Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / Cloufield/gwaslab issues and pull requests

#136 - Question regarding .get_lead()

Issue - State: open - Opened by MC4R 15 days ago - 1 comment

#135 - Add a variable changing the variant name for LD

Pull Request - State: closed - Opened by TakeuchiYohei 19 days ago

#134 - Downstream tutorials missing

Issue - State: open - Opened by igumnov-daniel 20 days ago - 1 comment
Labels: documentation

#133 - to_formats problem when no CHR column

Issue - State: open - Opened by fcliquet 20 days ago - 1 comment
Labels: bug

#132 - error at annotation

Issue - State: open - Opened by liukeweiaway 20 days ago - 1 comment

#131 - Miami plot issues

Issue - State: closed - Opened by MC4R about 1 month ago - 1 comment

#130 - Annotation using the sig_level_lead in Miami plot

Issue - State: open - Opened by bsb2014 about 1 month ago - 1 comment

#129 - Writing / reading parquet functionality request

Issue - State: closed - Opened by igumnov-daniel about 1 month ago - 2 comments
Labels: enhancement

#128 - Performance Optimization for pandas

Issue - State: open - Opened by 1511878618 about 1 month ago - 1 comment
Labels: enhancement

#127 - LDSC h2 bug

Issue - State: closed - Opened by igumnov-daniel about 2 months ago - 5 comments
Labels: bug

#126 - How to filter multiallelic snps

Issue - State: closed - Opened by 1511878618 about 2 months ago - 2 comments

#125 - Questions re assigning rsID and liftover

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

#124 - Regional plot

Issue - State: closed - Opened by MC4R about 2 months ago - 2 comments

#123 - assign_rsid

Issue - State: closed - Opened by MC4R about 2 months ago - 4 comments

#122 - Miami plot

Issue - State: closed - Opened by bsb2014 about 2 months ago - 4 comments
Labels: bug

#121 - How to set regional plot option: region_chromatin_files

Issue - State: open - Opened by jacklin9703 2 months ago - 9 comments
Labels: bug

#120 - Feedback on LocusZoom Plot Enhancements

Issue - State: open - Opened by Sandyyy123 2 months ago - 7 comments
Labels: enhancement

#119 - Unable to save stratified qq plot

Issue - State: closed - Opened by Sandyyy123 2 months ago - 8 comments

#118 - add fix ID before assign rsID

Pull Request - State: closed - Opened by joshchiou 3 months ago - 1 comment

#116 - Question about the QQ-plot

Issue - State: open - Opened by Youpu-Chen 3 months ago - 1 comment

#115 - gl.Sumstats.estimate_h2_by_ldsc and other LDSC functions can't use rsID columns

Issue - State: closed - Opened by igumnov-daniel 3 months ago - 1 comment
Labels: bug

#114 - unmatched p-value in data and regional plot

Issue - State: open - Opened by ryshi06 3 months ago - 4 comments

#113 - how to increase variant size for regional plot

Issue - State: closed - Opened by ryshi06 4 months ago - 4 comments

#112 - Unable to create effect size comparison plot without heterogeneity

Issue - State: open - Opened by Sandyyy123 4 months ago - 6 comments
Labels: bug, enhancement

#111 - Outdated urls?

Issue - State: closed - Opened by Sandyyy123 4 months ago - 1 comment

#110 - Miami plot Two GWAS incorrect aligned

Issue - State: open - Opened by XiaoyangDai1 4 months ago - 5 comments

#109 - liftover returning an empty dataframe

Issue - State: closed - Opened by apalmos 4 months ago - 2 comments

#108 - Lead SNP not found in reference

Issue - State: closed - Opened by chenyangjjj 5 months ago - 3 comments

#107 - Incorrect SSF file extension

Issue - State: open - Opened by yassineS 5 months ago - 1 comment
Labels: bug

#106 - Manhattan plot issue

Issue - State: closed - Opened by MC4R 6 months ago - 10 comments
Labels: bug

#105 - adjust y axis to be equal in miami plot

Issue - State: closed - Opened by lvilarribo9 6 months ago - 2 comments

#104 - liftover weird behaviour

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

#103 - get_lead 'boolean value of NA' issue localising to util_in_get_sig.py

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

#102 - Making merge of figures

Issue - State: open - Opened by migueep450 7 months ago - 1 comment

#101 - Abf

Pull Request - State: closed - Opened by TakeuchiYohei 7 months ago

#100 - Liftover returning only column headings

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

#99 - Inquiry on QC and GWAS Pipeline

Issue - State: open - Opened by buer19970329 8 months ago - 6 comments

#97 - mysumstats.to_finemapping not working

Issue - State: closed - Opened by halkelchen 8 months ago - 5 comments

#96 - Effect Allele select in 2SMR

Issue - State: closed - Opened by chide-org 9 months ago - 4 comments

#95 - Question about gwas

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

#94 - filter_value filters all data

Issue - State: closed - Opened by lbwfff 9 months ago - 2 comments

#93 - Installation error

Issue - State: closed - Opened by bsb2014 9 months ago - 10 comments
Labels: Installation

#92 - vcf_path in regional plot

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

#91 - Improve fix for when POS is not on ref_seq

Pull Request - State: closed - Opened by sup3rgiu 10 months ago - 1 comment

#90 - Issue on QQ plot visualization alone

Issue - State: closed - Opened by Youpu-Chen 10 months ago - 2 comments

#89 - out of memory error in basic_check()

Issue - State: open - Opened by evakoe 10 months ago - 4 comments
Labels: enhancement

#88 - Index out of bounds error in check_ref()

Issue - State: open - Opened by evakoe 10 months ago - 7 comments
Labels: bug

#87 - ImportError upon installation

Issue - State: closed - Opened by zhaiting 11 months ago - 8 comments

#86 - Add cache to speedup strand inference

Pull Request - State: closed - Opened by sup3rgiu 11 months ago - 5 comments

#85 - Fix missing logs, rename **args to **kwargs, fix typo

Pull Request - State: closed - Opened by sup3rgiu 11 months ago - 1 comment

#84 - error when setting anno="GENENAME"

Issue - State: open - Opened by Sheeya-Dong 11 months ago - 5 comments

#83 - Regional plots with LD

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

#82 - installation

Issue - State: open - Opened by YijiaWu1 11 months ago - 3 comments

#81 - Fast implementation to write VCF and CSV

Pull Request - State: closed - Opened by sup3rgiu 11 months ago - 1 comment

#80 - Vectorize checkref

Pull Request - State: closed - Opened by sup3rgiu 11 months ago - 4 comments

#79 - Highlighting significant loci in the trumpet plot?

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

#78 - scikit-allel build issues

Issue - State: closed - Opened by jonathangriffiths about 1 year ago - 2 comments

#77 - python version dependencies

Issue - State: closed - Opened by chenyangjjj about 1 year ago - 1 comment

#76 - Regional plot: unable to plot variants correctly.

Issue - State: closed - Opened by sakuramodokich about 1 year ago - 8 comments

#75 - rsID Annotation for need to be fixed

Issue - State: closed - Opened by chenyangjjj about 1 year ago - 2 comments

#73 - Filtering based on lookupstatus() and check_af()

Issue - State: open - Opened by swvanderlaan about 1 year ago - 4 comments

#72 - Naming convention mismatches fixed

Pull Request - State: closed - Opened by soumickmj about 1 year ago - 2 comments

#71 - Highlighting significant loci

Issue - State: open - Opened by soumickmj about 1 year ago - 2 comments
Labels: enhancement

#70 - arguments from manhattan don't exist in miami function

Issue - State: closed - Opened by igumnov-daniel about 1 year ago - 4 comments
Labels: enhancement

#69 - Bad statistics

Issue - State: closed - Opened by biomguler about 1 year ago - 7 comments
Labels: bug

#68 - installation issue with 3.4.30 version

Issue - State: open - Opened by chenyangjjj about 1 year ago - 4 comments
Labels: bug

#67 - plot_mqq() snpid problem

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

#66 - Typos

Pull Request - State: closed - Opened by gmauro over 1 year ago

#65 - seed error

Issue - State: open - Opened by swvanderlaan over 1 year ago - 1 comment
Labels: bug

#63 - rsid_to_chrpos failed

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

#62 - error while using rsid_to_chrpos

Issue - State: open - Opened by soumickmj over 1 year ago - 2 comments
Labels: bug

#61 - Lifting error

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

#60 - Error importing table to gl-format

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

#59 - miami image really huge

Issue - State: closed - Opened by swvanderlaan over 1 year ago - 3 comments
Labels: bug

#58 - effect size comparison

Issue - State: closed - Opened by swvanderlaan over 1 year ago - 2 comments
Labels: bug

#57 - Installation problem

Issue - State: closed - Opened by bsb2014 over 1 year ago - 2 comments

#56 - add extra parameters for pysam.tabix_index()

Pull Request - State: closed - Opened by gmauro over 1 year ago

#55 - VCF export

Issue - State: open - Opened by gmauro over 1 year ago - 2 comments
Labels: bug

#54 - issue about mqqplot anno="GENENAME"

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

#53 - inferring MAF from rsid for specific population

Issue - State: closed - Opened by chenyangjjj over 1 year ago - 2 comments
Labels: enhancement

#52 - Resolving Pysam Errors During GWASLab Installation

Issue - State: open - Opened by lphotoimpact over 1 year ago - 1 comment
Labels: Installation

#51 - Assigning rsID error

Issue - State: open - Opened by lphotoimpact over 1 year ago - 2 comments
Labels: enhancement

#50 - Different highlight lists and colors

Issue - State: closed - Opened by swvanderlaan over 1 year ago - 3 comments
Labels: enhancement

#49 - Error with .plot_daf() function

Issue - State: closed - Opened by swvanderlaan over 1 year ago - 3 comments
Labels: bug

#48 - More ancestries as download option?

Issue - State: closed - Opened by swvanderlaan over 1 year ago - 6 comments
Labels: enhancement

#47 - Could not retrieve index file

Issue - State: closed - Opened by chenyangjjj over 1 year ago - 14 comments
Labels: bug

#46 - coordinate conversion and infer rsid

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

#45 - Regional plot gene name issue

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

#44 - recombination data for hg38 is in the wrong format

Issue - State: closed - Opened by edg1983 over 1 year ago - 2 comments

#43 - gl.plot_miami : "local variable 'to_annotate5' referenced before assignment"

Issue - State: closed - Opened by chenyangjjj over 1 year ago - 8 comments
Labels: bug

#42 - Manhattan plotting issue

Issue - State: closed - Opened by swvanderlaan over 1 year ago - 5 comments
Labels: bug

#41 - Typo in `basic_check()`-log

Issue - State: closed - Opened by swvanderlaan over 1 year ago - 1 comment
Labels: documentation

#40 - Brisbane plotting error regarding 'SNPID'

Issue - State: closed - Opened by swvanderlaan over 1 year ago - 2 comments
Labels: bug

#39 - regional plot

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

#38 - Output exceeds the [size limit]

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

#37 - regional plot

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