Latest updates for Rna-Seq Benchmarking

Fresh curated links around RNA-seq benchmarking are collected here so marketers can spot useful updates and turn timely ideas into posts faster.

Recent items include:

  • Benchmarking RNA sequencing for more accurate alternative splicing analysis
  • A real-data approach to evaluating RNA transcript analysis methods
  • An end-to-end computational framework for “Record-seq” transcriptional recording data

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rna-seqblog.com /1 month ago

Benchmarking RNA sequencing for more accurate alternative splicing analysis

RNA sequencing benchmarking across 42 laboratories identifies data quality, sequencing depth, and bioinformatics choices that improve alternative splicing and isoform analysis...

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rna-seqblog.com /1 month ago

A real-data approach to evaluating RNA transcript analysis methods

RNA sequencing data provide a real-world framework for comparing differential transcript usage methods across bulk, single-cell, spatial, long-read, and short-read transcriptomics....

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rna-seqblog.com /1 month ago

An end-to-end computational framework for “Record-seq” transcriptional recording data

A new framework adapts RNA sequencing analysis for Record-seq, improving spacer extraction, transcription-unit quantification, normalization, differential expression, and modeling...

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rna-seqblog.com /1 week ago

Bulk RNA-seq Analysis: A Complete Beginner’s Guide

Bulk RNA sequencing helps researchers identify gene expression patterns associated with differences in drug response, supporting biomarker discovery and personalized medicine while...

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rna-seqblog.com /6 days ago

RNAmel simplifies RNA sequencing data analysis with a reproducible, integrated platform

RNAmel integrates RNA sequencing data analysis, gene expression profiling, pathway enrichment and visualization into a reproducible platform that simplifies...

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journals.plos.org /1 month ago

Not every gene is special: Modelling scale controls the false discovery rate when analysing high-throughput sequencing d...

by Scott J. Dos Santos, Andreea C. Murariu, Justin D. Silverman, Gregory B. Gloor Differential expression/abundance analyses are commonplace in studies employing high-throughput s...

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rna-seqblog.com /2 weeks ago

Nanopore direct RNA sequencing reveals the challenges of detecting RNA modifications

Direct RNA sequencing with Oxford Nanopore technology enables detection of RNA modifications, but benchmarking reveals substantial differences in accuracy among current computation...

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rna-seqblog.com /3 weeks ago

The Human RNome Project Consortium seeks to publish first-ever complete sequence of the body’s RNA

RNA sequencing efforts from the Human RNome Project aim to build a comprehensive reference of human RNA sequences, isoforms, processing states and chemical modifications...

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rna-seqblog.com /1 month ago

PotatoRTD and TomatoRTD: comprehensive reference transcript datasets for accurate transcriptome analysis and isoform dis...

RNA sequencing and Iso-Seq improve potato and tomato transcript annotations, revealing additional isoforms and enabling more accurate analysis of gene expression and alternative sp...

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rna-seqblog.com /2 weeks ago

How should biological replicates be handled in long-read RNA sequencing?

Long-read RNA sequencing analysis shows that handling biological replicates differently can influence transcript reconstruction and the discovery of novel RNA isoforms...

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rna-seqblog.com /3 weeks ago

scFlowReport brings multiple single-cell RNA sequencing analyses into one workflow

RNA sequencing analysis with scFlowReport integrates differential expression, pathway enrichment, regulatory networks and cell communication into a reproducible workflow for compar...

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rna-seqblog.com /2 weeks ago

DeCoRE – a computational method to resolve RNA structural heterogeneity from RNA structure probing data by direct RNA se...

Direct RNA sequencing with DeCoRE reveals alternative RNA structures and folding dynamics at single-nucleotide resolution, providing a detailed view of transcript-level structural....

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rna-seqblog.com /1 week ago

RiboBA improves detection of hidden protein-coding regions using ribosome profiling

RiboBA improves ribosome profiling and RNA sequencing analysis by correcting experimental biases, enabling more accurate identification of hidden protein-coding regions and transla...

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rna-seqblog.com /1 month ago

Eclipsebio expands its RNA characterization capabilities with multi-attribute nanopore-based sequencing assay eSTRAND RN...

Eclipsebio’s eSTRAND RNA QC uses direct RNA sequencing to measure multiple RNA quality attributes, including identity, poly(A) tails...

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rna-seqblog.com /4 weeks ago

Eclipsebio expands its RNA characterization capabilities with multi-attribute nanopore-based sequencing assay eSTRAND RN...

RNA sequencing with eSTRAND RNA QC enables simultaneous measurement of RNA identity, poly(A) tail length, capping efficiency, fragmentation hotspots, and dsRNA...

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rna-seqblog.com /1 month ago

Ultrafast and reference-free sequence discovery in single-cell data

Malva enables ultrafast, reference-free searches across massive single-cell RNA sequencing datasets for mutations, splice junctions, pathogens, transcripts, and other sequence-leve...

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rna-seqblog.com /1 month ago

Short-read RNA-seq yields lower estimates of A-to-I RNA editing levels than long-read cDNA sequencing

RNA sequencing comparisons show that short reads can underestimate A-to-I RNA editing, while long-read sequencing provides more accurate measurements through improved genomic align...

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rna-seqblog.com /3 weeks ago

ResolVI improves accuracy in spatial transcriptomics analysis

ResolVI improves spatial RNA sequencing analysis by correcting RNA assignment errors and technical variation, helping researchers distinguish cell states and detect subtle gene exp...

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journals.plos.org /4 weeks ago

Structural Variant benchmarking frameworks: Parameterization, matching logic, and evaluation assumptions presented throu...

by Gamze Maden, Mehmet Baysan, Nizamettin Aydın Structural Variants (SVs) constitute a significant yet complicated class of genomic changes. Due to their imprecise breakpoints, v...

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rna-seqblog.com /1 month ago

scLS – a computationally efficient differentially expressed gene detection algorithm

A new RNA sequencing analysis method uses the Lomb-Scargle periodogram to efficiently identify genes associated with pseudotime across complex single-cell trajectories...

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rna-seqblog.com /1 week ago

GARAGE improves rare cell detection in single-cell RNA sequencing analysis using AI

GARAGE uses artificial intelligence to generate realistic single-cell RNA sequencing data, improving rare cell representation, gene selection and cell clustering in complex biologi...

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rna-seqblog.com /1 month ago

ExoShorkie – predicting RNA-seq coverage of exogenous genomes in yeast by transfer learning

ExoShorkie uses RNA sequencing data and transfer learning to predict expression from exogenous DNA, supporting more accurate gene-regulation models and synthetic biology...

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rna-seqblog.com /3 days ago

Ribosome profiling reveals shared patterns in ribosome diversity and collisions

Researchers analyzed ribosomal RNA sequencing fragments to identify shared patterns of ribosome heterogeneity and collisions, improving computational detection of changes in protei...

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rna-seqblog.com /3 weeks ago

Therna Biosciences Releases Chronos, the Data Engine Behind its AI RNA Biologist

RNA sequencing with Therna’s Chronos platform measures millions of RNA behaviors across diverse human cell types, creating large datasets for modeling expression, stability a...

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rna-seqblog.com

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