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malariagen
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malariagen-data-python
Analyse MalariaGEN data from Python
https://malariagen.github.io/malariagen-data-python/latest/
MIT License
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'AssertionError' when trying to return 'variant_allele' from biallelic_snp_calls()
#516
tristanpwdennis
opened
3 months ago
0
Add plink converter function
#515
tristanpwdennis
opened
3 months ago
3
Add support for Python 3.12, drop support for Python 3.8
#514
alimanfoo
closed
3 months ago
1
Authenticate the user if accessing GCS
#513
alimanfoo
closed
3 months ago
4
Add support for Python 3.12
#512
alimanfoo
closed
3 months ago
0
Authenticate the user if accessing GCS
#511
alimanfoo
closed
3 months ago
2
Support authenticated access to GCS
#510
alimanfoo
closed
3 months ago
0
Fix random_region_str() to always select region within contig_size
#509
leehart
closed
3 months ago
1
A function or method to know what is under embargo and what is free to use
#508
sanjaynagi
opened
4 months ago
1
Implement diplotype clustering, refactor haplotype clustering, and fix random_region_str()
#507
sanjaynagi
closed
3 months ago
6
Add new discordant read calls version
#506
ahernank
closed
4 months ago
7
`af1.add_extra_metadata()` FileNotFoundError
#505
sanjaynagi
closed
5 months ago
2
Dash set lower wheel zoom sensitivity
#504
alimanfoo
opened
5 months ago
0
Refactor H12 and H1X
#503
alimanfoo
closed
6 months ago
1
Docs improvements
#502
alimanfoo
closed
6 months ago
0
Reduce memory usage when accessing SNP calls with site_class parameter
#501
alimanfoo
closed
6 months ago
3
Add the correct nomenclature for genes in anopheles.py to enable CNVs for Af
#500
jonbrenas
closed
6 months ago
5
Different nomenclature in genome_features between Ag and Af
#499
jonbrenas
closed
6 months ago
4
RAM use for Af diversity_stats
#498
jonbrenas
closed
6 months ago
3
Refactor Fst functions
#497
alimanfoo
closed
6 months ago
2
Add ENA run accessions function
#496
ahernank
closed
4 months ago
6
Refactor G123
#495
alimanfoo
closed
6 months ago
1
Maintenance 2024-01-08
#494
alimanfoo
closed
6 months ago
1
Improve G123 and H12 performance
#493
alimanfoo
closed
6 months ago
3
Include project description on PyPI
#492
alimanfoo
closed
6 months ago
0
Exclude samples with unassigned taxon from advanced allele frequencies cohorts
#491
alimanfoo
closed
6 months ago
0
Refactor SNP frequencies
#490
alimanfoo
closed
6 months ago
3
Refactor handling of virtual contigs
#489
alimanfoo
closed
7 months ago
1
Link to training course in API docs
#488
alimanfoo
closed
6 months ago
1
Misc maintenance 2023-12-19
#487
alimanfoo
closed
7 months ago
2
Update URL in reprs
#486
alimanfoo
opened
7 months ago
0
Migrate to ruff
#485
alimanfoo
closed
7 months ago
0
Migrate to pydantic validate_call() for public API parameter type validation
#484
alimanfoo
opened
7 months ago
0
Refactor Anopheles IGV
#483
alimanfoo
closed
7 months ago
3
Add __init__() to API docs
#482
alimanfoo
opened
7 months ago
0
Anopheles refactor PCA functions
#481
alimanfoo
closed
7 months ago
2
Misc bug fixes
#480
alimanfoo
closed
7 months ago
3
Gaps in progress while computing biallelic SNP calls
#479
alimanfoo
closed
7 months ago
0
TypeError: plot_pca_coords() should accept dict for category_orders param
#478
alimanfoo
closed
7 months ago
0
plot_pca_coords() and plot_pca_coords_3d() should copy the input data before modifying
#477
alimanfoo
closed
7 months ago
0
TypeError: plot_pca_coords() does not accept dict for color param
#476
alimanfoo
closed
7 months ago
0
Reduce plotly legend trace gaps
#475
alimanfoo
closed
7 months ago
0
Xarray use Dataset.sizes rather than Dataset.dims
#474
alimanfoo
closed
7 months ago
0
Plot samples as scatter on a map
#473
alimanfoo
opened
7 months ago
1
Use xarray datasets for more return values
#472
alimanfoo
opened
7 months ago
0
Standardise biallelic diplotypes and handling of missing calls
#471
alimanfoo
opened
7 months ago
0
Biallelic pairwise distances and neighbour joining trees
#470
alimanfoo
closed
7 months ago
4
Simplify memory caching
#469
alimanfoo
opened
7 months ago
0
Biallelic SNP calls and diplotypes
#468
alimanfoo
closed
7 months ago
3
Remove dependency on jupyter-dash
#467
alimanfoo
closed
7 months ago
3
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