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CHANGELOG.md

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Changelog

[0.4.6] - 2024-04-17

Added

Changed

Fixed

  • fix bugs in cojo cond

[0.4.5] - 2024-04-17

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Changed

Fixed

  • fix bugs in polyfun+finemap and polyfun+susie

[0.4.4] - 2023-11-09

Added

Changed

  • discard progress bar, because it is not compatible with multiprocessing

Fixed

  • fix bugs in cojo cond

[0.4.3] - 2023-10-25

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Changed

  • env add data.table
  • fix inf beta and se in sumstats

Fixed

[0.4.2] - 2023-10-23

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Changed

  • load sumstat after multiprocessing
  • aviod error when no intersection ldref with input sumstat
  • fix bugs in cojo cond

Fixed

[0.4.1] - 2023-10-15

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  • docs

Changed

Fixed

[0.4.0] - 2023-10-12

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  • docs

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Fixed

[0.3.9] - 2023-09-26

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Fixed

  • fix dependency

[0.3.5] - 2023-06-13

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  • fix smunger independency

Fixed

[0.3.4] - 2023-06-12

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Changed

  • fix bugs in loci by ldblock

Fixed

[0.3.3] - 2023-06-12

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  • fix bugs in loci by ldblock

Fixed

[0.3.2] - 2023-05-25

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  • remove pathos

Fixed

[0.3.1] - 2023-05-25

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  • locus plot

Changed

Fixed

[0.3.0] - 2023-05-24

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  • annotate R2 for locus plot

Changed

Fixed

[0.2.9] - 2023-05-24

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  • Speed up susie by using fread

Fixed

[0.2.8] - 2023-05-23

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Changed

  • Speed up conditional analysis by intersect ldref with input sumstat first

Fixed

[0.2.7] - 2023-05-20

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Changed

  • Use tabix to load sumstats when finemap

Fixed

[0.2.6] - 2023-05-19

Added

  • Support polyfun for finemap and susie

Changed

  • Use the most significant SNP as lead SNP when COJO fails

Fixed

[0.2.5] - 2023-03-30

Added

  • set the most significant SNP as SNP, if there are no SNPs with P-value ≤ threshold.

Changed

Fixed

[0.2.4] - 2023-03-30

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  • support susie

Changed

Fixed

[0.2.3] - 2023-03-24

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  • suppor using LD blocks as loci boudaries.

Changed

Fixed

[0.2.2] - 2023-03-22

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Changed

  • deleted format function

Fixed

[0.2.1] - 2023-01-10

Added

  • Instruction of installation

Changed

Fixed

  • typo in easyfinemap.py line519

[0.2.0] - 2023-01-10

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  • add CAVIARBF

Changed

Fixed

[0.1.4] - 2023-01-10

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  • add PAINTOR

Changed

Fixed

[0.1.3] - 2023-01-09

Added

  • output credible sets

Changed

Fixed

[0.1.2] - 2023-01-07

Added

  • update summary statistics using cojo-cond
  • make ld matrix using plink --r2
  • fine-mapping tools: FINEMAP

Changed

Fixed

[0.1.1] - 2023-01-07

Added

  • add temp dir decorator
  • identify lead SNPs by LD clumping
  • identify lead SNPs by conditional analysis

Changed

Fixed

[0.0.5] - 2022-12-26

Added

  • validate GWAS summary statistics

Changed

Fixed

[0.0.4] - 2022-12-26

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  • prepare and validate LD reference panel

Changed

Fixed

[0.0.1] - 2022-12-20

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  • merge the overlapped independent loci (optional).

Changed

Fixed

[0.0.2] - 2022-12-22

Added

  • identify the independent lead snps by distance only
  • expand the independent lead snps to independent loci by given range.

Changed

Fixed

[0.0.3] - 2022-12-22

Added

  • extract LD ref plink bfile and clean it.

Changed

Fixed