
#147
szhan
closed
1 year ago
1
Refactor sample path vis code
#146
szhan
closed
1 year ago
0
Refactor code to visualise sample paths
#145
szhan
closed
1 year ago
0
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