gaow/neuro-twas

Issues

• Document the path of the input files we used for our project

  #7 opened 4 years ago by gaow
  8

• Error at ED step with updated mashr packages.

  #42 opened 3 years ago by hsun3163
  7

• Missing data pattern is inconsistent between Bhat and Shat

  #41 opened 3 years ago by hsun3163
  2

• Issues in installing "mashr"

  #30 opened 4 years ago by hsun3163
  3

• Consideration on the optimization of TWAS analysis

  #40 opened 3 years ago by hsun3163
  0

• Try MR-JIT as a new method for multivariate tissue prediction

  #35 opened 4 years ago by gaow
  6

• Potential issues in mv-susie cross-validation

  #36 opened 4 years ago by hsun3163
  12

• Project aims and action plans

  #1 opened 4 years ago by gaow
  1

• Explain how summary stats works for TWAS

  #6 opened 4 years ago by gaow
  5

• parallel environments for the CSG cluster.

  #15 opened 4 years ago by hsun3163
  6

• SVA vs PEER model.

  #3 opened 4 years ago by hsun3163
  1

• Look into strand flip issues in summary data

  #8 opened 4 years ago by gaow
  2

• Alternate method for GWAS Z score imputation

  #21 opened 4 years ago by hsun3163
  4

• Question arise after univariate analysis

  #27 opened 4 years ago by hsun3163
  6

• Quality control protocol for TWAS

  #2 opened 4 years ago by gaow
  4

• Gene region extraction workflow

  #4 opened 4 years ago by gaow
  1

• Literature and methods for multivariate TWAS

  #9 opened 4 years ago by gaow
  4

• Part of the alzheimer paper gene are missing from the ROSMAP dataset.

  #20 opened 4 years ago by hsun3163
  5

• When calculating the TWAS Z score, shall heritability be taken into consideration.

  #22 opened 4 years ago by hsun3163
  0

• Question and summary: what is a good way to conduct TWAS for risk locus with low expression heritability via multi-tissue dataset ?

  #29 opened 4 years ago by hsun3163
  2

• Metric to show improvement of multivariate predictions

  #31 opened 4 years ago by hsun3163
  1

• Whole Genome SNP-heritability of gene expression

  #33 opened 4 years ago by hsun3163
  0

• Problem with the flash() function in the flash_no_constraint pipeline step.

  #34 opened 4 years ago by hsun3163
  9

• Problem resulting in large amount of NULL in mv_susie initial run

  #32 opened 4 years ago by hsun3163
  0

• Discrepancy in the result of the three tissue fusion run

  #24 opened 4 years ago by hsun3163
  0

• P value for the hsq computed by susie

  #26 opened 4 years ago by hsun3163
  1

• Lack of justification of using a sparse model for prediction and new structure of story.

  #28 opened 4 years ago by hsun3163
  1

• file not found error in Workflow

  #25 opened 4 years ago by hsun3163
  0

• New Issues in TWAS.FUSION

  #23 opened 4 years ago by hsun3163
  2

• New Issue in reading genotype file after the mount point changed.

  #19 opened 4 years ago by hsun3163
  2

• SNP not scaled issues.

  #18 opened 4 years ago by hsun3163
  4

• Issues in running the twas_fusion pipeline on cluster

  #16 opened 4 years ago by hsun3163
  7

• Issues in job naming of SOS submission

  #17 opened 4 years ago by hsun3163
  3

• Comments on first draft of pipeline implementation

  #12 opened 4 years ago by gaow
  1

• Using Singularity for SOS, docker daemon not running problem

  #14 opened 4 years ago by hsun3163
  1

• Documenting how to setup fusion

  #13 opened 4 years ago by hsun3163
  1

• Performance issues when running on laptop

  #11 opened 4 years ago by hsun3163
  2

• Heritability change with partitioned sample size.

  #10 opened 4 years ago by hsun3163
  1

• Reasons for genes that gets excluded from analysis

  #5 opened 4 years ago by gaow
  1