New ribozyme can make #RNA molecules accessible for #clickchemistry in living cells https://phys.org/news/2023-09-ribozyme-rna-molecules-accessible-click.html

Damn this is hot - imagine the possibilities for single sell #RNAseq @nanopore
#sequencing

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

MicroRNA Gene Reports now display high-throughput RNA-Seq expression data from FlyAtlas2 (Leader et al 2018 http://flybase.org/reports/FBrf0237746) & meta-analysis of Lai lab experiments (http://flybase.org/reports/FBrf0230987).
These datasets are presented in the High-Throughput Expression Data sub-section of the gene report’s Expression Data section; data for any given microRNA gene can be downloaded.
#RNAseq

What is an industry-academia gap? It's when every 5th presentation in a conference is about a new method for #RNAseq to stratify #cancer patients, but only 0.0X% (!) of patients ever get RNAseq test (and even those are to support a proposal to develop yet another RNAseq method)

"**MetaPro: a scalable and reproducible data processing and analysis pipeline for metatranscriptomic investigation of microbial communities"**

https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-023-01562-6

#RNAseq #metatranscriptomics #microbes #bioinformatics #pipeline

For #RNA sequencing results data analysis, a rich alternative to Cluster3 (http://bonsai.hgc.jp/~mdehoon/software/cluster/software.htm) and the no longer maintained Java TreeView (https://sourceforge.net/projects/jtreeview/) is #Phantasus.

An evolution of Morpheus (https://software.broadinstitute.org/morpheus/), Phantasus can be used online (https://artyomovlab.wustl.edu/phantasus/) or as an R package via Bioconductor (https://bioconductor.org/packages/release/bioc/vignettes/phantasus/inst/doc/phantasus-tutorial.html)

#rstats #rnaseq #datavisualization

Videos of the #SIB course “Gene expression made useful easily: tools and database of Bgee” (Frederic Bastian & @marcrr):
Introduction of trainers https://www.youtube.com/watch?v=vjrTq0fGCTk
Overview of Bgee https://www.youtube.com/watch?v=x8Fypkwlmuw
Data integration in Bgee https://www.youtube.com/watch?v=hTx4fk77DZ4
Bgee data access https://www.youtube.com/watch?v=5cbXWL9quCA
Bgee tools https://www.youtube.com/watch?v=iUSjT9wDbmU
#biocuration #bioinformatics #RNAseq #SingleCell #GeneExpression #training

What an incredibly engaging bunch of participants delving into exceptionally cool systems, accompanied by two phenomenal instructors! Our #singlecell #RNASeq with #rstats/@Bioconductor
course was an absolute blast!🙏🚀

What an incredibly engaging bunch of participants delving into exceptionally cool systems, accompanied by two phenomenal instructors! Our #singlecell #RNASeq with #rstats/@Bioconductor
course was an absolute blast!🙏🚀

And this simulation #rstats code, shows why one must use use very short seeds when using #blast to map #nanopore #transcriptomic #RNAseq data (Q10 quality scores are not unheard of, in such datasets).

Take home message, one has got to work for their database searches for long read platforms
(R code in the alt description)

New #RNAseq, #metabolomics protocol offers more efficient extraction that maintains #data integrity.

#proteomics #transcriptomics

https://phys.org/news/2023-05-rna-seq-metabolomics-protocol-efficient.html

We still have some seats available for the #SIB course on:
Gene expression made useful easily: tools and database of Bgee
live-streamed on 26 May 2023
https://www.sib.swiss/training/course/20230526_BGEEL
#biocuration #bioinformatics #RNAseq #SingleCell #GeneExpression #training

Hi #biocuration2023 @biocuration2023! All the team is here, and we invite you to explore our newly released pages to browse and select annotated raw data https://bgee.org/search/raw-data and gene expression calls https://bgee.org/search/expression-calls #biocuration #bioinformatics #RNAseq #SIB

All of the Bgee team will be at #biocuration2023 @biocuration2023 this Monday-Wednesday, meet us to discuss #RNAseq bulk & #singlecell, anatomical and developmental #ontologies, and how to make #GeneExpression data useful. #SIB #bioinformatics #biocuration

RT @AhmedMoustafa
NCBI just released the count matrices for thousands of RNA-Seq 🧬 experiments on GEO 🎉 an amazing resource 🤩 #RNASeq #Transcriptomics #Bioinformatics #OpenScience #OpenData https://ncbiinsights.ncbi.nlm.nih.gov/2023/04/19/human-rna-seq-geo/

🥁There are still a few seats available for some of our courses in May and June!
#Python #Rstats #singlecell #RNAseq #transposableElements #Metagenomics #GLMs #rspatial #Genomics #DataScience

A substantial base calling quality improvement observed beta testing the #nanopore RNA004 direct #rnaseq protocol.
This is empirical data from commercial, multi-tissue RNA after poly(A) selection, aligned to hg38 with miminap2 -a -x splice --secondary=no.
Alignments (especially at splice junctions) look exceptional; I could see potential RNA modifications directly from basecalling output as mutations in IGV

Can confirm the Snapchat AI chat can provide basic #RNASeq analysis code 🤣

#rstats #bioinformatics #genomics

RT @hagentilgner
Andrey & Alla put out the newest version of Isoquant
(https://www.nature.com/articles/s41587-022-01565-y); Results unchanged but memory usage down ~10-15 fold and disk usage down ~5-fold;
https://github.com/ablab/IsoQuant/releases/tag/v3.2.0
#LongRead #RNA @iRnaCosi
#nanopore #pacbio #genomics
#Transcripomics #RNAseq #Splicing

Very cool preprint by Adam P Cribbs's group: "Correcting PCR amplification errors in unique molecular identifiers to generate absolute numbers of sequencing molecules." https://www.biorxiv.org/content/10.1101/2023.04.06.535911v1 with lots of innovative ideas to a) measure and b) correct PCR induced errors in RNA-seq experiments. #rnaseq #ngs #singlecells #compbio #illumina #nanopore