New ribozyme can make molecules accessible for in living cells phys.org/news/2023-09-ribozyme

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

#RNA #clickchemistry #rnaseq #sequencing

Last updated 1 year ago

Thomas Sandmann · @thomas_sandmann
366 followers · 1147 posts · Server genomic.social

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 ๐Ÿš€ - even on my laptop! Here's a blog post with what I learned: tomsing1.github.io/blog/posts/

#til #RStats #duckdb #parquet #spark #compBio #rnaseq

Last updated 1 year ago

FlyBase · @FlyBase
77 followers · 22 posts · Server mstdn.science

MicroRNA Gene Reports now display high-throughput RNA-Seq expression data from FlyAtlas2 (Leader et al 2018 flybase.org/reports/FBrf023774) & meta-analysis of Lai lab experiments (flybase.org/reports/FBrf023098).
These datasets are presented in the High-Throughput Expression Data sub-section of the gene reportโ€™s Expression Data section; data for any given microRNA gene can be downloaded.

#rnaseq

Last updated 1 year ago

TanyaAneichyk · @tanyaaneichyk
57 followers · 47 posts · Server genomic.social

What is an industry-academia gap? It's when every 5th presentation in a conference is about a new method for to stratify 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)

#rnaseq #cancer

Last updated 1 year ago

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

microbiomejournal.biomedcentra

#rnaseq #metatranscriptomics #microbes #bioinformatics #pipeline

Last updated 1 year ago

Cosmin Saveanu · @cosminribo
135 followers · 501 posts · Server framapiaf.org
Bgee database · @bgeedb
45 followers · 53 posts · Server genomic.social

Videos of the course โ€œGene expression made useful easily: tools and database of Bgeeโ€ (Frederic Bastian & @marcrr):
Introduction of trainers youtube.com/watch?v=vjrTq0fGCT
Overview of Bgee youtube.com/watch?v=x8Fypkwlmu
Data integration in Bgee youtube.com/watch?v=hTx4fk77DZ
Bgee data access youtube.com/watch?v=5cbXWL9quC
Bgee tools youtube.com/watch?v=iUSjT9wDbm

#SIB #biocuration #bioinformatics #rnaseq #singlecell #geneexpression #training

Last updated 1 year ago

Physalia-courses · @PhysaliaCourses
409 followers · 221 posts · Server mas.to

What an incredibly engaging bunch of participants delving into exceptionally cool systems, accompanied by two phenomenal instructors! Our with /@Bioconductor
course was an absolute blast!๐Ÿ™๐Ÿš€

#rstats #rnaseq #singlecell

Last updated 1 year ago

Physalia-courses · @PhysaliaCourses
410 followers · 227 posts · Server mas.to

What an incredibly engaging bunch of participants delving into exceptionally cool systems, accompanied by two phenomenal instructors! Our with /@Bioconductor
course was an absolute blast!๐Ÿ™๐Ÿš€

#rstats #rnaseq #singlecell

Last updated 1 year ago

And this simulation code, shows why one must use use very short seeds when using to map 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)

#rstats #blast #nanopore #transcriptomic #rnaseq

Last updated 1 year ago

CellBioNews · @cellbionews
50 followers · 1199 posts · Server scientificnetwork.de
Bgee database · @bgeedb
46 followers · 41 posts · Server genomic.social

We still have some seats available for the course on:
Gene expression made useful easily: tools and database of Bgee
live-streamed on 26 May 2023
sib.swiss/training/course/2023

#SIB #biocuration #bioinformatics #rnaseq #singlecell #geneexpression #training

Last updated 2 years ago

Bgee database · @bgeedb
45 followers · 35 posts · Server genomic.social

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

#biocuration2023 #biocuration #bioinformatics #rnaseq #SIB

Last updated 2 years ago

Bgee database · @bgeedb
43 followers · 32 posts · Server genomic.social

All of the Bgee team will be at @biocuration2023 this Monday-Wednesday, meet us to discuss bulk & , anatomical and developmental , and how to make data useful.

#biocuration2023 #rnaseq #singlecell #Ontologies #geneexpression #SIB #bioinformatics #biocuration

Last updated 2 years ago

Victor Chano · @vchano
55 followers · 80 posts · Server ecoevo.social

RT @AhmedMoustafa
NCBI just released the count matrices for thousands of RNA-Seq ๐Ÿงฌ experiments on GEO ๐ŸŽ‰ an amazing resource ๐Ÿคฉ ncbiinsights.ncbi.nlm.nih.gov/

#rnaseq #Transcriptomics #bioinformatics #OpenScience #opendata

Last updated 2 years ago

Physalia-courses · @PhysaliaCourses
404 followers · 201 posts · Server mas.to
Martin Smith · @Martinalexsmith
404 followers · 316 posts · Server genomic.social

A substantial base calling quality improvement observed beta testing the RNA004 direct 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

#nanopore #rnaseq

Last updated 2 years ago

Feargal Ryan :rna: · @feargal
263 followers · 189 posts · Server genomic.social

Can confirm the Snapchat AI chat can provide basic analysis code ๐Ÿคฃ

#rnaseq #RStats #bioinformatics #genomics

Last updated 2 years ago

Robert Castelo · @robertclab
98 followers · 371 posts · Server genomic.social
Thomas Sandmann · @thomas_sandmann
287 followers · 583 posts · Server genomic.social

Very cool preprint by Adam P Cribbs's group: "Correcting PCR amplification errors in unique molecular identifiers to generate absolute numbers of sequencing molecules." biorxiv.org/content/10.1101/20 with lots of innovative ideas to a) measure and b) correct PCR induced errors in RNA-seq experiments.

#rnaseq #ngs #singlecells #compBio #illumina #nanopore

Last updated 2 years ago