bulik/ldsc issues and pull requests

#456 - valid alleles QC

Issue - State: open - Opened by Sophia20230711 17 days ago - 1 comment

#455 - snpsvalid alleles

Issue - State: closed - Opened by Sophia20230711 17 days ago

#454 - Other species

Issue - State: open - Opened by xmliu01 22 days ago

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

Issue - State: closed - Opened by ElizabethWallace97 about 1 month ago - 1 comment

#452 - Is enrichment same when using LD scores with different combination of categories?

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

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

Issue - State: closed - Opened by Jesson-mark about 1 month ago - 4 comments

#450 - Cannot run tutorial

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

#449 - Fix installation error

Pull Request - State: open - Opened by HelloWorldLTY about 2 months ago

#448 - How to update the partitioned LDscore?

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

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

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

#446 - munge_sumstats issue: Usecols do not match names

Issue - State: open - Opened by ElizabethWallace97 about 2 months ago - 1 comment

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

Issue - State: closed - Opened by dhlee1013 2 months ago - 3 comments

#444 - Estimating bivariate LDSC intercept when h2 is low

Issue - State: open - Opened by tom-a-bond 2 months ago - 3 comments

#443 - Error # terms in --M must match # of LD Scores in --ref-ld

Issue - State: open - Opened by soumodip15 2 months ago

#442 - Syntax Error

Issue - State: open - Opened by FrederickGri 3 months ago - 4 comments

#441 - Individual variant heritabilities?

Issue - State: closed - Opened by danieljrichard 3 months ago - 4 comments

#440 - make_annot.py does not run

Issue - State: closed - Opened by VitorAguiar 3 months ago - 2 comments

#439 - Filtering of munge_sumstats.py

Issue - State: open - Opened by yesyj-yuns 3 months ago - 5 comments

#438 - Prop._h2 is negative

Issue - State: open - Opened by dqq0404 3 months ago - 15 comments

#437 - Partition heritability for UKB data

Issue - State: open - Opened by reshu23 4 months ago

#436 - Filtration of partition heritability results

Issue - State: open - Opened by reshu23 4 months ago - 2 comments

#435 - Error parsing .annot file

Issue - State: open - Opened by reshu23 4 months ago - 7 comments

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

Issue - State: open - Opened by jodithea 4 months ago - 6 comments

#433 - African data analysis

Issue - State: open - Opened by xEmz 4 months ago - 1 comment

#432 - Is python 2.7 no longer available to download using code in ldsc tutorial?

Issue - State: open - Opened by laleoarrow 5 months ago - 4 comments

#431 - INTERCEPT FLAG

Issue - State: open - Opened by zara03 5 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 5 months ago - 3 comments

#429 - https://data.broadinstitute.org/alkesgroup/LDSCORE/eur_w_ld_chr.tar.bz2 download problem?

Issue - State: open - Opened by zara03 6 months ago - 4 comments

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

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

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

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

#426 - MemoryError: When running LDSCORE analysis

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

#425 - Is it necessary to use the --merge-alleles parameter when doing genetic correlation in ldsc?

Issue - State: open - Opened by dqq0404 7 months ago - 13 comments

#424 - Missing frequency from GWAS

Issue - State: open - Opened by ariadnacilleros 7 months ago - 1 comment

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

Issue - State: open - Opened by xiaomu125 7 months ago - 1 comment

#422 - NotImplementedError: iLocation based boolean indexing on an integer type is not available

Issue - State: open - Opened by XochitlDiaz 7 months ago

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

Issue - State: open - Opened by chirrie 7 months ago - 6 comments

#420 - munge_sumstats.py taking forever to complete analysis

Issue - State: open - Opened by chirrie 7 months ago - 5 comments

#419 - rg with sample overlap

Issue - State: open - Opened by Cui4399 7 months ago - 1 comment

#418 - ERROR: P<1e-300

Issue - State: open - Opened by jielab 7 months ago - 3 comments

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

Issue - State: open - Opened by eightYao2 7 months ago - 2 comments

#416 - how to get the filtered snps

Issue - State: open - Opened by yingyuan830 8 months ago

#415 - Sample size with repeated observations

Issue - State: open - Opened by ldehoyos 8 months ago - 1 comment

#414 - Need LDSC file

Issue - State: open - Opened by zainab-cpu 8 months ago - 1 comment

#413 - How to draw the visialization of the LDSC regression plot like its NG paper?

Issue - State: open - Opened by laleoarrow 9 months ago - 3 comments

#411 - Partitioned genetic correlation

Issue - State: open - Opened by AEAEAESSC 10 months ago - 1 comment

#410 - correlation value higher than 1

Issue - State: open - Opened by yildizkoca 10 months ago - 1 comment

#409 - bucket seems to be unavailable

Issue - State: open - Opened by M-xiao815 10 months ago - 1 comment

#408 - Error running LD score regression

Issue - State: open - Opened by yildizkoca 11 months ago

#407 - Suitable w_hm3.snplist for AFR?

Issue - State: open - Opened by beckse 12 months ago - 6 comments

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

Issue - State: open - Opened by lannandc 12 months ago

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

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

#404 - ，

Issue - State: closed - Opened by yankvss about 1 year ago

#403 - 1kg_eur.tar.bz2 not found

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

#402 - Could anyone send me the "eas_ldscores.tar.bz2"? I wanted to calculate the ldsc of Asia, but I found I didn't have such file. And I can't download it from cloud. If anyone can send me it, my e-mail is [email protected]. Thank you so much.

Issue - State: open - Opened by MikeKiki101 about 1 year ago - 2 comments

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

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

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

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

#399 - Fix indentation

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

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

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

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

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

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

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

#395 - tutorial request

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

#394 - s-LDSC continuous annotations

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

#385 - Error: Missing some LD scores from cts files. Are you sure all SNPs in ref-ld-chr are also in ref-ld-chr-cts

Issue - State: open - Opened by danyfersa over 1 year ago - 4 comments

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

Issue - State: open - Opened by keypanqi over 1 year ago - 7 comments

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

Issue - State: open - Opened by Tengjun0520 over 1 year ago

#382 - eas_ldscores.tar.bz2

Issue - State: closed - Opened by 1667857557 over 1 year ago - 3 comments

#381 - Help in replicating heritability estimates

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

#380 - LDSC requires pandas version >= 0.17.0

Issue - State: open - Opened by pinliang168 over 1 year ago

#379 - LDSC requires pandas version >= 0.17.0

Issue - State: open - Opened by pinliang168 over 1 year ago

#378 - Unable to download from google bucket

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

#377 - Reference files - 1000G LD scores

Issue - State: open - Opened by alejocrojo09 over 1 year ago - 2 comments

#376 - weights for non-European populations

Issue - State: open - Opened by meghanasp21 over 1 year ago

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

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

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

Issue - State: open - Opened by ZyRose1 over 1 year ago - 12 comments

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

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

#372 - No module named bz2

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

#371 - link to reference files does not work

Issue - State: open - Opened by sn-GT over 1 year ago - 11 comments

#370 - questions about pre-computed ldscore

Issue - State: open - Opened by WZo0o over 1 year ago - 6 comments

#369 - Getting module parse has no attibute error

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

#368 - Fix a bug when parsing annotations

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

#367 - parse.py error?

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

#366 - IndexError: list index out of range

Issue - State: open - Opened by cwnag-c almost 2 years ago - 11 comments

#365 - Unalignable boolean Series provided as indexer (index of the boolean Series and of the indexed object do not match).

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

#364 - how to make my own baseline model?

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

#363 - Sample overlap

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

#362 - h2 estimate and intercept

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

#361 - make_annot.py_error "AttributeError: 'float' object has no attribute 'isdigit'"

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

#360 - Port ldsc to Python 3

Pull Request - State: open - Opened by pettyalex almost 2 years ago - 2 comments

#359 - LDSC is not available for Python 3

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

GitHub / bulik/ldsc issues and pull requests