gaow neuro-twas issues - Githubissues

gaow / neuro-twas

Development code (private repo) for TWAS related multiomic gene-mapping in Alzheimer's disease data

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Error at ED step with updated mashr packages.

#42 hsun3163 closed 3 years ago
7
Missing data pattern is inconsistent between Bhat and Shat

#41 hsun3163 closed 3 years ago
2
Consideration on the optimization of TWAS analysis

#40 hsun3163 opened 3 years ago
0
add parameters notes for mv_susie output

#39 nickluo1313 closed 8 months ago
2
Redo upload original script and function script

#38 nickluo1313 closed 3 years ago
0
add original JTI.r

#37 nickluo1313 closed 3 years ago
4
Potential issues in mv-susie cross-validation

#36 hsun3163 closed 3 years ago
12
Try MR-JIT as a new method for multivariate tissue prediction

#35 gaow opened 3 years ago
6
Problem with the flash() function in the flash_no_constraint pipeline step.

#34 hsun3163 closed 3 years ago
9
Whole Genome SNP-heritability of gene expression

#33 hsun3163 closed 3 years ago
0
Problem resulting in large amount of NULL in mv_susie initial run

#32 hsun3163 closed 3 years ago
0
Metric to show improvement of multivariate predictions

#31 hsun3163 opened 3 years ago
1
Issues in installing "mashr"

#30 hsun3163 closed 3 years ago
3
Question and summary: what is a good way to conduct TWAS for risk locus with low expression heritability via multi-tissue dataset ?

#29 hsun3163 closed 3 years ago
2
Lack of justification of using a sparse model for prediction and new structure of story.

#28 hsun3163 closed 3 years ago
1
Question arise after univariate analysis

#27 hsun3163 closed 3 years ago
6
P value for the hsq computed by susie

#26 hsun3163 closed 3 years ago
1
file not found error in Workflow

#25 hsun3163 closed 3 years ago
0
Discrepancy in the result of the three tissue fusion run

#24 hsun3163 closed 3 years ago
0
New Issues in TWAS.FUSION

#23 hsun3163 closed 3 years ago
2
When calculating the TWAS Z score, shall heritability be taken into consideration.

#22 hsun3163 opened 3 years ago
0
Alternate method for GWAS Z score imputation

#21 hsun3163 closed 3 years ago
4
Part of the alzheimer paper gene are missing from the ROSMAP dataset.

#20 hsun3163 closed 3 years ago
5
New Issue in reading genotype file after the mount point changed.

#19 hsun3163 closed 3 years ago
2
SNP not scaled issues.

#18 hsun3163 closed 3 years ago
4
Issues in job naming of SOS submission

#17 hsun3163 closed 3 years ago
3
Issues in running the twas_fusion pipeline on cluster

#16 hsun3163 closed 3 years ago
7
parallel environments for the CSG cluster.

#15 hsun3163 closed 3 years ago
6
Using Singularity for SOS, docker daemon not running problem

#14 hsun3163 closed 3 years ago
1
Documenting how to setup fusion

#13 hsun3163 closed 4 years ago
1
Comments on first draft of pipeline implementation

#12 gaow closed 3 years ago
1
Performance issues when running on laptop

#11 hsun3163 closed 4 years ago
2
Heritability change with partitioned sample size.

#10 hsun3163 closed 4 years ago
1
Literature and methods for multivariate TWAS

#9 gaow opened 4 years ago
4
Look into strand flip issues in summary data

#8 gaow closed 4 years ago
2
Document the path of the input files we used for our project

#7 gaow closed 3 years ago
8
Explain how summary stats works for TWAS

#6 gaow opened 4 years ago
5
Reasons for genes that gets excluded from analysis

#5 gaow closed 4 years ago
1
Gene region extraction workflow

#4 gaow closed 3 years ago
1
SVA vs PEER model.

#3 hsun3163 closed 4 years ago
1
Quality control protocol for TWAS

#2 gaow opened 4 years ago
4
Project aims and action plans

#1 gaow opened 4 years ago
1