Ecosyste.ms: Issues

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GitHub / bulik/ldsc issues and pull requests

#472 - rg values not in the [-1,1] bound&NAN Values

Issue - State: open - Opened by AyselenKuru about 1 month ago - 2 comments

#471 - how to build my own input weight files for --w-ld-chr

Issue - State: open - Opened by FangrenLan97 about 1 month ago - 3 comments

#470 - LDSC on build38 data

Issue - State: open - Opened by mvab 2 months ago - 2 comments

#468 - Unexpected genetic correlation (rg) estimate

Issue - State: closed - Opened by dtomi0223 2 months ago

#466 - Index error/ list index out of range

Issue - State: open - Opened by ruimin-1212 3 months ago - 3 comments

#465 - LD Hub Website Inaccessibility

Issue - State: open - Opened by xikanfeng2 3 months ago

#464 - Heritability Estimation Error!!

Issue - State: open - Opened by Taylor19973 3 months ago

#461 - How to generate one own cts annotation file?

Issue - State: open - Opened by Crazzy-Rabbit 3 months ago

#459 - Update LDSC to python3

Pull Request - State: closed - Opened by thomas-reimonn 4 months ago

#458 - Genetic correlation > 1

Issue - State: open - Opened by HelenYSLin 4 months ago

#457 - Extension of S-LDSC

Issue - State: open - Opened by cybluetree 4 months ago

#456 - valid alleles QC

Issue - State: open - Opened by Sophia20230711 5 months ago - 1 comment

#455 - snpsvalid alleles

Issue - State: closed - Opened by Sophia20230711 5 months ago

#454 - Other species

Issue - State: open - Opened by xmliu01 5 months ago

#453 - Compute LD scores fails: no module named ldscore.ldscore

Issue - State: closed - Opened by ElizabethWallace97 6 months ago - 1 comment

#451 - How to obtain per-SNP heritability by LDSC?

Issue - State: closed - Opened by Jesson-mark 6 months ago - 4 comments

#450 - Cannot run tutorial

Issue - State: open - Opened by HelloWorldLTY 6 months ago - 2 comments

#449 - Fix installation error

Pull Request - State: open - Opened by HelloWorldLTY 6 months ago

#448 - How to update the partitioned LDscore?

Issue - State: closed - Opened by Jesson-mark 6 months ago - 2 comments

#447 - Questions Regarding S-LDSC Analysis with --ref-ld-chr-cts

Issue - State: open - Opened by YingkaiSun 6 months ago - 8 comments

#446 - munge_sumstats issue: Usecols do not match names

Issue - State: open - Opened by ElizabethWallace97 6 months ago - 1 comment

#445 - "Pip subprocess error" during installation of LDSC

Issue - State: closed - Opened by dhlee1013 7 months ago - 3 comments

#444 - Estimating bivariate LDSC intercept when h2 is low

Issue - State: open - Opened by tom-a-bond 7 months ago - 3 comments

#442 - Syntax Error

Issue - State: open - Opened by FrederickGri 7 months ago - 4 comments

#441 - Individual variant heritabilities?

Issue - State: closed - Opened by danieljrichard 7 months ago - 4 comments

#440 - make_annot.py does not run

Issue - State: closed - Opened by VitorAguiar 8 months ago - 2 comments

#439 - Filtering of munge_sumstats.py

Issue - State: open - Opened by yesyj-yuns 8 months ago - 5 comments

#438 - Prop._h2 is negative

Issue - State: open - Opened by dqq0404 8 months ago - 15 comments

#437 - Partition heritability for UKB data

Issue - State: open - Opened by reshu23 8 months ago

#436 - Filtration of partition heritability results

Issue - State: open - Opened by reshu23 8 months ago - 2 comments

#435 - Error parsing .annot file

Issue - State: open - Opened by reshu23 9 months ago - 7 comments

#434 - Lowest limit of rg p-value reported?

Issue - State: open - Opened by jodithea 9 months ago - 6 comments

#433 - African data analysis

Issue - State: open - Opened by xEmz 9 months ago - 1 comment

#431 - INTERCEPT FLAG

Issue - State: open - Opened by zara03 9 months ago - 1 comment

#430 - p values in version Version 1.0.1 are different from v 2.0.0

Issue - State: open - Opened by zara03 10 months ago - 3 comments

#428 - where can i find ENSG_coord.txt or similiar plain file in different build?

Issue - State: open - Opened by yc-long 11 months ago - 2 comments

#427 - Causes for Ratio < 0 other than GC?

Issue - State: closed - Opened by tgbrooks 11 months ago - 2 comments

#426 - MemoryError: When running LDSCORE analysis

Issue - State: open - Opened by chirrie 11 months ago - 4 comments

#424 - Missing frequency from GWAS

Issue - State: open - Opened by ariadnacilleros 11 months ago - 1 comment

#423 - ./ldsc.py -h Illegal instruction (core dumped)

Issue - State: open - Opened by xiaomu125 11 months ago - 1 comment

#421 - lsdc :IndexError: list index out of range

Issue - State: open - Opened by chirrie 12 months ago - 7 comments

#420 - munge_sumstats.py taking forever to complete analysis

Issue - State: open - Opened by chirrie 12 months ago - 5 comments

#419 - rg with sample overlap

Issue - State: open - Opened by Cui4399 12 months ago - 1 comment

#418 - ERROR: P<1e-300

Issue - State: open - Opened by jielab 12 months ago - 3 comments

#417 - Can't run ldsc under screen at Linux

Issue - State: open - Opened by eightYao2 12 months ago - 2 comments

#416 - how to get the filtered snps

Issue - State: open - Opened by yingyuan830 about 1 year ago

#415 - Sample size with repeated observations

Issue - State: open - Opened by ldehoyos about 1 year ago - 1 comment

#414 - Need LDSC file

Issue - State: open - Opened by zainab-cpu about 1 year ago - 1 comment

#412 - Cell type specific analyses

Issue - State: open - Opened by AEAEAESSC about 1 year ago - 2 comments

#411 - Partitioned genetic correlation

Issue - State: open - Opened by AEAEAESSC about 1 year ago - 3 comments

#410 - correlation value higher than 1

Issue - State: open - Opened by yildizkoca about 1 year ago - 1 comment

#409 - bucket seems to be unavailable

Issue - State: open - Opened by M-xiao815 about 1 year ago - 1 comment

#408 - Error running LD score regression

Issue - State: open - Opened by yildizkoca about 1 year ago

#407 - Suitable w_hm3.snplist for AFR?

Issue - State: open - Opened by beckse over 1 year ago - 6 comments

#406 - Add CM and MAF file to LD Score output .gz

Issue - State: open - Opened by lannandc over 1 year ago

#405 - 'Could not find a signed summary statistic column.')

Issue - State: open - Opened by yuupei over 1 year ago

#404 - ，

Issue - State: closed - Opened by yankvss over 1 year ago - 1 comment

#403 - 1kg_eur.tar.bz2 not found

Issue - State: open - Opened by kf-cuanschutz over 1 year ago - 5 comments

#401 - how to add annotation to the baseline model???

Issue - State: open - Opened by fanjiacheng-max over 1 year ago

#400 - TypeError: a bytes-like object is required, not 'str'

Issue - State: open - Opened by yijiesung over 1 year ago - 1 comment

#399 - Fix indentation

Pull Request - State: open - Opened by evlim over 1 year ago

#398 - Error with 'python mtag.py -h'

Issue - State: closed - Opened by isobel16 over 1 year ago

#397 - Error with 'python mtag.py -h'

Issue - State: closed - Opened by isobel16 over 1 year ago

#396 - --overlap-annot does not recognize path in --annot

Issue - State: open - Opened by nickorka over 1 year ago

#395 - tutorial request

Issue - State: open - Opened by astrid12345 over 1 year ago - 2 comments

#394 - s-LDSC continuous annotations

Issue - State: closed - Opened by aiim-lab over 1 year ago - 2 comments

#393 - Why is the number of SNPs in a cell type the same to the control's one?

Issue - State: open - Opened by ohmiyajohn2 over 1 year ago - 2 comments

#392 - IndexError: list index out of range

Issue - State: closed - Opened by aydanasg over 1 year ago - 1 comment

#391 - Update munge_sumstats.py

Pull Request - State: open - Opened by evlim over 1 year ago - 5 comments

#390 - How to test the null hypothesis of rg=1

Issue - State: open - Opened by Apprentice2 over 1 year ago

#389 - Error calculating heritability

Issue - State: open - Opened by DelnazRoshandel over 1 year ago - 1 comment

#388 - Question about partitioned LDSC

Issue - State: open - Opened by syuxuan over 1 year ago - 1 comment

#387 - merge-alleles: command not found

Issue - State: open - Opened by Hisewetty over 1 year ago

#386 - Where to obtain "hapmap3_snps.tgz"?

Issue - State: open - Opened by juditcd almost 2 years ago - 2 comments

#384 - How to obtain the file "w_hm3.snplist.bz2"

Issue - State: open - Opened by keypanqi almost 2 years ago - 7 comments

#383 - Could I set the number of chromosomes in LDSC?

Issue - State: open - Opened by Tengjun0520 almost 2 years ago - 2 comments

#382 - eas_ldscores.tar.bz2

Issue - State: closed - Opened by 1667857557 almost 2 years ago - 3 comments

#381 - Help in replicating heritability estimates

Issue - State: closed - Opened by littlehegemon almost 2 years ago - 1 comment

#380 - LDSC requires pandas version >= 0.17.0

Issue - State: open - Opened by pinliang168 almost 2 years ago

#379 - LDSC requires pandas version >= 0.17.0

Issue - State: open - Opened by pinliang168 almost 2 years ago

#378 - Unable to download from google bucket

Issue - State: open - Opened by mohammedmsk almost 2 years ago - 6 comments

#377 - Reference files - 1000G LD scores

Issue - State: open - Opened by alejocrojo09 almost 2 years ago - 2 comments

#376 - weights for non-European populations

Issue - State: open - Opened by meghatron21 almost 2 years ago - 4 comments

#375 - About A1 / A2 allele definition in wiki and `munge_sumstats.py`

Issue - State: open - Opened by liangyy almost 2 years ago - 6 comments

#374 - Why do I keep reporting an error: Could not find SNP column？

Issue - State: open - Opened by ZyRose1 almost 2 years ago - 25 comments

#373 - Presence of ldsc 2.0.1 on PyPI but not on GitHub

Issue - State: open - Opened by kirilledition almost 2 years ago - 1 comment