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feat: finish running platelet_count pipeline on UKB #46

Merged
merged 69 commits into from
Dec 5, 2024
Merged

feat: finish running platelet_count pipeline on UKB #46

merged 69 commits into from
Dec 5, 2024

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aryarm
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@aryarm aryarm commented Sep 25, 2024

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aryarm added 30 commits June 11, 2024 14:43
@aryarm
bump maf down to make happler runtimes reasonable
0600885
@aryarm
adjust timing and memory of all rules for UKB based on linear regress…
887a349 
…ions
@aryarm
subset pheno files by samples in all happler steps
18f0982
@aryarm
add verbosity to happler workflow
a1f1541
@aryarm
try to fix problem with overlapping bars of table in allele heatmaps
32f98f4
@aryarm
support multiple haps in cond_linreg plots and add orange dots to ori…
dd0b7a1 
…ginal manhattans
@aryarm
recalibrate cond_linreg
7c7f7e4
@aryarm
handle even super strong pvals
7c8472d
@aryarm
add SuSiE L param as a parameter of our workflow
6bd0348
@aryarm
add new strategy of inverting the parent hap and testing it against t…
a4d75d5 
…he current one
@aryarm
try new independence test strategy
f689b29
@aryarm
use set instead of tuple for samples in transform
50f87b6
@aryarm
create script for midway manhattan plot
9f8b5a6
@aryarm
also allow for creating t-test midway manhattan plots
41a4f84
@aryarm
refmt with black
4b84ac8
@aryarm
try again to refmt with black
6331382
@aryarm
Merge branch 'feat/ukb' into feat/inverted-hap
1b5b37e
@aryarm
Merge pull request #45 from gymrek-lab/feat/inverted-hap
76ca938 
feat: regress out parent and child haps when checking whether to terminate
@aryarm
create script for midway manhattan summaries
773595a
@aryarm
allow for filtering displayed pvals in midway manhattan plots
a826509
@aryarm
display r-squared in explained_variance_plot
d8af216
@aryarm
delete finemappers.smk which was combined into happler.smk
d01d25c
@aryarm
fix issue where sample IDs would sometimes be strings rather than ints
36a5529
@aryarm
import sklearn only if needed when running midway manhattans
63ac111
@aryarm
fix MAF message in tree builder to mention allele as int not bool
fc10730
@aryarm
allow for transforming just a few variants
fe0d3ac
@aryarm
allow pipeline to run on geuvadis
1b0cc0a
@aryarm
create first iteration of forest builder
b420ee2
@aryarm
use new config file for simulations
c937bb6
@aryarm
use new --max-signals param in happler
0bcf1b2
aryarm added 28 commits October 22, 2024 17:43
@aryarm
allow for setting output threshold as a param in the config
4edfd01
@aryarm
clean up and update scripts README
8371c80
@aryarm
handle empty hap files in utils.R
1b5a9ed
@aryarm
allow for reordering rows of parameter_plot
c8e2eb5
@aryarm
allow for leniency when estimating pvals in happler
4f5b24b
@aryarm
make thresh more lenient
46fe5ca
@aryarm
split pheno for happler rules
1584890
@aryarm
set up workflow for running on geuvadis again
63bd60b
@aryarm
switch to geuvadis config
eeb4659
@aryarm
enable pickling as a parameter plot option
1dbe559
@aryarm
start to try to handle multiple haps in summarize_results.R
4383e3f
@aryarm
enable computing mean and stderr of finemapping metrics in parameter_…
23735cf 
…plot
@aryarm
adjust the amount of time for the multiline rule
b9a1c22
@aryarm
start on STR analysis
e1f01c3
@aryarm
revert to min for now. need to come up with a better way of doing thi…
321ced6 
…s eventually
@aryarm
allow for pickled output for explained_variances.png
f0b5b38
@aryarm
upgrade to newest susie
03f9eef
@aryarm
recalibrate timing and mem
32f1a32
@aryarm
collapse sim configs
f0164e0
@aryarm
switch to dev version of haptools
2ac2c27
@aryarm
ci: handle deprecations in gh actions and devcontainer
f6d5a93
@aryarm
update lock file for latest haptools
786db1d
@aryarm
update min python to 3.9 and add 3.13 ci test
592bf88
@aryarm
fix failing example tests with --out-thresh
b08162f
@aryarm
refmt with black
b291264
@aryarm
adapt workflow to simulate STRs
c4f1dcf
@aryarm
update lock file
e0dec77
@aryarm
Merge pull request #47 from gymrek-lab/feat/forests
3090781 
feat: iterative approach
@aryarm aryarm merged commit 2bad3c3 into main Dec 5, 2024
7 of 10 checks passed
@aryarm aryarm deleted the feat/ukb branch December 5, 2024 23:47
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@aryarm