Issues

• --max-missing does not exclude variants with >5% missing genotypes in VCF

  mgalardini/pyseer#310 · Filter by author cywanggis opened on Sep 6, 2026

• Add multi-thread option for BWA utils

  mgalardini/pyseer#308 · Filter by author hgrandjean opened on Sep 2, 2026
  2

• "Lineage file and similarity matrix contain different sets of samples" error is misleading if phenotype and similarity matrices have different sets of samples

  mgalardini/pyseer#307 · Filter by author arinwongprommoon opened on Aug 27, 2026
  1

• Making kinship matrix for viral GWAS

  mgalardini/pyseer#303 · Filter by author Rohit-Satyam opened on Jun 15, 2026

• IndexError when running Elastic Net model in prediction tutorial

  mgalardini/pyseer#290 · Filter by author 1nessh opened on May 1, 2025

• ValueError: endog must be in the unit interval.

  mgalardini/pyseer#280 · Filter by author ktmeaton opened on Oct 22, 2024
  3

• manhattan plot

  mgalardini/pyseer#273 · Filter by author xqzangnolan opened on Jul 19, 2024
  1

• SNP and COG association with fixed effects model

  mgalardini/pyseer#271 · Filter by author OtakuZerg opened on Jul 12, 2024
  4

• k-mer annotation

  enhancementhelp wanted
  mgalardini/pyseer#270 · Filter by author beryl-au opened on Jul 12, 2024
  6

  

• K-mer association with mixed effects model

  mgalardini/pyseer#265 · Filter by author komaltilwani53 opened on May 1, 2024
  6

• Number of significant genes different with several runs of Pyseer

  bug
  mgalardini/pyseer#264 · Filter by author Samriddhi0906 opened on Feb 29, 2024
  6

  

• rsync webhook for docs

  mgalardini/pyseer#258 · Filter by author johnlees opened on Nov 21, 2023

• Improve error messages when wrong format is used

  improvements
  mgalardini/pyseer#216 · Filter by author mgalardini opened on Aug 2, 2022
  

• Mapping hits using a pangenome

  improvementsscripts
  mgalardini/pyseer#183 · Filter by author LeonardosMageiros opened on Nov 22, 2021
  4

  

• Lineage-associated mutations

  bug
  mgalardini/pyseer#180 · Filter by author sydelstan opened on Nov 9, 2021
  10

• SNP vs K-mer

  mgalardini/pyseer#174 · Filter by author neginmb opened on Oct 19, 2021
  1

• Gene description in the significant hits summary

  improvementsscripts
  mgalardini/pyseer#172 · Filter by author LeonardosMageiros opened on Sep 27, 2021
  

• Enet/lasso fails with "ValueError: negative dimensions are not allowed"

  bugimprovementsinterface
  mgalardini/pyseer#165 · Filter by author mgalardini opened on Jul 21, 2021
  2

  

• missing data is ignored with variant files but not .Rtab

  improvements
  mgalardini/pyseer#157 · Filter by author julibeg opened on Jun 3, 2021
  4

  

• Interpretation of the results of Wald test for association between lineages and phenotype

  question
  mgalardini/pyseer#156 · Filter by author neginmb opened on May 26, 2021
  3

• ValueError when input has variants that don't occur in a single sample

  improvements
  mgalardini/pyseer#153 · Filter by author julibeg opened on May 24, 2021
  2

• Do you apply any transformation for the continuous trait in case it does not follow a normal distribution?

  question
  mgalardini/pyseer#136 · Filter by author neginmb opened on Jan 29, 2021
  9

• RuntimeWarning: line buffering (buffering=1) isn't supported in binary mode .....

  scriptswarning
  mgalardini/pyseer#118 · Filter by author EricDeveaud opened on Apr 8, 2020
  2

  

• Problem when running LMM tutorial

  docsquestion
  mgalardini/pyseer#109 · Filter by author flashton2003 opened on Jan 23, 2020
  12

  

• Logistic mixed models?

  improvements
  mgalardini/pyseer#79 · Filter by author cizydorczyk opened on Jun 12, 2019
  3