In this preprint biorxiv.org/content/10.110… with @sindri_e we compared seven widely used methods for batch correction of single cell RNA-seq data. We found that all but one of the methods introduce batch effects when there are none. 1/N
Pall Melsted
3,714 posts
Pall Melsted
@pmelsted
Professor @hi.is in CS, head of rna seq data analysis at decode genetics (views are mine). Bioinformatician, epistemic trespasser, &c. ps. I hate GTF files
Joined January 2013
- I'm pretty sure my morning coffee changes my gene expression by more than 7%
- Exactly one month ago Iceland had 1045 active diagnosed infections. Today we have 99 active, and added 608 new cases during this time, most of which have recovered. #TestTraceIsolate
- Today I am doing proper bioinformatics. Matching up gene symbols between databases
- Next time your kid loses a tooth, put it in a coke-bath and have them watch what happens. There is an important lesson to be learned 1/n
- New release of kallisto is out github.com/pachterlab/kal… kallisto can now produce BAM files in genomic coordinates, sorted and indexed for IGV consumption, details in a new blogpost pmelsted.wordpress.com/2018/01/29/bam/ Oh, and it runs on a tiny computer liorpachter.wordpress.com/2018/01/29/bio…
- Replying to @pmelstedSociety will teach your kids about dental hygiene, dangers of soda drinks, but who is going to talk to them about experimental design? 4/4
- Speed is crucial in fighting this epidemic. In Iceland we use test-trace-isolate to curb the spread in addition to restrictions on social gathering, 2m social distancing and mask wearing in public. Here is a rough timeline of what happens for a positive diagnosis
- I can solve every problem with a combination of cut,grep,sed,sort,uniq, and awkThis post is unavailable.
- Transcripts are real, genes are a useful abstraction #gi2017
- I am a real bioinformagician, I can do analysis stuff without first converting data into tabular form
- New preprint out w @lpachter & @vntranos on the Barcode, UMI, Set format (BUS) for processing of single cell RNA-Seq datasets. Shows how to create modular frameworks for processing scRNA-Seq data, fast using kallisto (v 0.45.0 just released) and simple biorxiv.org/content/early/…
- Recursive vaccinations! My brother got his first and only J&J/Jansen shot today. Yes, that’s a tattoo of himself
