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Bioinformatics : Recent Questions and Answers

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

calculateQCMetrics defunct, how to calculate the quality metrics by perCellQCMetrics

I am trying to follow a tutorial from Sanger institute (from May 2019) on analysis of single cell RNA Seq data. They use calculateQCMetric function to calculate the quality metrics,...

Asked on 01/01/2022

2 answer

Changing active.ident in Seurat

Im trying to change the active.ident to another column in metadata but this error keeps popping up! I recently upgraded to R version 4.0.2 from 3.6.1 The older version was...

Asked on 01/01/2022

1 answer

How to compact variant data to their genes without bias?

I have a dataset of genes I am trying to collect data on from public databases, to use as features in machine learning. I am trying to take some features...

Asked on 12/30/2021

1 answer

can I download DESeq2 in R 3.6.3 in Linux MInt?

I am trying to download DESeq2 in R 3.6.3. Is it possible?This is printed when I am trying: Warning in install.packages : package ‘DESeq2’ is not available (for R...

Asked on 12/30/2021

2 answer

Interpretion of my coronavirus 2019-nCov, Wuhan, China BLAST tree?

This is the BLAST tree of the latest coronavirus out of China (from Wuhan Institute of Virology, China). It seems strange that there is so much divergence from all the...

Asked on 12/27/2021

1 answer

europmc and tidypmc R library for extracting or making metadata from publication

I'm trying to use this europmc r libray where I have a list of pmids to look for. I tried with pubtator but its bit complicated.In Europmc...

Asked on 12/27/2021

1 answer

RNASeq read coverage in protein space?

I used samtools depth to find the per base-pair read coverage over a number of isoform contigs from my Trinity assembly.I have also conducted a multiple sequence...

Asked on 12/23/2021

1 answer

Number of reactions per metabolic pathway

What is the quickest way to calculate the number of chemical reactions present in each pathway for a given organism and which online database such as Kegg,...

Asked on 12/23/2021

0 answer

no result from heat map WGCNA

I have created a heat map using WGCNA using R. But the heat map command is not showing the plot and there is no error. I have a large number...

Asked on 12/22/2021

2 answer

Ancestry of the coronavirus 2019-nCov, WuHan city, China

In one of the answers to another question about the corona virus a link was given to this phylogenetic analysis of the virus. Can somebody assist...

Asked on 12/20/2021

1 answer

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