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omerwe
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polyfun
PolyFun (POLYgenic FUNctionally-informed fine-mapping)
MIT License
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suspected problem in create_finemapper_jobs.py - regions with a single snp are dropped
#207
nettam
closed
2 weeks ago
2
PolyFun approach 3: Stage3 Compute LD-scores for each SNP bin
#206
liangcheng-hrbmu
closed
3 weeks ago
1
Modifying precomputed UKB LD matrix for trans-ancestry fine-mapping
#205
zhangchuyi
closed
1 month ago
2
Feature request: LD matrix as an R object
#204
cdiazmun
closed
1 month ago
1
Fix `assert df_snp.shape[0]==1` error in compute_ld_bgen
#203
mkanai
closed
3 months ago
1
All LD Scores have zero variance
#202
gdgdandsz
closed
1 month ago
2
Limited annotation
#201
gdgdandsz
closed
4 months ago
1
Error in aggregate_finemapper_results.py - output file for chromosome 1 bp 1-3000001 doesn't exist
#200
aydanasg
closed
4 months ago
0
functional annotations in hg38 version
#199
cybluetree
closed
1 month ago
9
Guidance on generating per-SNP heritabilities with custom annotations
#198
Al-Murphy
closed
4 months ago
6
Some doubts about the standard error of calculating R-square using the jackknife method
#197
Y-Isaac
closed
5 months ago
5
negative weights appear in the. mixweights file without arg --allow-neg-mixweights
#196
Y-Isaac
closed
5 months ago
2
The linear combination of ploypred with ployfun and bolt-lmm results in poorer prediction performance compared to using bolt-lmm alone
#195
Y-Isaac
closed
5 months ago
19
Issues on the number of chromosomes in different species (2)
#194
heebokp
closed
1 month ago
6
How to divide individual ancestry background based on UKB datafield 21000？
#193
Y-Isaac
closed
6 months ago
5
how to use sumstats from other methods(except bolt-lmm refered in WIKI) in PolyPred?
#192
Y-Isaac
closed
7 months ago
4
Issue with polyfun.py and memory allocation
#191
mkoromina
closed
7 months ago
2
a question about Polypred+
#190
Y-Isaac
closed
8 months ago
7
Issues on the number of chromosomes in different species
#189
heebokp
closed
1 month ago
2
Some changes on `finemapper.py` with data parsing, and if unnecessary, i'll only submit the code with bug fix for bgen file
#188
1511878618
opened
8 months ago
0
Bgen input with an error caused by an incorrect variable invocation.
#187
1511878618
opened
8 months ago
2
Scaled prior variance should be no greater than 1 when standardize = TRUE
#186
Y-Isaac
closed
8 months ago
4
The warning: IBSS algorithm did not converge in 100 iterations!
#185
Y-Isaac
closed
8 months ago
2
AttributeError: module 'networkx' has no attribute 'from_numpy_matrix' when I use arg --hess
#184
Y-Isaac
closed
8 months ago
4
Remove arg `normalize` from `Lasso()` (no longer exists)
#183
jdblischak
closed
8 months ago
1
TypeError: __init__() got an unexpected keyword argument 'normalize'
#182
Y-Isaac
closed
8 months ago
6
Missing SNPs in merging summary statistics with reference panel
#181
Y-Isaac
closed
9 months ago
1
Some problems in Computing LD-scores using existing functional annotation files
#180
Y-Isaac
closed
8 months ago
8
Some question about "best-practice recommendations" in article
#179
Y-Isaac
closed
9 months ago
7
Missing LD files
#178
kkupkova
closed
11 months ago
1
Locus has no credible set
#177
AI-10
closed
11 months ago
1
LD matrix genome assembly
#176
kkupkova
closed
11 months ago
1
susie_suff_stat no longer accept bhat input
#175
lruizcalico
closed
1 year ago
2
Flag --n of finemapper.py confused `conda run -n polyfun`
#174
lruizcalico
closed
1 year ago
4
Test_polyfun.py failed: extract_snpvar command failed
#173
noeri-mohamed-hoesein
closed
1 year ago
2
per-SNP heritability?
#172
humanpaingeneticslab
closed
1 year ago
3
Can extract_snpvar.py accept sumstats in hg38 coordinates instead of hg19?
#171
qiyanghong2020
closed
1 year ago
2
There appear to be 1 leaked semaphore objects to clean up at shutdown warnings.warn('resource_tracker: There appear to be %d '
#170
gustavahlberg
closed
1 year ago
3
LD matrix snps
#169
gbloeb
closed
1 year ago
1
Help with PolyPred-S
#168
jumentib
closed
1 year ago
3
susie_rss has replaced susie_suff_stat? finemapper.py calling error
#167
devibole
closed
1 year ago
5
Migrate to mamba-org/setup-micromamba@v1
#166
jdblischak
closed
1 year ago
0
PolyPred not recognizing my bed file
#165
bcoombes
closed
1 year ago
1
PolyLoc bfile suggestion?
#164
teresa-sansan
closed
1 year ago
4
'nan' in LD matrix (.bcor)/
#163
chunt28
closed
1 year ago
2
Memory Issues with polyfun.py
#162
BideZ
closed
1 year ago
2
per-SNP sample size N
#161
piganoemi
closed
1 year ago
4
All PIPs were zero
#160
poppy-yingying
closed
1 year ago
1
UKBB Annotation files missing A1, A2 columns
#159
taboltz
closed
1 year ago
3
Exact path to UKBB LD files on new google cloud space
#158
johnacurtin
closed
1 year ago
6
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