Galaxy

PEA-m6A: an ensemble learning framework for accurately predicting N6-methyladenosine modifications in plants

N6-methyladenosine (m6A), which is the mostly prevalent modification in eukaryotic mRNAs, is involved in gene expression regulation and many RNA metabolism processes. Accurate prediction of m6A modification is important for understanding its …

Interactive Web-based Annotation of Plant MicroRNAs with iwa-miRNA

MicroRNAs (miRNAs) are important regulators of gene expression. The large-scale detection and profiling of miRNAs has accelerated with the development of high-throughput small RNA sequencing (sRNA-Seq) techniques and bioinformatics tools. However, …

iwa-RNA

Interactive Web-based Annotation of Plant MicroRNAs with iwa-miRNA

deepEA

deepEA a containerized web server for interactive analysis of epitranscriptome sequencing data

deepEA: a containerized web server for interactive analysis of epitranscriptome sequencing data

RNA molecules are decorated with a variety of chemical modifications, which make up an epitranscriptome that extensively regulates gene expression and biological processes. With the recent development of high-throughput experimental technologies, …

deepTS

Exploring transcriptional switches from pairwise, temporal, and population RNA-Seq data using deepTS

Exploring transcriptional switches from pairwise, temporal, and population RNA-Seq data using deepTS

Transcriptional switch (TS) is a widely observed phenomenon caused by changes in the relative expression of transcripts from the same gene, in spatial, temporal, or other dimensions. TS has been associated with human diseases, plant development, and …

CAFU

A bioinformatics framework for comprehensive assembly and functional annotation

CAFU: a Galaxy framework for exploring unmapped RNA-Seq data

A widely used approach in transcriptome analysis is the alignment of short reads to a reference genome. However, owing to the deficiencies of specially designed analytical systems, short reads unmapped to the genome sequence are usually ignored, …