PotatoRTD and TomatoRTD: comprehensive reference transcript datasets for accurate transcriptome analysis and isoform discovery
Genes can produce more than one RNA transcript, allowing a single gene to generate different versions of RNA that may ultimately produce different proteins. Accurately identifying these transcript variants, known as isoforms, is important for understanding how genes function ...
Bonsai reconstructs tree representations for distortion-free visualization and exploration of high-dimensional data
Modern biology research can now generate valuable data on an unprecedented scale. But there is one major obstacle: making sense of these complex high-dimensional datasets. A team at the University of Basel, Switzerland, has developed a new tool that ...
MiRQuery – a user-friendly web app for the interactive analysis and visualization of microRNA sequencing data
MicroRNAs, or miRNAs, are small RNA molecules that help control how genes are expressed. Rather than coding for proteins themselves, miRNAs can bind to messenger RNAs, or mRNAs, and reduce the amount of protein those messages produce. Because a ...
Tidesurf improves RNA velocity analysis for modern single-cell RNA sequencing
Single-cell RNA sequencing allows researchers to examine gene activity in thousands of individual cells. While a conventional analysis provides a snapshot of each cell at the time it was collected, researchers often want to understand something more dynamic, where ...
New RNA sequencing model improves sequencing depth planning for UMI transcriptomics
RNA sequencing experiments depend on collecting enough sequencing data to reliably measure the RNA molecules present in a sample. Sequencing too little can cause researchers to miss important molecules, while sequencing more than necessary increases costs without providing equivalent ...
MitoClipSplice – machine learning improves RNA sequencing analysis of mitochondrial RNA processing
Mitochondria are best known for producing energy for cells, but they also contain their own DNA and produce their own RNA molecules. These mitochondrial RNAs must be carefully processed before they can function properly. Errors in this processing have ...
Machine learning improves RNA sequencing annotation of active genes
Understanding which parts of the genome are active is essential for studying how cells develop, specialize, and respond to disease. RNA sequencing provides researchers with information about gene activity, but turning sequencing signals into accurate maps of genes and ...
NextLongIso – a comprehensive Nextflow pipeline for multi-dimensional long-read RNA-seq analysis
Long-read RNA sequencing has given researchers a powerful way to examine the full range of RNA molecules produced by cells. Technologies from Pacific Biosciences, or PacBio, and Oxford Nanopore Technologies, or ONT, can sequence much longer stretches of RNA ...
ISAtools improves full-length RNA isoform analysis from long-read RNA sequencing
Long-read RNA sequencing has made it possible for researchers to study complete RNA molecules instead of assembling them from many short fragments. This provides a much clearer picture of how genes produce different RNA isoforms through alternative splicing. However, ...
Deep learning improves cell cycle prediction from single-cell RNA sequencing
Single-cell RNA sequencing has given researchers an unprecedented view of how individual cells behave. One important piece of information scientists often want to know is where each cell is in the cell cycle, the series of stages that cells ...
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Most Shared Posts
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- Upcoming Workshop – Advanced Topics in Single Cell RNA-Seq Analysis: Multiomics ATAC-Seq & RNA-Seq
- BAP-seq – bioorthogonal masked acylating agents for proximity-dependent RNA labelling
- Single-cell RNA-seq of the rare virosphere reveals the native hosts of giant viruses in the marine environment
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