Issues

• Missing/incomplete protocols

  StatFunGen/xqtl-protocol#1400 · Filter by author danielnachun opened on Aug 10, 2026
  1

• iQTL interaction factors center

  StatFunGen/xqtl-protocol#1276 · Filter by author gaow opened on Dec 4, 2025

• TWAS/cTWAS codes needs to support dropping event patterns

  StatFunGen/xqtl-protocol#1160 · Filter by author gaow opened on Mar 25, 2025

• rare events detection in impution pipeline

  StatFunGen/xqtl-protocol#1073 · Filter by author rfeng2023 opened on Sep 24, 2024

• bug in TensorQTL for sQTL analysis

  StatFunGen/xqtl-protocol#1072 · Filter by author rfeng2023 opened on Sep 24, 2024

• pipeline/extract_effects.ipynb file not found

  StatFunGen/xqtl-protocol#1024 · Filter by author neeteshpandey opened on Aug 2, 2024
  1

• error in association analysis

  StatFunGen/xqtl-protocol#985 · Filter by author rfeng2023 opened on Apr 27, 2024

• Gene annotation should also generate relevant files for --phenoIDFile

  StatFunGen/xqtl-protocol#942 · Filter by author gaow opened on Mar 26, 2024

• Some reference data download link nolonger work, pending investigation.

  StatFunGen/xqtl-protocol#758 · Filter by author hsun3163 opened on Dec 1, 2023
  3

• RNA_calling.ipynb rsem_call error when using BAM files from STAR with wasp filter

  StatFunGen/xqtl-protocol#696 · Filter by author grennfp opened on Oct 5, 2023
  1

• Error message - BAM file shares no contigs with GTF - Knight eQTL rnaseq call

  StatFunGen/xqtl-protocol#571 · Filter by author Chunmingl opened on Apr 20, 2023
  13

• * in snp is not allowed in MASH pipeline rds_to_vcf

  StatFunGen/xqtl-protocol#551 · Filter by author rfeng2023 opened on Mar 13, 2023
  6

• How to deal with NA column in MASH analysis

  StatFunGen/xqtl-protocol#550 · Filter by author rfeng2023 opened on Mar 13, 2023
  1

• Different result from available results

  StatFunGen/xqtl-protocol#546 · Filter by author rfeng2023 opened on Mar 10, 2023
  2

• Running gene_annotation.ipynb map_leafcutter_cluster_to_gene

  StatFunGen/xqtl-protocol#544 · Filter by author grennfp opened on Mar 6, 2023

• Bug in bulk_expression_QC.ipynb RLE candidate outlier output

  StatFunGen/xqtl-protocol#533 · Filter by author grennfp opened on Feb 17, 2023
  1

• Bug in TensorQTL - pandas & numpy conflict

  StatFunGen/xqtl-protocol#528 · Filter by author m-mews opened on Feb 15, 2023
  1

• Remaining problem in unisusie pipeline

  StatFunGen/xqtl-protocol#527 · Filter by author SamuelSun2000 opened on Feb 15, 2023
  5

• Different format of snp for Knight(WashU) genotype data

  StatFunGen/xqtl-protocol#525 · Filter by author zining-qi opened on Feb 14, 2023
  2

  

• Bug in extracting sample id from script aggregate_rsem_results.py

  StatFunGen/xqtl-protocol#524 · Filter by author mw201608 opened on Feb 8, 2023
  1

• Accommodation for region_list header that are not started with #chr

  StatFunGen/xqtl-protocol#509 · Filter by author hsun3163 opened on Jan 26, 2023

• Wishlist for susie finemapping piepline

  StatFunGen/xqtl-protocol#505 · Filter by author SamuelSun2000 opened on Jan 23, 2023

• Bug fix in RNA calling pipeline

  StatFunGen/xqtl-protocol#475 · Filter by author gouwh29 opened on Dec 6, 2022
  8

• Annotation source for visualization of result

  StatFunGen/xqtl-protocol#474 · Filter by author hsun3163 opened on Dec 5, 2022

• Adding a part to the pipeline to automatically generate the required objects in analysis_unit_list

  StatFunGen/xqtl-protocol#470 · Filter by author floutt opened on Nov 17, 2022