Expression and Quantification

Differential expression analysis of RNA sequencing (RNA-seq) data typically relies on reconstructing transcripts or counting reads that overlap known gene structures. Previously, researchers at Johns Hopkins Bloomberg School of Public Health introduced an intermediate approach called differentially expressed region (DER) finder ...

Transcriptomes are routinely compared in term of a list of differentially expressed genes followed by functional enrichment analysis. Due to the technology limitations of microarray, the molecular mechanisms of differential expression is poorly understood. Using RNA-seq data, researchers at Wayne ...

High-throughput RNA-sequencing (RNA-seq) technology provides an attractive platform for gene expression analysis. In many experimental settings, RNA-seq read counts are measured from matched samples or taken from the same subject under multiple treatment conditions. The induced correlation therefore should be ...

EMASE is a software program written in Python to quantify allele-specific expression and gene expression simultaneously from RNA-seq data. EMASE takes in the diploid transcriptome alignment BAM file and GTF file as inputs and estimates expression abundance for each isoforms ...

limma is an R/Bioconductor software package that provides an integrated solution for analysing data from gene expression experiments. It contains rich features for handling complex experimental designs and for information borrowing to overcome the problem of small sample sizes. Over ...

RNA-seq is a powerful tool for gene expression profiling and differential expression analysis. Its power depends on sequencing depth which limits its high-throughput potential, with 10-15 million reads considered as optimal balance between quality of differential expression calling and cost ...

With the advances in high-throughput DNA sequencing technologies, RNA-seq has rapidly emerged as a powerful tool for the quantitative analysis of gene expression and transcript variant discovery. In comparative experiments, differential expression analysis is commonly performed on RNA-seq data to ...

High-throughput RNA sequencing (RNA-Seq) enables quantification and identification of transcripts at single-base resolution. Recently, longer sequence reads become available thanks to the development of new types of sequencing technologies as well as improvements in chemical reagents for the Next Generation ...

Recent studies on single cells and population transcriptomics have revealed striking differences in global gene expression distributions. Single cells display highly variable expressions between cells, while cell populations present deterministic global patterns. The mechanisms governing the reduction of transcriptome-wide variability ...

Mix-Square is a software tool for the accurate quantification of transcript isoforms for RNA-Seq data generated from NGS Lexogen is seeking participants for an early access program for this novel algorithm Mix-Square, a new algorithm for accurate RNA-seq data analysis ...