Article

GeneTEFlow: A Nextflow-based pipeline for analysing gene and transposable elements expression from RNA-Seq data

2020-04-28

Abstract excerpt

Transposable elements (TEs) are mobile genetic elements in eukaryotic genomes. Recent research highlights the important role of TEs in the embryogenesis, neurodevelopment, and immune functions. However, there is a lack of a one-stop and easy to use computational pipeline for expression analysis of both genes and locus-specific TEs from RNA-Seq data. Here, we present GeneTEFlow, a fully automated, reproducible and...

Topics

Open a Topic to create a Post that cites this publication.

Identifiers and source

Literature Corpus work: b69ef336-e007-5f4d-9f75-1ee04a461a38
DOI: 10.1101/2020.04.28.065862

Open publication

Related research

Semantic proximity does not establish scientific evidence.

Click a neighbor to travelStep 1 · 12 closest

GeneTEFlow: A Nextflow-based pipeline for analysing gene and transposable elements expression from RNA-Seq dataDOI 10.1101/2020.04.28.065862Read

TEITbase: a database for transposable element (TE)-initiated transcripts in human cancersSemantic proximity Read

PERREO: An integrated pipeline for repetitive elements analysis enables the repeatome expression profiling in cancerSemantic proximity Read

TEscape: Defining the human transposable element transcriptome using multiplatform long-read sequencingSemantic proximity Read

A standalone software platform for the interactive management and pre-processing of ATAC-seq samplesSemantic proximity Read

Benchmarking computational tools for locus-specific analysis of transposable elements in single-cell RNA-seq datasetsSemantic proximity Read

FREDDIE: A comprehensive tool for detecting exonization of retrotransposable elements in short and long RNA sequencing dataSemantic proximity Read

TransXplorer: an automated translational discovery platform for RNA-seq dataSemantic proximity Read

Viewing RNA-seq data on the entire human genomeSemantic proximity Read

TEDEdb: a large-scale resource and multi-cohort analysis of transposable element differential expression in cancerSemantic proximity Read

SQuIRE: Software for Quantifying Interspersed Repeat ElementsSemantic proximity Read

TransAtlasDB: an integrated database connecting expression data, metadata and variants.Semantic proximity Read

<tt>recount</tt> : A large-scale resource of analysis-ready RNA-seq expression dataSemantic proximity Read