STAARpipeline-Tutorial

STAARpipeline-Tutorial copied to clipboard

Hi. I would like to also get the plots for the gene centric noncoding ncRNA regions. I see that the default (NULL) would be used for `ncRNA_pos` in the `STAARpipeline-Tutorial/STAARpipelineSummary_Gene_Centric_Noncoding.r`...

samreenzafer

Conditional analysis - Summary Gene Centric Noncoding not running to completion

6

Thanks for a great easy to use tool. I've finally reached the step where I would like to do a Gene Centric Noncoding conditional analysis on some select rare variants...

samreenzafer

#SNVs per case/control?

1

Hello, For the gene-centric analyses, is there any possible way to obtain the number of SNVs per case and control samples? The output from the summary functions only lists the...

kwdoyle

[Suggestion-Implementation] Add information to summary and annotations of results

1

Hello Xihao! I would suggest two types of information that would be very informative in the summary and annotation of all steps. For quantitative phenotype, a simple mean/median of the...

GACGAMA

gnomAD AF & family-based vcf analysis

3

Hi Xihao, Thanks for your useful tool! And I've met some problems really confused me: 1. I noticed that allele frequencies of gnomAD and 1000G are contained in FAVOR full...

XiaKwan

Controls / cases counts inverted when using binary model

7

Hello! I've finished analyzing a large cohort using 0/1 numerical values for control/case status respectively. Then I went to my vcf to count the distributions of variants for each group....

GACGAMA

What is the difference between the "results_temp" and "results_m" results?

2

When summarizing the results of the coding region, what is the difference between the "results_temp" and "results_m" results?

jingydz

Error : Mat::operator(): index out of bounds & Error in apply(emthr_SCANG_O, 2, max) :

1

Is it acceptable for a few samples to exhibit the following error during the Dynamic_window step? #######-- Dynamic_window Start time is 2024/08/22--16:22 --####### used (Mb) gc trigger (Mb) max used...

jingydz