malariagen/malariagen-data-python

Issues

• Contig colors in GWSS plots

  #583 opened 4 months ago by jonbrenas
  0

• More plotting options in plot_* functions

  #582 opened 4 months ago by jonbrenas
  0

• explanation of site_annotations output

  #548 opened 7 months ago by EricRLucas
  2

• plot_pairwise_average_fst may change the order of the cohorts when using a cohort dict

  #539 opened 4 months ago by jonbrenas
  1

• Diplotype clustering fails on sample sets without CNV calls

  #555 opened 5 months ago by sanjaynagi
  5

• Pandas FutureWarning: Setting an item of incompatible dtype is deprecated

  #532 opened 5 months ago by jonbrenas
  0

• Should Fst be clipped between 0 and 1?

  #543 opened 5 months ago by sanjaynagi
  0

• 'AssertionError' when trying to return 'variant_allele' from biallelic_snp_calls()

  #516 opened 9 months ago by tristanpwdennis
  2

• Study URL in sample_metadata() is hard-coded rather than sourced from manifest.tsv

  #562 opened 5 months ago by leehart
  1

• FST plotting function error

  #567 opened 5 months ago by KellyLBennett
  5

• A function or method to know what is under embargo and what is free to use

  #508 opened 5 months ago by sanjaynagi
  2

• Cannot always select older versions from docs switcher

  #578 opened 5 months ago by leehart
  0

• Update docs version switcher

  #573 opened 5 months ago by leehart
  0

• Handle missing discordant read calls for Af1.x

  #551 opened 6 months ago by leehart
  3

• Anopheles pca() and plot_njt() functions should have sensible defaults for min_minor_ac and max_missing_an

  #568 opened 5 months ago by alimanfoo
  7

• UserWarnings when using bokeh.layouts.gridplot for GWSS

  #521 opened 8 months ago by jonbrenas
  4

• Dash set lower wheel zoom sensitivity

  #504 opened a year ago by alimanfoo
  0

• Amend anoph snp_data.py where GQ, AD, MQ are still expected to be alongside GT

  #525 opened 7 months ago by leehart
  2

• Pairwise Fst plots - Only plotting one information on each plot

  #542 opened 7 months ago by jonbrenas
  1

• Upgrade latest_docs.yml to use Node.js 20

  #552 opened 6 months ago by leehart
  0

• Consider adding more documentation for sample set metadata

  #553 opened 6 months ago by leehart
  0

• codecov/project CI check fails but seems to require additional coverage on code unrelated to the PR

  #554 opened 6 months ago by leehart
  0

• Add option to filter samples by max heterozygosity in advanced diplotype clustering

  #557 opened 6 months ago by alimanfoo
  2

• Advanced diplotype clustering orders genes in the CNV section by label rather than by genomic position

  #558 opened 6 months ago by alimanfoo
  6

• Display normal copy number (2) differently from missing CNV call (NaN) in advanced diplotype clustering

  #559 opened 6 months ago by alimanfoo
  3

• Add Ag3.cross_metadata() to API docs

  #566 opened 6 months ago by alimanfoo
  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 opened 5 months ago by alimanfoo
  0

• Allow fractional value for max_missing_an, e.g. 0.01

  #572 opened 5 months ago by leehart
  0

• SNP browser to replace Panoptes

  #563 opened 6 months ago by EricRLucas
  2

• Diplotype clustering title reports the number of amino acid snps, not total snps used in clustering

  #556 opened 5 months ago by sanjaynagi
  0

• Z score for Fst

  #536 opened 6 months ago by jonbrenas
  0

• Make the released sequence QC summary stats available

  #547 opened 6 months ago by leehart
  2

• Anopheles pca() should use default site mask

  #545 opened 7 months ago by alimanfoo
  0

• sample_query argument for cnv_discordant_read_calls function

  #522 opened 7 months ago by EricRLucas
  0

• Bokeh BokehDeprecationWarning: 'circle() method with size value' was deprecated in Bokeh 3.4.0 and will be removed, use 'scatter(size=...) instead'

  #530 opened 7 months ago by jonbrenas
  0

• Pandas FutureWarning: ChainedAssignmentError: behaviour will change in pandas 3.0

  #531 opened 7 months ago by jonbrenas
  0

• Pandas FutureWarning: 'A' is deprecated and will be removed in a future version, please use 'Y' instead

  #526 opened 7 months ago by alimanfoo
  0

• Key errors on `snp_calls()`

  #524 opened 7 months ago by ahernank
  1

• Update mailing address on API client info

  #518 opened 8 months ago by ahernank
  0

• Add support for Python 3.12

  #512 opened 9 months ago by alimanfoo
  0

• Support authenticated access to GCS

  #510 opened 9 months ago by alimanfoo
  0

• Fix random_region_str() to always select region within contig_size

  #509 opened 9 months ago by leehart
  1

• `af1.add_extra_metadata()` FileNotFoundError

  #505 opened a year ago by sanjaynagi
  2

• Link to training course in API docs

  #488 opened a year ago by alimanfoo
  1

• Different nomenclature in genome_features between Ag and Af

  #499 opened a year ago by jonbrenas
  4

• RAM use for Af diversity_stats

  #498 opened a year ago by jonbrenas
  3

• Exclude samples with unassigned taxon from advanced allele frequencies cohorts

  #491 opened a year ago by alimanfoo
  0

• Include project description on PyPI

  #492 opened a year ago by alimanfoo
  0

• Update URL in reprs

  #486 opened a year ago by alimanfoo
  0

• Migrate to ruff

  #485 opened a year ago by alimanfoo
  0