malariagen malariagen-data-python issues

malariagen / malariagen-data-python

Analyse MalariaGEN data from Python

https://malariagen.github.io/malariagen-data-python/latest/

MIT License

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issues

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SNP browser to replace Panoptes

#563 EricRLucas opened 4 days ago
1
Study URL in sample_metadata() is hard-coded rather than sourced from manifest.tsv

#562 leehart opened 6 days ago
0
dipclust - fix n_snps in title

#561 sanjaynagi opened 6 days ago
1
Add terms-of-use info to sample_metadata()

#560 leehart opened 1 week ago
1
Display normal copy number (2) differently from missing CNV call (NaN) in advanced diplotype clustering

#559 alimanfoo opened 1 week ago
2
Advanced diplotype clustering orders genes in the CNV section by label rather than by genomic position

#558 alimanfoo opened 1 week ago
5
Add option to filter samples by max heterozygosity in advanced diplotype clustering

#557 alimanfoo opened 1 week ago
2
Diplotype clustering title reports the number of amino acid snps, not total snps used in clustering

#556 sanjaynagi opened 1 week ago
0
Diplotype clustering fails on sample sets without CNV calls

#555 sanjaynagi opened 1 week ago
3
codecov/project CI check fails but seems to require additional coverage on code unrelated to the PR

#554 leehart opened 2 weeks ago
0
Consider adding more documentation for sample set metadata

#553 leehart opened 2 weeks ago
0
Upgrade latest_docs.yml to use Node.js 20

#552 leehart opened 2 weeks ago
0
Handle missing discordant read calls for Af1.x

#551 leehart opened 2 weeks ago
1
Advanced diplotype clustering - follow-up

#550 alimanfoo closed 3 weeks ago
1
Add sequence QC metadata to sample_metadata()

#549 leehart closed 2 weeks ago
0
explanation of site_annotations output

#548 EricRLucas opened 3 weeks ago
1
Make the released sequence QC summary stats available

#547 leehart closed 2 weeks ago
2
Ensure a site mask is used by default for Anopheles popgen functions

#546 alimanfoo closed 1 month ago
1
Anopheles pca() should use default site mask

#545 alimanfoo closed 1 month ago
0
Add clip_min parameter for Fst GWSS analyses

#544 sanjaynagi opened 1 month ago
1
Should Fst be clipped between 0 and 1?

#543 sanjaynagi opened 1 month ago
0
Pairwise Fst plots - Only plotting one information on each plot

#542 jonbrenas opened 1 month ago
1
Updated parasite test buckets from staging to release

#541 nw20 closed 1 month ago
0
plot_pairwise_average_fst may change the order of the cohorts when using a cohort dict

#540 jonbrenas opened 1 month ago
8
plot_pairwise_average_fst may change the order of the cohorts when using a cohort dict

#539 jonbrenas opened 1 month ago
0
Option to annotate upper-right corner of Fst plots with Z scores.

#538 jonbrenas closed 2 weeks ago
16
Advanced diplotype clustering

#537 sanjaynagi closed 3 weeks ago
16
Z score for Fst

#536 jonbrenas closed 2 weeks ago
0
Pandas FutureWarning: Setting an item of incompatible dtype is deprecated

#535 jonbrenas opened 1 month ago
7
Bokeh BokehDeprecationWarning: 'circle() method with size value' was deprecated in Bokeh 3.4.0 and will be removed, use 'scatter(size=...) instead'

#534 jonbrenas closed 1 month ago
1
Pandas FutureWarning: ChainedAssignmentError: behaviour will change in pandas 3.0

#533 jonbrenas closed 1 month ago
1
Pandas FutureWarning: Setting an item of incompatible dtype is deprecated

#532 jonbrenas opened 1 month ago
0
Pandas FutureWarning: ChainedAssignmentError: behaviour will change in pandas 3.0

#531 jonbrenas closed 1 month ago
0
Bokeh BokehDeprecationWarning: 'circle() method with size value' was deprecated in Bokeh 3.4.0 and will be removed, use 'scatter(size=...) instead'

#530 jonbrenas closed 1 month ago
0
Pandas FutureWarning: 'A' is deprecated and will be removed in a future version, please use 'Y' instead

#529 jonbrenas closed 1 month ago
1
Add sample_query argument for cnv_discordant_read_calls function

#528 jonbrenas closed 1 month ago
0
Update poetry lock file

#527 alimanfoo closed 1 month ago
0
Pandas FutureWarning: 'A' is deprecated and will be removed in a future version, please use 'Y' instead

#526 alimanfoo closed 1 month ago
0
Amend anoph snp_data.py where GQ, AD, MQ are still expected to be alongside GT

#525 leehart opened 1 month ago
2
Key errors on `snp_calls()`

#524 ahernank closed 1 month ago
1
Add automatic selection of regional GCS storage

#523 alimanfoo closed 1 month ago
5
sample_query argument for cnv_discordant_read_calls function

#522 EricRLucas closed 1 month ago
0
UserWarnings when using bokeh.layouts.gridplot for GWSS

#521 jonbrenas opened 1 month ago
4
Update support mailing address

#520 ahernank closed 2 months ago
0
Update support mailing address

#519 ahernank closed 2 months ago
1
Update mailing address on API client info

#518 ahernank closed 2 months ago
0
Detect permission error

#517 alimanfoo closed 3 months ago
1
'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