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Forum: Site Use Guidelines
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Forum: Improvement on automatic annotation of single-cell RNA-seq data from the literature using LLM
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Answer: NGS forensics: how to know if data is fabricated
Comment: NGS forensics: how to know if data is fabricated
correcting for a batch in DESeq2
Comment: NGS forensics: how to know if data is fabricated
Answer: NGS forensics: how to know if data is fabricated
Comment: how to combine multiple RNAseq count files into a single dataframe in R and unix
NGS forensics: how to know if data is fabricated
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Comment: NGS forensics: how to know if data is fabricated by dsull ★ 5.8k
I don't think people have undertaken the effort to create an anomaly detector for RNAseq -- people's efforts are dedicated towards developi…
Comment: NGS forensics: how to know if data is fabricated by dsull ★ 5.8k
I'd say post on pubpeer -- it's the best forum for this sort of discussion. As for what additional analysis I recommend: I'd say look at s…
Comment: NGS forensics: how to know if data is fabricated by noodle ▴ 520
> This is a super-interesting question from an algorithmic standpoint Ya, I was hoping to find some algorithm that would compare say a 're…
Comment: ScRNAseq-How to correctly choose cell type marker genes by Francesco ▴ 10
Thank you for your valuable suggestion!
Comment: NGS forensics: how to know if data is fabricated by noodle ▴ 520
> My first question would be how strong your background in such analysis > is. Very strong. PhD+several years working in the field. > Wot…
Comment: NGS forensics: how to know if data is fabricated by ATpoint 82k
My first question would be how strong your background in such analysis is. Claim of fabrication is very serious, so be 100% sure to back it…
Answer: NGS forensics: how to know if data is fabricated by Jeremy Leipzig 22k
This is a super-interesting question from an algorithmic standpoint (devising a model that can distinguish real from synthetic reads) but I…
Answer: absolute path for symbolic links in Snakefile by Jesse ▴ 740
It's nothing to do with Snakemake, just the ordinary confusion of making relative symlinks when your working directory is somewhere else. …
Answer: Hide positions in alignment with 99% "–" characters to ignore single sequence in by Jesse ▴ 740
[seqmagick](https://github.com/fhcrc/seqmagick/) has a `--squeeze-threshold` option that does just this. For example with an MSA of five s…
Comment: Source other conda environments in a nextflow pipeline when nextflow itself is i by Arup Ghosh 3.2k
Use the standalone version of Nextflow and specify the process-specific conda environments paths.
Comment: gvcf joint calling by Jeremy Leipzig 22k
can you show us an exonic position in your VCF file that is all `./.`?
Comment: Help understanding how KEGG Ortholog `K00004 ` has 3 ECs associated with it (EC: by O.rka ▴ 710
Thank you. This answers my question. The reason I am asking is because I’m trying to do set enrichment analysis with BRENDA pathways using…
Answer: Source other conda environments in a nextflow pipeline when nextflow itself is i by colindaven 6.4k
I used to use nextflow in a conda env. That requires the env to be active when a pipeline is started. Also I have productive pipelines whic…
Comment: different FeatureCounts output for the same data by Istvan Albert 100k
just to clarify, it is not that the program algorithm works differently but the meaning of the flags changed; before -p was sufficient to…
Comment: how to combine multiple RNAseq count files into a single dataframe in R and unix by BioinfGuru ★ 1.7k
Thanks Ram. Using merge maxed out my ram on a large list, but your suggestion directed me to purrr::reduce which works great.
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