Amy Willis @AmyDWillis
about to present on model misspecification in microbiome studies at #bioc2022

An April '22 preprint from David Clausen and Dr. Willis:

arxiv.org/abs/2204.12733 @AmyDWillis Great and simple motivation from looking at mock communities (over-detection) as to why to move away from:

E(W_ij) = c_j mu_ij (just size factor scaling)

instead use:

Eric Davis @ericscottdavis1 & Wancen Mu @WancenM presenting two branches of functionality in the {nullranges} pkg: finding matched sets of genomic ranges based on covariates & bootstrapping blocks of genomic ranges. Both play well w/ {plyranges} for downstream analysis

#bioc2022 Both methods are based statistical methods for refining null comparisons. E.g. we were inspired by {MatchIt}, {cobalt} and other matching packages, as well as {GSC} for the block bootstrap (method described in Bickel et al 2010)

Got an RNA-seq dataset with 50, 100, 200+ samples? Plug it into a differential expression tool and hope for the best? No! You need to consider QC, EDA, and modeling technical variation, or else risk generating spurious results. A thread on papers, methods, and best practices: Short version:
1) look for outliers (QC) and technical variation with PCA plots
2) consider problems with confounding: model unwanted variation with methods like RUV / SVA / PEER
3) include technical factors in linear model, iterate with respect to positive and negative controls

This #EOSS funding from @cziscience for #DESeq2 and #tximeta wrapped up at the end of 2021.

Reporting in this 🧵 on what we developed:

https://twitter.com/mikelove/status/1330840564091252737

1. @kwame_forbes wrote DESeq2::integrateWithSingleCell() which helps user locate publicly available SC datasets followed by visualization with his own R package:

kwameforbes.github.io/vizWithSCE/

Kwame was then a @UNCPREP scholar, now a first year BCB student at UNC 🧬💻🎉

New preprint from first author Scott Van Buren, we look at various aspects of quantification uncertainty for scRNA-seq counts: interval coverage, trajectory analysis, and DE testing. 1/7

biorxiv.org/content/10.110… Last year, in the alevin publication, @k3yavi et al showed that assignment of all the reads in scRNA-seq was critical for accurate estimation of abundance across categories of genes by uniqueness. 2/7

genomebiology.biomedcentral.com/articles/10.11…