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Transposable element expression software tools | RNA sequencing data analysis

Most RNA-seq data analysis software packages are not designed to handle the complexities involved in properly apportioning short sequencing reads to highly repetitive regions of the genome. These regions are often occupied by transposable elements…
TEtools
Desktop

TEtools transposable elements tools

Provides analysis of TE expression. TEtools takes into account the TE sequence…

Provides analysis of TE expression. TEtools takes into account the TE sequence diversity of the genome. It can be applied to unannotated or unassembled genomes and is freely available under the GPL3.…

G T A T C G C T A
LIONS
Desktop

LIONS

Quantifies the contribution of Transposable Elements (TE) promoters to the…

Quantifies the contribution of Transposable Elements (TE) promoters to the transcriptome from RNA-seq data. LIONS can annotate the intersection between the assembly, a reference gene set and repeat…

G T A T C G C T A
TEToolkit
Desktop

TEToolkit

A method and software package for including both gene- and TE-associated…

A method and software package for including both gene- and TE-associated ambiguously mapped reads in differential expression analysis. TEtranscripts shows improved recovery of TE transcripts over…

G T A T C G C T A
piPipes
Desktop

piPipes

A coordinated set of pipelines, 'piPipes', to analyze piRNA and…

A coordinated set of pipelines, 'piPipes', to analyze piRNA and transposon-derived RNAs from a variety of high-throughput sequencing libraries, including small RNA, RNA, degradome or…

G T A T C G C T A
RepEnrich
Desktop

RepEnrich

A computational method to study genome-wide transcriptional regulation of…

A computational method to study genome-wide transcriptional regulation of repetitive elements. RepEnrich supports analysis for ChIP-seq and RNA-seq for any organism where a reference genome and…

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