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Commits on Jul 30, 2025

• convert all sample id to strings

  zixuanzhang

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  e297340

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Commits on Jul 25, 2025

• update sim_sc and sim_bulk file

  zixuanzhang

  committed
  7943e6b

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Commits on Jul 24, 2025

• run cis in simulated null genes

  zixuanzhang

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  0cddd52

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Commits on Jul 23, 2025

• clean up _ACAT; fix PCA solver to be SVD full; fix bug in tutorial code

  zixuanzhang

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  60d2b6e

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Commits on Jul 22, 2025

• fix _ACAT bug of jax.array selector

  zixuanzhang

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  0998954

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Commits on Jul 18, 2025

• merge main into dev

  zixuanzhang

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  c126cbc

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• fix bug of fitting PCA twice

  zixuanzhang

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  65a2afa

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Commits on Jul 17, 2025

• change y from integer to float64

  zixuanzhang

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  fe97565

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Commits on Jul 2, 2025

• fix donor feature file name in tutorial code

  zixuanzhang

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  036938c

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• add data for benchmark

  zixuanzhang

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  b8142ea

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Commits on Jun 20, 2025

• debug x64 config for tpu

  zixuanzhang

  committed
  494e299

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• TPU doesn't support x64, so fall back to f32 if choosing --platform tpu

  zixuanzhang

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  07aa153

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• set platform before update x64

  zixuanzhang

  committed
  578b732

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Commits on Jun 19, 2025

• clear caches for every 50 genes to work around OOM for now

  zixuanzhang

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  19c6c3a

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• change back to previous cis cutter

  zixuanzhang

  committed
  941f030

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• remove chr prefix when cutting cis window, allow pheno to have chr prefix for automosomal only filter

  zixuanzhang

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  f010abf

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Commits on Jun 15, 2025

• add suffix to phenotype bulk out file

  zixuanzhang

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  f5b42e9

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Commits on May 14, 2025

• remove clear caches in nominal scan

  zixuanzhang

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  e6d0065

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Commits on May 10, 2025

• write ld matrix one at a time

  zixuanzhang

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  f1702df

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Commits on Apr 25, 2025

• change README title names

  zixuanzhang

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• delete jupyter notebook

  zixuanzhang

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  fe46169

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Commits on Apr 23, 2025

• update README

  zixuanzhang

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  12b7da9

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• edit README

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  53db2dc

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Commits on Apr 19, 2025

• use projecting method for linear model

  zixuanzhang

  committed
  c1b2839

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Commits on Apr 18, 2025

• set converged to True

  zixuanzhang

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  8449a38

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Commits on Apr 17, 2025

• add fast scan for lm model using wald test

  zixuanzhang

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  a8e2d6d

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Commits on Mar 30, 2025

• del object to save memory

  zixuanzhang

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  2471817

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• add raw ld at request

  zixuanzhang

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  64f6dac

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• write LD calculated using glm wt matrix, no glm weight and raw ld

  zixuanzhang

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  4072548

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Commits on Mar 28, 2025

• add snp position to cis output

  zixuanzhang

  committed
  68fde3a

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• write test result; put minus 1 back to df_cost

  zixuanzhang

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  a2e33b4

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• add test file for lm wald; clean chr in gene_info

  zixuanzhang

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Commits on Mar 26, 2025

• change celltype_path to None

  zixuanzhang

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  7a08ac3

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• make write_bed more flexible

  zixuanzhang

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  a7c6a52

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• extract cell type in write_bed

  zixuanzhang

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  2d701a2

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