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 ...
DeepSAP – improved RNA-seq alignment by integrating transcriptome guidance with transformer-based splice junction scoring
RNA sequencing (RNA-seq) has opened up new frontiers in our understanding of gene expression and the complexities of how genes are regulated. One of the most significant breakthroughs in this field is the ability to examine how RNA is ...
New AI tool pinpoints gene splicing with unmatched precision
A recent innovation from Johns Hopkins researchers enables deeper insights into gene function and disease-linked mutations Johns Hopkins researchers have developed a powerful new AI tool called Splam that can identify where splicing occurs in genes—an advance that could help scientists ...
nf-rnaSeqCount – a Nextflow pipeline for obtaining raw read counts from RNA-seq data
The rate of raw sequence production through Next-Generation Sequencing (NGS) has been growing exponentially due to improved technology and reduced costs. This has enabled researchers to answer many biological questions through "multi-omics"...
Characterization and sequence mapping of large RNA and mRNA therapeutics using mass spectrometry
Large RNA including mRNA (mRNA) has emerged as an important new class of therapeutics. Recently, this has been demonstrated by two highly efficacious vaccines based on mRNA sequences encoding for a modified version of the SARS-CoV-2 spike protein. There is ...
Enhanced recovery of single-cell RNA-sequencing reads for missing gene expression data
Droplet-based 3’ single-cell RNA-sequencing (scRNA-seq) methods have proved transformational in characterizing cellular diversity and generating valuable hypotheses throughout biology. Researchers from the University of Texas Southwestern Medical...
Dictionary learning for integrative, multimodal, and scalable single-cell analysis
Mapping single-cell sequencing profiles to comprehensive reference datasets represents a powerful alternative to unsupervised analysis. Reference datasets, however, are predominantly constructed from single-cell RNA-seq data, and cannot...
MGcount – a total RNA-seq quantification tool to address multi-mapping and multi-overlapping alignments ambiguity in non-coding transcripts
Total-RNA sequencing (total-RNA-seq) allows the simultaneous study of both the coding and the non-coding transcriptome. Yet, computational pipelines...
LR-Split-seq – mapping and modeling the genomic basis of differential RNA isoform expression at single-cell resolution
Alternative RNA isoforms are defined by promoter choice, alternative splicing, and polyA site selection. Although differential isoform expression is known to play a large regulatory role in eukaryotes, it has proved challenging to study with standard short-read RNA-seq because of ...
CoCo – RNA-seq Read Assignment Correction for Nested Genes and Multimapped Reads
Next generation sequencing techiques revolutionized the study of RNA expression by permitting whole transcriptome analysis. However, sequencing reads generated from nested and multi-copy genes are often either misassigned or discarded, which greatly reduces both quantification accuracy and gene coverage. Here ...
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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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