Expression and Quantification

Feed Subscription

QuasR – Quantification and annotation of short reads in R

QuasR – Quantification and annotation of short reads in R

QuasR is a package for the integrated analysis of high-throughput sequencing data in R, covering all steps from read preprocessing, alignment and quality control to quantification. QuasR supports different experiment types (including RNA-seq, ChIP-seq and Bis-seq) and analysis variants (e.g. ...

Read More »

A ratiometric-based measure of gene co-expression

A ratiometric-based measure of gene co-expression

Gene co-expression analysis has previously been based on measures that include correlation coefficients and mutual information, as well as newcomers such as MIC. These measures depend primarily on the degree of association between the RNA levels of two genes and ...

Read More »

miRNA Temporal Analyzer (mirnaTA) – for identifying differentially expressed microRNAs in temporal studies using normal quantile transformation

miRNA Temporal Analyzer (mirnaTA) – for identifying differentially expressed microRNAs in temporal studies using normal quantile transformation

Many open-source bioinformatics tools to identify existing and/or discover novel miRNAs in next-generation sequencing (NGS) reads have become available. While miRNA identification and discovery tools are significantly improved, the development of miRNA differential expression analysis tools, especially in temporal studies, ...

Read More »

Rcount – simple and flexible RNA-Seq read counting

Rcount – simple and flexible RNA-Seq read counting

Analysis of differential gene expression by RNA sequencing (RNA-Seq) is frequently done using feature counts, i.e. the number of reads mapping to a gene. However, commonly used count algorithms (e.g. HTSeq) do not address the problem of reads aligning with ...

Read More »
Scroll To Top