cumc/xqtl-protocol

Issues

• Bug in running univariate fine mapping

  #1026 opened 2 months ago by rfeng2023
  1

• pipeline/extract_effects.ipynb file not found

  #1024 opened 2 months ago by neeteshpandey
  1

• TensorQTL indices possible bug

  #998 opened 3 months ago by minqiao
  1

• error in association analysis

  #985 opened 5 months ago by rfeng2023
  0

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

  #942 opened 6 months ago by gaow
  0

• RNA_calling.ipynb rnaseqc_call stalls

  #791 opened 7 months ago by Travyse
  3

• TensorQTL - trans error

  #548 opened 7 months ago by m-mews
  1

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

  #696 opened a year ago by grennfp
  1

• methylation.sif container not working on BU cluster

  #582 opened 7 months ago by AlexandrePelletier
  1

• Issue using SuSiE to do metaQTLs fine mapping

  #596 opened 7 months ago by jackytao18
  0

• Python not found rna_quantification container

  #784 opened 9 months ago by Travyse
  4

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

  #758 opened 10 months ago by hsun3163
  3

• TensorQTL Cis not able to handle multiple cis windows in the regionlist covering the same position.

  #641 opened 10 months ago by hsun3163
  2

• Update on susie break the code

  #746 opened 10 months ago by hsun3163
  3

• Inconsistency between the example and workflow code

  #717 opened a year ago by mw201608
  1

• gtf files different positions

  #645 opened a year ago by SamuelSun2000
  2

• Error when running VCF_QC under new container

  #611 opened a year ago by zq2209
  5

• singularity environment conflict with the host

  #614 opened a year ago by gaow
  0

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

  #571 opened a year ago by Chunmingl
  13

• New error in vcfQC

  #576 opened a year ago by hsun3163
  3

• Bug sumstat_to_vcf

  #540 opened a year ago by m-mews
  4

• TensorQTL - cis results error

  #549 opened 2 years ago by m-mews
  1

• * in snp is not allowed in MASH pipeline `rds_to_vcf`

  #551 opened 2 years ago by rfeng2023
  6

• Different result from available results

  #546 opened 2 years ago by rfeng2023
  2

• How to deal with NA column in MASH analysis

  #550 opened 2 years ago by rfeng2023
  1

• [Expression] TypeError: '<=' not supported

  #543 opened 2 years ago by Chunmingl
  0

• Running gene_annotation.ipynb map_leafcutter_cluster_to_gene

  #544 opened 2 years ago by grennfp
  0

• Bug in bulk_expression_QC.ipynb RLE candidate outlier output

  #533 opened 2 years ago by grennfp
  1

• Remaining problem in unisusie pipeline

  #527 opened 2 years ago by SamuelSun2000
  5

• Bug in TensorQTL - pandas & numpy conflict

  #528 opened 2 years ago by m-mews
  1

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

  #525 opened 2 years ago by zq2209
  2

• Bug in extracting sample id from script aggregate_rsem_results.py

  #524 opened 2 years ago by mw201608
  1

• Wishlist for susie finemapping piepline

  #505 opened 2 years ago by SamuelSun2000
  0

• Unreasonably large RDS files

  #510 opened 2 years ago by hsun3163
  3

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

  #509 opened 2 years ago by hsun3163
  0

• Impracticality of saving the LD matrix with the SuSiERSS results.

  #506 opened 2 years ago by hsun3163
  1

• Sumstat standardizer fail to handle reverse strand

  #495 opened 2 years ago by hsun3163
  3

• allele flip in LD file.

  #493 opened 2 years ago by hsun3163
  7

• FileNotFoundError in susie_rss pipeline

  #502 opened 2 years ago by hsun3163
  1

• non-conformable arrays error from susie_rss via rpy2 but not via native r.

  #500 opened 2 years ago by hsun3163
  12

• Strange error occurs while loading the susieR from stephenlab.sif

  #499 opened 2 years ago by hsun3163
  1

• updates in rpy2 render the polyfun code unusable

  #496 opened 2 years ago by hsun3163
  3

• Large amount of snps discarded by sumstat standardizer for ADGWAS

  #490 opened 2 years ago by hsun3163
  1

• Bug fix in RNA calling pipeline

  #475 opened 2 years ago by gouwh29
  8

• Adding a parameter for "check_prior" with susie_rss

  #469 opened 2 years ago by floutt
  2

• Annotation source for visualization of result

  #474 opened 2 years ago by hsun3163
  0

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

  #470 opened 2 years ago by floutt
  0

• another sumstat error with sqtl nominal data: Boolean index has wrong length

  #465 opened 2 years ago by hsun3163
  3

• susie by tad give snps that are not in tad region.

  #466 opened 2 years ago by hsun3163
  3

• Issue on Projection of related individuals phase

  #464 opened 2 years ago by frarosamilia
  3