Recent single-cell RNA-seq protocols based on droplet microfluidics use massively multiplexed barcoding to enable simultaneous measurements of transcriptomes for thousands of individual cells. The increasing complexity of such data creates challenges for subsequent computational processing...
Read More »Potential pitfalls in analyzing and quantifying lowly-expressed genes and small RNAs with alignment-free pipelines
Alignment-free RNA quantification tools have significantly increased the speed of RNA-seq analysis. However, it is unclear whether these state-of-the-art RNA-seq analysis pipelines can quantify...
Read More »SAVER – gene expression recovery for single-cell RNA sequencing
In single-cell RNA sequencing (scRNA-seq) studies, only a small fraction of the transcripts present in each cell are sequenced. This leads to unreliable...
Read More »Gene expression distribution deconvolution in single-cell RNA sequencing
Single-cell RNA sequencing (scRNA-seq) enables the quantification of each gene’s expression distribution across cells, thus allowing the assessment of the...
Read More »Researchers develop a better method to compare gene expression in single cells
St. Jude Children’s Research Hospital investigators have developed a software package to help identify biomarkers that differentiate between cell...
Read More »FADU – a feature counting tool for prokaryotic RNA-Seq analysis
The major algorithms for quantifying transcriptomics data for differential gene expression analysis were designed for analyzing data from human or human-like genomes, specifically those with single...
Read More »New tool enables big-scale analysis of single-cell RNA-Seq data
New research led by Holger Heyn at the Centro Nacional de Análisis Genómico of the Centre for Genomic Regulation (CNAG-CRG), presents a sophisticated computational framework to analyze single-cell gene expression levels, scalable to process...
Read More »miR-MaGiC improves quantification accuracy for small RNA-seq
Many tools have been developed to profile microRNA (miRNA) expression from small RNA-seq data. These tools must contend with several issues: the small...
Read More »Bias correction for single cell RNA-seq quantification
With rapid technical advances, single cell RNA-seq (scRNA-seq) has been used to detect cell subtypes exhibiting distinct gene expression profiles and to trace cell transitions in development and disease...
Read More »DEsingle – detecting three types of differential expression in single-cell RNA-seq data
The excessive amount of zeros in single-cell RNA-seq data include “real” zeros due to the on-off nature of gene transcription in single cells and “dropout”...
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