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Bioinformatics : Recent Questions and Answers (Page 2)

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

Alternatives to imputation for single-cell RNA-Seq analysis to increase statistical power of DE analysis

I have a small scRNA-Seq dataset (n = 357, inhibitory neurons). This set of cells is split almost evenly between two conditions (Case and Control). I would like to test...

Asked on 12/16/2021

0 answer

Output the linear predictor from a stratified cox model?

I have fitted a cox model on a pooled dataset of multiple studies, say studies A, B, and C. As these studies have different baseline hazard functions, I stratified for...

Asked on 12/13/2021

1 answer

RNAseq biological replicates not clustering in PCA plots

I have RNAseq data from 4 samples with 3 biological replicates per sample. I am currently trying to do the differential expression analysis with DESeq2 but the biological replicates will...

Asked on 12/13/2021

3 answer

Kraken2 or metaphlan2 report to phyloseq

I wish to convert a kraken2 or metaphlan2 report into the R package to analyze using Phyloseq. I have performed obtained an importation and Phyloseq analysis, but the result was...

Asked on 12/11/2021

0 answer

Prevent Snakemake from changing wildcards: sample for every rule

EDIT: I posted this as a bug, perhaps wait for the result of that? github All, I am using Snakemake to build a pipeline. To define input...

Asked on 12/11/2021

2 answer

Which sequence alignment tools support codon alignment?

Sometimes it useful to perform a nucleotide protein coding gene sequence alignment based on codons, not on individual nucleotides. For example for further codon model analysis it is important to...

Asked on 12/09/2021

3 answer

Why does the SARS-Cov2 coronavirus genome end in aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa (33 a's)?

The SARS-Cov2 coronavirus's genome was released, and is now available on Genbank. Looking at it... 1 attaaaggtt tataccttcc caggtaacaa accaaccaac tttcgatctc ttgtagatct 61...

Asked on 12/09/2021

4 answer

A new paper suggests the Corona Virus has "Uncanny similarity of unique inserts in the 2019-nCoV spike protein to HIV-1" - What does this mean?

Quote:We found 4 insertions in the spike glycoprotein (S) which are unique to the 2019-nCoV and are not present in other coronaviruses. Importantly, amino acid residues in all the 4...

Asked on 12/09/2021

3 answer

parsimony and maximum likelihood tree comparison in R

Maximum Likelihood analysis compares the tips or the species based on their sequence similarity while Parsimony analysis compares the characteristic features among the species. So far I did comparison of...

Asked on 12/09/2021

2 answer

Comparing aligned amino acids to codon

I have a set of 4 amino acids which i have aligned,but i want to compare then with respective nucleotide sequence in terms of change codon level. I have...

Asked on 12/07/2021 by kcm

1 answer

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