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Comment: Tools or R / Python packages to perfom ML models

Comment: p-value combination methods

Answer: bcftools mpileup --max depth : What would be a reasonable setting for this optio

Answer: What type of cancer did they study in this paper?

Answer: How to filter .fasta file based on conditional statement

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Teacher to i.sudbery 18k

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Recent Replies

Comment: Tools or R / Python packages to perfom ML models by Matthias Zepper 4.2k

Just to clarify: Many ML models are trained and executed using dedicated software libraries for machine learning and artificial intellige…

Answer: Problematic fastq files...How can we trust them? by ATpoint 78k

> I assume that maybe all these are fixable with a script but my question is, can we trust these files? Is it worth spending time and effor…

Comment: Tools or R / Python packages to perfom ML models by sil_bioinfo ▴ 30

My main idea is to be able to classify patients with active TB, LTBI and healthy patients as well as possible. The problem is that within t…

Comment: scRNA-seq: Consistent low number of cells and low fraction reads across the samp by rpolicastro 12k

They could have saved themselves a ton of money by sequencing this on a miseq.

Comment: Annotate Unplaced Scaffold with Chromosome Information by cmdcolin ★ 3.4k

I think there are tools like ragtag https://github.com/malonge/RagTag that could help. you can also align your reads back to your new assem…

Comment: An incomprehensible error with R package gggenes by ATpoint 78k

It's not stupid, just a bit lazy ;-)

Comment: Adding functional annotation and meta-data of MAKER/BRAKER GFF by ben@f • 0

Hi, did you find an effective solution for this problem? beside Agat and

Comment: An incomprehensible error with R package gggenes by alice005201314 • 0

Thank you. I asked a stupid question.

Answer: An incomprehensible error with R package gggenes by ATpoint 78k

First hit on google: https://stackoverflow.com/questions/73935357/error-in-grid-callc-convert-x-as-integerwhatfrom-as-integerwhatto-vie

Answer: Should I scale all genes in single cell Seurat? by antonioggsousa 3.0k

Hi, Scaling all features might be useful to plot genes that are not among the 2k HVG in a heatmap. Otherwise than that, I never encounter…

Comment: How to filter .fasta file based on conditional statement by rob_DNA ▴ 20

Oh wow that was a bit stupid.. I downloaded 39.06 but I accidentally used 39.01... anyway, thank you very much for your help!! I now used t…

Comment: How can I map coordinates between two strains of yeast? by Jimmy ▴ 10

Yes (S. cerevisiae)

Comment: scRNA-seq: Consistent low number of cells and low fraction reads across the samp by GenoMax 136k

> less than 100 for some samples Hmm. That is surprising but then in light of that fact ~20% recovery of cells does not sound bad.

Comment: scRNA-seq: Consistent low number of cells and low fraction reads across the samp by newbee ▴ 40

Thanks for raising these valid points. I do not have the answer right now. Lately, I heard from the PI that they started with a small numbe…

Comment: How to get multiple protein domain database domain name from id's by GenoMax 136k

A list of InterPro domains is available: https://ftp.ebi.ac.uk/pub/databases/interpro/current_release/entry.list

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