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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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Install failing on Colab (package incompatibility)
#586
ahernank
opened
19 hours ago
3
Support single-region buckets only
#585
ahernank
opened
1 day ago
0
Add plink converter function (shadow PR)
#584
alimanfoo
opened
1 week ago
1
Colors in GWSS plots
#583
jonbrenas
opened
1 week ago
1
More plotting options in plot_* functions
#582
jonbrenas
opened
1 week ago
0
Update switcher.json
#581
leehart
opened
2 weeks ago
0
Add clip_min parameter for Fst GWSS analyses
#580
alimanfoo
closed
2 weeks ago
0
Fix and improve plotting pairwise average fst
#579
alimanfoo
closed
2 weeks ago
3
Cannot always select older versions from docs switcher
#578
leehart
opened
3 weeks ago
0
Raise ValueError for missing CNV HMM
#577
leehart
closed
2 weeks ago
1
Raise ValueError for missing CNV DRCs
#576
leehart
closed
2 weeks ago
3
Skip sample sets missing CNV HMM
#575
leehart
closed
2 weeks ago
1
Update switcher.json
#574
leehart
closed
3 weeks ago
0
Update docs version switcher
#573
leehart
closed
3 weeks ago
0
Allow fractional value for max_missing_an, e.g. 0.01
#572
leehart
opened
1 month ago
0
FAILED tests/anoph/test_g123.py::test_g123_calibration[af1_sim] - IndexError: index -1 is out of bounds for axis 0 with size 0
#571
alimanfoo
opened
1 month ago
0
Add defaults for min_minor_ac, max_missing_an
#570
leehart
closed
1 month ago
0
Add defaults for min_minor_ac, max_missing_an
#569
leehart
closed
3 weeks ago
12
Anopheles pca() and plot_njt() functions should have sensible defaults for min_minor_ac and max_missing_an
#568
alimanfoo
closed
3 weeks ago
7
FST plotting function error
#567
KellyLBennett
closed
2 weeks ago
5
Add Ag3.cross_metadata() to API docs
#566
alimanfoo
opened
1 month ago
0
Handle missing CNV data
#565
leehart
closed
3 weeks ago
0
SNP browser to replace Panoptes
#563
EricRLucas
opened
1 month ago
2
Study URL in sample_metadata() is hard-coded rather than sourced from manifest.tsv
#562
leehart
closed
2 weeks ago
1
Anopheles diplotype clustering - fix n_snps in title
#561
sanjaynagi
closed
1 month ago
2
Add terms-of-use info to sample_metadata()
#560
leehart
closed
2 weeks ago
7
Display normal copy number (2) differently from missing CNV call (NaN) in advanced diplotype clustering
#559
alimanfoo
opened
2 months ago
3
Advanced diplotype clustering orders genes in the CNV section by label rather than by genomic position
#558
alimanfoo
opened
2 months ago
6
Add option to filter samples by max heterozygosity in advanced diplotype clustering
#557
alimanfoo
opened
2 months ago
2
Diplotype clustering title reports the number of amino acid snps, not total snps used in clustering
#556
sanjaynagi
closed
1 month ago
0
Diplotype clustering fails on sample sets without CNV calls
#555
sanjaynagi
closed
2 weeks ago
5
codecov/project CI check fails but seems to require additional coverage on code unrelated to the PR
#554
leehart
opened
2 months ago
0
Consider adding more documentation for sample set metadata
#553
leehart
opened
2 months ago
0
Upgrade latest_docs.yml to use Node.js 20
#552
leehart
opened
2 months ago
0
Handle missing discordant read calls for Af1.x
#551
leehart
opened
2 months ago
3
Advanced diplotype clustering - follow-up
#550
alimanfoo
closed
2 months ago
1
Add sequence QC metadata to sample_metadata()
#549
leehart
closed
2 months ago
0
explanation of site_annotations output
#548
EricRLucas
opened
2 months ago
2
Make the released sequence QC summary stats available
#547
leehart
closed
2 months ago
2
Ensure a site mask is used by default for Anopheles popgen functions
#546
alimanfoo
closed
2 months ago
1
Anopheles pca() should use default site mask
#545
alimanfoo
closed
2 months ago
0
Add clip_min parameter for Fst GWSS analyses
#544
sanjaynagi
closed
2 weeks ago
2
Should Fst be clipped between 0 and 1?
#543
sanjaynagi
closed
2 weeks ago
0
Pairwise Fst plots - Only plotting one information on each plot
#542
jonbrenas
opened
3 months ago
1
Updated parasite test buckets from staging to release
#541
nw20
closed
3 months ago
0
plot_pairwise_average_fst may change the order of the cohorts when using a cohort dict
#540
jonbrenas
closed
2 weeks ago
9
plot_pairwise_average_fst may change the order of the cohorts when using a cohort dict
#539
jonbrenas
closed
2 weeks ago
1
Option to annotate upper-right corner of Fst plots with Z scores.
#538
jonbrenas
closed
2 months ago
16
Advanced diplotype clustering
#537
sanjaynagi
closed
2 months ago
16
Z score for Fst
#536
jonbrenas
closed
2 months ago
0
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