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Bioinformatics : Recent Questions and Answers (Page 23)

Find answers to your questions about Bioinformatics or help others by answering their Bioinformatics questions.

COVID-19 GWAS: what is a cross-replicating association?

In a genomic study of patients infected with SARS-CoV-2, the authors detected cross-replicating associations with rs11385942 at locus 3p21.31 , the association signal spanned the genes SLC6A20, LZTFL1, CCR9,...

Asked on 05/23/2021

1 answer

Are there any databases for gene co-expression or expression pattern clustering?

I am currently working on gene clustering based on co-expression pattern in mouse brain. The problem is I do not have some solid way to test my result. Are there...

Asked on 05/23/2021 by jasperhyp

1 answer

Is SNPRelate the goto package for PCA of SNP data in R?

I'm trying to evaluate a method that I'm not familiar with. They used SNPRelate. I'm wondering if this is the best / only choice... what other tools would you recommend?...

Asked on 05/23/2021 by Dan Bolser

0 answer

data visualization RNAseq : scaling data for PCA and cluster dendogram

I have count data from a RNAseq experiment (2 samples are from normal cells and 3 samples are cells with a disease), and the data is already standardized by trimmed...

Asked on 05/20/2021

1 answer

I do not understand the output of ssGSEA using GSVA package in R

I am using the GSVA package in R to do single sample gene set enrichment analysis (ssgsea) using method = ssgsea. This works, but I do not understand the output....

Asked on 05/19/2021 by Sylvia Rodriguez

0 answer

Failed run beast v2.6.3 using test1.xml in STAECY v1.2.5 pacakage

I am using the package STAECY v1.2.5 in beast v2.6.3. But it failed in testing the test1.xml in STACEY example package. I am attaching the beast running log below....

Asked on 05/19/2021

0 answer

Which database is good to store (metagenomic) relative abundance data?

The simple question is: how to store relative abundance data in a database? Which database to choose? I am talking here about metagenomics data, relative abundance of species or some...

Asked on 05/19/2021 by Art

0 answer

NO_COOR reads not in a single block at the end 0 -1

I am doing an RNA seq analysis with mouse samples. I had my reads in several lanes, so I concatenated those fastq reads. Then I've mapped my reads with Hisat2...

Asked on 05/19/2021 by user9393

1 answer

MUMmer plot error. Line 884. What to do?

My third year comp sci friend got me this far, I hope you guys can help me with the last inch! For the record, I have practically no coding experience....

Asked on 05/18/2021 by DansterBoy

0 answer

BAM to gene expression matrix (UMI counts per gene per cell),10X

I am trying to reproduce some results of a scRNASeq experiment. However I am new to the server-side aspect of such analyses and am very confused at the moment. The...

Asked on 05/18/2021 by h3ab74

2 answer

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