BioconductorMay 22, 2023

🎓 #biocsmorgasbord! starts today! New workshop added ✨ Learn "Introduction to SpatialOmicsOverlay" with the #NanoString #GeoMx Team 🧬💻

📅 May 22-26
➡️ https://gallantries.github.io/video-library/modules/bioconductor
#Bioinformatics #RStats #SpatialOmics

Bioconductor R analyses

Eli Roberson (he/him)Mar 28, 2023
Adventures in #GeoMx data analysis. The available tools are fine for loading info from a nanostring software processed DSP file. They suggest some segment (tissue piece) QC based on the area of the slide and number of trimmed reads, etc. Also fine.
Eli Roberson (he/him)Feb 17, 2023

#bioinformatics #genomics

Do I know anyone working with #nanostring #GeoMx? This is the first GeoMx dataset we've received.

There appear to be several packages for upfront QC and transfer to Seurat of the *processed* data in R. But I wasn't sure if there was anyone with recommendations for taking FASTQ to DCC. The instructions for installing and running the Nanostring pipeline don't seem very friendly to pure command-line interaction on a local server of in self-contained docker image.