rmflight, 17 days ago to bioinformatics

What RNA-Seq datasets are everyone using for RNA-Seq differential analysis workshops, using {DESeq2} or {limma} #RStats?

Two or three categories, and ideally a good (4 or 5+) number of replicates, human or mouse?

We have some new methods in ontology enrichment, and we really could use some more datasets to try them on.

I've found the {airways} dataset, and lung adenocarcinoma from {recount3} (as an easy pull). Looking for others. TIA.

#bioinformatics #RnaSeq

Genomique_ENS, 5 months ago to random French

Hello !

We are a Genomics core facility located in the centre of Paris, France, within the Ecole normale supérieure.

✅ We support our collaborators by providing access to high-throughput sequencing, with particular expertise in functional genomics applications in eukaryotes. We propose transcriptomics: #RNAseq (low input, short-read and long-read, single-cell #scRNA-seq).

thomas_sandmann, 8 months ago to til

Today I learned how to store gene expression data in (multiple) parquet files, and query them as a single dataset from R with the {arrow}, {duckdb} or {sparklyr} packages. I am amazed by {duckdb}'s speed 🚀 - even on my laptop! Here's a blog post with what I learned: https://tomsing1.github.io/blog/posts/parquet/ #TIL #RStats #duckdb #parquet #spark #compbio #rnaseq