gaow/neuro-twas issues and pull requests

#42 - Error at ED step with updated mashr packages.

Issue - State: closed - Opened by hsun3163 over 3 years ago - 7 comments

#41 - Missing data pattern is inconsistent between Bhat and Shat

Issue - State: closed - Opened by hsun3163 over 3 years ago - 2 comments

#40 - Consideration on the optimization of TWAS analysis

Issue - State: open - Opened by hsun3163 almost 4 years ago

#39 - add parameters notes for mv_susie output

Pull Request - State: closed - Opened by nickluo1313 almost 4 years ago - 2 comments

#38 - Redo upload original script and function script

Pull Request - State: closed - Opened by nickluo1313 almost 4 years ago

#37 - add original JTI.r

Pull Request - State: closed - Opened by nickluo1313 almost 4 years ago - 4 comments

#36 - Potential issues in mv-susie cross-validation

Issue - State: closed - Opened by hsun3163 almost 4 years ago - 12 comments
Labels: Question to gaow, Discussions

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

Issue - State: open - Opened by gaow almost 4 years ago - 6 comments
Labels: Reference, Current action, New ideas

#34 - Problem with the flash() function in the flash_no_constraint pipeline step.

Issue - State: closed - Opened by hsun3163 almost 4 years ago - 9 comments

#33 - Whole Genome SNP-heritability of gene expression

Issue - State: closed - Opened by hsun3163 about 4 years ago
Labels: Reference

#32 - Problem resulting in large amount of NULL in mv_susie initial run

Issue - State: closed - Opened by hsun3163 about 4 years ago

#31 - Metric to show improvement of multivariate predictions

Issue - State: open - Opened by hsun3163 about 4 years ago - 1 comment
Labels: Immediately next, Discussions

#30 - Issues in installing "mashr"

Issue - State: closed - Opened by hsun3163 about 4 years ago - 3 comments

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

Issue - State: closed - Opened by hsun3163 about 4 years ago - 2 comments
Labels: Reference

#28 - Lack of justification of using a sparse model for prediction and new structure of story.

Issue - State: closed - Opened by hsun3163 about 4 years ago - 1 comment

#27 - Question arise after univariate analysis

Issue - State: closed - Opened by hsun3163 over 4 years ago - 6 comments
Labels: FIXME

#26 - P value for the hsq computed by susie

Issue - State: closed - Opened by hsun3163 over 4 years ago - 1 comment

#25 - file not found error in Workflow

Issue - State: closed - Opened by hsun3163 over 4 years ago

#24 - Discrepancy in the result of the three tissue fusion run

Issue - State: closed - Opened by hsun3163 over 4 years ago

#23 - New Issues in TWAS.FUSION

Issue - State: closed - Opened by hsun3163 over 4 years ago - 2 comments

#22 - When calculating the TWAS Z score, shall heritability be taken into consideration.

Issue - State: open - Opened by hsun3163 over 4 years ago
Labels: Discussions, Question from gaow

#21 - Alternate method for GWAS Z score imputation

Issue - State: closed - Opened by hsun3163 over 4 years ago - 4 comments
Labels: Discussions

#20 - Part of the alzheimer paper gene are missing from the ROSMAP dataset.

Issue - State: closed - Opened by hsun3163 over 4 years ago - 5 comments
Labels: Discussions

#19 - New Issue in reading genotype file after the mount point changed.

Issue - State: closed - Opened by hsun3163 over 4 years ago - 2 comments

#18 - SNP not scaled issues.

Issue - State: closed - Opened by hsun3163 over 4 years ago - 4 comments

#17 - Issues in job naming of SOS submission

Issue - State: closed - Opened by hsun3163 over 4 years ago - 3 comments

#16 - Issues in running the twas_fusion pipeline on cluster

Issue - State: closed - Opened by hsun3163 over 4 years ago - 7 comments

#15 - parallel environments for the CSG cluster.

Issue - State: closed - Opened by hsun3163 over 4 years ago - 6 comments
Labels: FIXME

#14 - Using Singularity for SOS, docker daemon not running problem

Issue - State: closed - Opened by hsun3163 over 4 years ago - 1 comment

#13 - Documenting how to setup fusion

Issue - State: closed - Opened by hsun3163 over 4 years ago - 1 comment

#12 - Comments on first draft of pipeline implementation

Issue - State: closed - Opened by gaow over 4 years ago - 1 comment

#11 - Performance issues when running on laptop

Issue - State: closed - Opened by hsun3163 over 4 years ago - 2 comments

#10 - Heritability change with partitioned sample size.

Issue - State: closed - Opened by hsun3163 over 4 years ago - 1 comment

#9 - Literature and methods for multivariate TWAS

Issue - State: open - Opened by gaow over 4 years ago - 4 comments
Labels: Reference

#8 - Look into strand flip issues in summary data

Issue - State: closed - Opened by gaow over 4 years ago - 2 comments
Labels: Reference, Discussions

#7 - Document the path of the input files we used for our project

Issue - State: closed - Opened by gaow over 4 years ago - 8 comments
Labels: Reference, FIXME

#6 - Explain how summary stats works for TWAS

Issue - State: open - Opened by gaow over 4 years ago - 5 comments
Labels: Current action, Discussions, New ideas

#5 - Reasons for genes that gets excluded from analysis

Issue - State: closed - Opened by gaow over 4 years ago - 1 comment

#4 - Gene region extraction workflow

Issue - State: closed - Opened by gaow over 4 years ago - 1 comment

#3 - SVA vs PEER model.

Issue - State: closed - Opened by hsun3163 over 4 years ago - 1 comment
Labels: Reference

#2 - Quality control protocol for TWAS

Issue - State: open - Opened by gaow over 4 years ago - 4 comments
Labels: Reference, Current action, Discussions

#1 - Project aims and action plans

Issue - State: open - Opened by gaow over 4 years ago - 1 comment

GitHub / gaow/neuro-twas issues and pull requests