It was a pleasure to contribute to this work (w/ our section led by Dongze He w/contributions by Y & Avi Srivastava). We’re particularly grateful to Lukas Heumos, @AnnaCSchaar, & Fabian Theis for inviting us to be part of this great effort (& are already working on updates)!

Understanding and evaluating ambiguity in single-cell and single-nucleus RNA-sequencing biorxiv.org/cgi/content/sh… #bioRxiv

Are you interested in performing splice-aware quantification of your #scrnaseq data, obtaining unspliced, spliced, and ambiguous UMI counts quickly & in <3GB of RAM? If so, check out the new manuscript by Dongze He, @CSoneson and me on #bioRxiv bit.ly/3vJr0Ji. 1/🧵

In case you missed it, important thread on quantification in #scRNAseq of spliced vs unspliced reads, with a careful examination of recent benchmarks. From Dongze He @CSoneson 𝕐 x.com/nomad421/statu…

The new pyroe release pypi.org/project/pyroe/ supports construction of the "spliceu” in addition to the “splici” transcriptome (thanks Dongze He). Read more about quantifying expression & spicing status in #scrnaseq in this thread & the linked preprint! x.com/nomad421/statu…

simpleaf: A simple, flexible, and scalable framework for single-cell transcriptomics data processing using alevin-fry biorxiv.org/cgi/content/sh… #bioRxiv

I'm excited to see this out! Dongze He & I have been working on simpleaf for a while, and it's already become our daily driver & preferred interface for single-cell processing. It has also been important in easing integration of alevin-fry into nf-core's scRNA-seq pipeline! 1/2

A massive thanks to the whole consortium that contributed to this effort and made it what it is now. We could not have done it without you!

Workflow templates are an exciting new feature for simpleaf; check out the docs simpleaf.readthedocs.io/en/latest/work…! They provide an easy way to process protocols that may involve many commands (like CITE-seq, 10X feature-barcoding & beyond), by just filling in a simple template. 1/13

Do you ever look at something amazing someone in your lab has done and say "Wow; this is awesome!"? Well, here's a very short story starring Dongze He! As part of simpleaf (github.com/COMBINE-lab/si…), we rely on another package we wrote called pyroe (github.com/COMBINE-lab/py…). 1/15

DifferentialRegulation pre-print online -> doi.org/10.1101/2023.0… *DifferentialRegulation* studies how splicing dynamics change between experimental conditions. It is based on a Bayesian hierarchical method (multiple samples) with latent states (for multi-mapping reads).

The simpleaf (simple-AF) paper by Dongze He & me was recently published in @OUPBioinfo academic.oup.com/bioinformatics…. It describes the simpleaf tool, written in #rustlang, designed to track best practices & make processing #SingleCell #scrna data with alevin-fry even easier. 1/x

Just tested out the github action creator from cargo dist (github.com/axodotdev/carg…) & WOW! Initial setup w/cargo dist, add a few keys to my manifest and bam — releases across 3 platforms & an installer script! Check out autogenerated piscem release page :) github.com/COMBINE-lab/pi…

Our newest preprint is out! We introduce Forseti, a model to predict the splicing status of individual fragments in tagged-end #scRNAseq experiments (biorxiv.org/content/10.110…). 1/

This is more great work by Dongze He, and Yuan Gao, and done in collaboration with Skyler Chan (now a postbac at NIH who worked on this as an undergrad researcher) and Natalia Quintana-Parrilla (an REU student in the lab this past summer). Longer thread soon! 4/4

Forseti: A mechanistic and predictive model of the splicing status of scRNA-seq reads biorxiv.org/cgi/content/sh… #biorxiv_bioinfo

Forseti: A mechanistic and predictive model of the splicing status of scRNA-seq reads biorxiv.org/content/10.110…

We've been thinking about what information is & isn't contained in single-cell seq. data for quite some time now. With respect to splicing in particular we've been thinking about this since it became clear that typical #scRNAseq data contain many reads of unspliced origin 1/

Perhaps the first step is optimally aggregating the fragment-level scores to the level of the UMIs, which are the ultimate unit of quantification in these experiments. Anyway, thanks for reading to the end of the thread and we're happy to chat with folks interested in this! 22/22

We just released oarfish 0.4.0! The key addition is that we now compute a Sequence Collection digest for each quant file on the basis of the header information in the alignment file. This is the first step toward automated metadata propagation as we do with salmon -> tximeta.