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Comment: how can i fix this problem in R
by
cpad0112
20k
Package ‘S4Vectors’ could not be loaded
Check the permissions and try reinstalling the mentioned package.
Comment: [R] Differential Co-Expression ?
by
ali
▴
20
I use edgeR , that is the point, I dont know if I need log-scale or not.
Comment: How to find DEG within a cluster between two groups without any replication info
by
Zahra
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Thanks for your reply. I mean the biological replicates information. Indeed the dataset is for the 3 conditions (ctrl, treat1, treat2) and …
Answer: Multiple copies of same gene annotated
by
Mensur Dlakic
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Gene duplication.
It could be a contamination with contigs that do not belong to that bin and also happen to contain a copy of the same ge…
Comment: Confusion on downloading SRA run data
by
crx6xw
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Nope, I simply just didn't use this dataset. I think it's probably better to just download the count matrices directly instead of processin…
Comment: Use of Scater for QC in scRNA-seq Analysis: How to remove cells with less than c
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otieno43
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Thanks let me try and see how it goes.
Comment: Is Stringtie a suitable tool for both gene and transcript quantification?
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virajbdeshpande
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Thanks for this comment. Could you point to some example benchmarks you are referring to?
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by
GenoMax
117k
Looks like this is *Aceinetobacter baumanii* genome.
Using [**EntrezDirect**][1]:
$ esearch -db nuccore -query "H0N27_00020 [locus]" …
Comment: Retrieve protein sequence from Mgnify given only accession code
by
GenoMax
117k
Are these accessions private? It looks like most of the study accessions available on https://www.ebi.ac.uk/metagenomics/search/studies?pag…
Comment: [R] Differential Co-Expression ?
by
ATpoint
62k
That depends what the package you use instructs you to do. Do you need log-scale or not?
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by
Mensur Dlakic
★
19k
There is no pairwise alignment in MSA, because pairwise alignment by definition means that a pair of sequences is involved. There are *many…
Answer: Use of Scater for QC in scRNA-seq Analysis: How to remove cells with less than c
by
ATpoint
62k
If you use scater or scuttle it's really just simple subsetting:
library(scuttle)
sce <- scuttle::addPerCellQCMetrics(sce)
…
Comment: Retrieve protein sequence from Mgnify given only accession code
by
jscience
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It does not return any hits when you do a text search, but it is a valid accession for protein data.
See https://www.ebi.ac.uk/metagenomic…
Answer: Find motif position given a set of enrich peaks
by
tobiaminuxy
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Try looking at FIMO find individual occurence of motifs.
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