xiw588

Unable to perform CNA vs. gene expression analysis in TCGA pan-cancer

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Hi Shixiang, I was trying to perform analysis on CNA and gene expression in HLA genes in the TCGA pan-cancer setting using the shiny app. Unfortunately, there have been errors...

HLA typing for SNP2HLA output

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Hi, I wonder if I could feed the bed, bim and fam files output from SNP2HLA into HIBAG to get the HLA class I and II typing. Thank you in...

Hi, I am trying to apply it to panel data, but found the sum of all the exp_sigs is not equal to the number of total_snvs. Some samples have the...

Hi, I want to apply your algorithm to the data output from SNP2HLA, but I realized that the vcf file your specified doesn't really match what I got from SNP2HLA....

Hi I want to apply the function you kindly provided, but was running into some issues of using my own data, probably due to the format. Can you please provide...

I try to install RFmix in command line on cluster, but failed in both ways you provided. I am new to genetic ancestry and it will be helpful if you...

Hi, I wonder if there is any efficient way to covert SNP2HLA dosage file to HPED that can be fed into your downstream analysis pipeline? Thanks

Questions about MATH score

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**Describe the issue** I wonder if MATH score implemented in maftools took CNA into account? **Command** Please post your commands and the output (errors or any unexpected output) ```r ```...

Hi, I got the following error messages when running calculate_sig_score (), any ideas? Error in .Call("matrix_density_R", as.double(t(expr[, sample.idxs, drop = FALSE])), : Incorrect number of arguments (7), expecting 6 for...

Can you explain the results running batch_kruskal ()? Does it provide the mean or median by group variable? I also checked the results running batch_wilcoxon (), and it seems to...