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KARR-seq reveals cellular higher-order RNA structures and RNA–RNA interactions
RNA fate and function are affected by their structures and interactomes. However, how RNA and RNA-binding proteins (RBPs) assemble into higher-order...
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RNA Sequencing (RNA-seq)
RNA sequencing (or popularly known as RNA-seq) or whole transcriptome shortgun sequencing (WTSS) is a useful next-generation sequencing (NGS)...
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Metatranscriptomic RNA-Seq Data Analysis of Virus-Infected Host Cells
RNA sequencing (RNA-seq)RNA sequencing (RNA-seq) analysis of virus-infected host cells enables researchers to study a wide range of phenomena...
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RNA Preparation and RNA-Seq Bioinformatics for Comparative Transcriptomics
The principal transcriptome analysis is the determination of differentially expressed genes across experimental conditions. For this, the...
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A comprehensive workflow for optimizing RNA-seq data analysis
BackgroundCurrent RNA-seq analysis software for RNA-seq data tends to use similar parameters across different species without considering...
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RNA-clique: a method for computing genetic distances from RNA-seq data
BackgroundAlthough RNA-seq data are traditionally used for quantifying gene expression levels, the same data could be useful in an integrated...
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rMATS-turbo: an efficient and flexible computational tool for alternative splicing analysis of large-scale RNA-seq data
Pre-mRNA alternative splicing is a prevalent mechanism for diversifying eukaryotic transcriptomes and proteomes. Regulated alternative splicing plays...
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Curare and GenExVis: a versatile toolkit for analyzing and visualizing RNA-Seq data
Even though high-throughput transcriptome sequencing is routinely performed in many laboratories, computational analysis of such data remains a...
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Computational Analysis of Single-Cell RNA-Seq Data
Single-cell RNA sequencing (scRNA-seq) is gaining popularity as this allows you to profile a large number of individual cells. However, as the volume...
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Machine learning on alignment features for parent-of-origin classification of simulated hybrid RNA-seq
BackgroundParent-of-origin allele-specific gene expression (ASE) can be detected in interspecies hybrids by virtue of RNA sequence variants between...
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Transcriptome Analysis Using RNA-seq and scRNA-seq
Differential gene expression profile is a powerful tool to identify changes in cell or tissue transcriptomes. It allows understanding complex...
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Decoder-seq enhances mRNA capture efficiency in spatial RNA sequencing
Spatial transcriptomics technologies with high resolution often lack high sensitivity in mRNA detection. Here we report a dendrimeric DNA coordinate...
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Single-cell RNA-seq of maize meiocytes and pollen grains
RNA-sequencing (RNA-seq) provides invaluable knowledge on developmental pathways and the effects of mutant phenotypes. Plant reproductive cells have...
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Bulk and Single-Cell RNA-Seq Analyses for Studies of Spermatogonia
Robust methods have been developed that leverage next-generation sequencing (NGS) to measure abundance of all mRNAs (RNA-seq) in samples as small as...
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A Workflow Guide to RNA-Seq Analysis of Chaperone Function and Beyond
RNA sequencing (RNA-seq) is a powerful method of transcriptional analysis that allows for the sequence identification and quantification of cellular...
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Splice_sim: a nucleotide conversion-enabled RNA-seq simulation and evaluation framework
Nucleotide conversion RNA sequencing techniques interrogate chemical RNA modifications in cellular transcripts, resulting in mismatch-containing...
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scDIOR: single cell RNA-seq data IO software
BackgroundSingle-cell RNA sequencing is becoming a powerful tool to identify cell states, reconstruct developmental trajectories, and deconvolute...
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TORNADO-seq: A Protocol for High-Throughput Targeted RNA-seq-Based Drug Screening in Organoids
Organoids are 3D ex vivo cell aggregates derived from primary tissue and shown to closely recapitulate tissue homeostasis. Organoids deliver certain...
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A sco** review on deep learning for next-generation RNA-Seq. data analysis
In the last decade, transcriptome research adopting next-generation sequencing (NGS) technologies has gathered incredible momentum amongst functional...
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Integrative analysis of Iso-Seq and RNA-seq data reveals transcriptome complexity and differential isoform in skin tissues of different hair length Yak
BackgroundThe hair follicle development process is regulated by sophisticated genes and signaling networks, and the hair grows from the hair...
