Jack Kamm
@snackematician.bsky.social
Statistician working in genomics. https://jackkamm.github.io/
Perhaps related, but I think this paper is also a good explanation for why these streaks commonly occur in PCA (not just in popgen demographic inference), due to sparse structure in the data -- a lot of this was figured out by people doing factor analysis in the 40s
academic.oup.com/jrsssb/artic...
academic.oup.com/jrsssb/artic...
Vintage factor analysis with Varimax performs statistical inference
Abstract. In the 1930s, Psychologists began developing Multiple-Factor Analysis to decompose multivariate data into a small number of interpretable factors
academic.oup.com
July 22, 2025 at 6:57 PM
Perhaps related, but I think this paper is also a good explanation for why these streaks commonly occur in PCA (not just in popgen demographic inference), due to sparse structure in the data -- a lot of this was figured out by people doing factor analysis in the 40s
academic.oup.com/jrsssb/artic...
academic.oup.com/jrsssb/artic...
Thanks for the tip, I will have to check it out :)
December 4, 2024 at 9:39 PM
Thanks for the tip, I will have to check it out :)
Totally agree. I also like this paper on the topic:
genomebiology.biomedcentral.com/articles/10....
Unfortunately the package isn't easily installable from CRAN/Bioconductor. But more flexible to just use velocyto/kallisto anyways. Really wish cellranger would output this statistic to begin with.
genomebiology.biomedcentral.com/articles/10....
Unfortunately the package isn't easily installable from CRAN/Bioconductor. But more flexible to just use velocyto/kallisto anyways. Really wish cellranger would output this statistic to begin with.
DropletQC: improved identification of empty droplets and damaged cells in single-cell RNA-seq data - Genome Biology
Background Advances in droplet-based single-cell RNA-sequencing (scRNA-seq) have dramatically increased throughput, allowing tens of thousands of cells to be routinely sequenced in a single experiment...
genomebiology.biomedcentral.com
December 4, 2024 at 9:25 PM
Totally agree. I also like this paper on the topic:
genomebiology.biomedcentral.com/articles/10....
Unfortunately the package isn't easily installable from CRAN/Bioconductor. But more flexible to just use velocyto/kallisto anyways. Really wish cellranger would output this statistic to begin with.
genomebiology.biomedcentral.com/articles/10....
Unfortunately the package isn't easily installable from CRAN/Bioconductor. But more flexible to just use velocyto/kallisto anyways. Really wish cellranger would output this statistic to begin with.