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Xanthi - Lida Katopodi - Student • Master's degree
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Xanthi - Lida Katopodi

Student • Master's degree

National Technical University of Athens • Athens, Greece

Transposable Elements

tools for studying transposable elements

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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…

LTRharvest
Desktop

LTRharvest

An efficient software tool delivering high quality annotation of LTR…

An efficient software tool delivering high quality annotation of LTR retrotransposons. LTRharvest can, for example, process the largest human chromosome in approx. 8 minutes on a Linux PC with 4 GB…

RepeatExplorer
Web

RepeatExplorer

A collection of software tools for characterization of repetitive elements,…

A collection of software tools for characterization of repetitive elements, which is accessible via web interface. A key component of the server is the computational pipeline using a graph-based…

VisualTE
Desktop

VisualTE

A JAVA stand-alone graphical interface that allows users to visualize and…

A JAVA stand-alone graphical interface that allows users to visualize and analyze all occurrences of transposable element families in annotated genomes. VisualTE reads and extracts transposable…

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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…

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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…

TEtools
Desktop

transposable elements tools TEtools

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.…

TEclass
Desktop
Web

TEclass

Classifies unknown transposable element (TE) consensus sequences into four…

Classifies unknown transposable element (TE) consensus sequences into four categories, according to their mechanism of transposition: DNA transposons, Long Terminal Repeats (LTRs), Long Interspersed…

EnHERV
Web

Human Endogenous Retrovirus Enrichment Tool EnHERV

Provides the identified endogenous retrovirus repetitive sequences from Repbase…

Provides the identified endogenous retrovirus repetitive sequences from Repbase Update that are present in the human genome. EnHERV offers an enrichment analysis function that allows users to perform…

REannotate
Desktop

Repetitive Element re-annotation REannotate

Processes REPEAT MASKER annotation for automated i) defragmentation of…

Processes REPEAT MASKER annotation for automated i) defragmentation of dispersed repetitive elements, ii) resolution of the temporal order of insertions in clusters of nested elements, and iii)…

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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…

STEAK
Desktop

Specific Transposable Element Aligner (HERV-K) STEAK

Detects integrations of any sort in high-throughput sequencing (HTS) data.…

Detects integrations of any sort in high-throughput sequencing (HTS) data. STEAK was built for validating and discovering transposable element (TE) and retroviral integrations in a variety of HTS…

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SalmonTE
Desktop

SalmonTE

Offers an approach for quantifying transposable elements (TEs) from next…

Offers an approach for quantifying transposable elements (TEs) from next generation sequencing (NGS) data. SalmonTE performs its analysis in three mains steps: first; it builds a mapping index from…

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REPET
Desktop

REPET

Serves for the association of all the meta-data obtained for a given…

Serves for the association of all the meta-data obtained for a given transposable element (TE) family. REPET is a program designed to improve tractability by: (1) interacting with MySQL tables at…

ConTExt
Desktop

ConTExt

Detects a wide range of structural variation within repetitive sequence…

Detects a wide range of structural variation within repetitive sequence including tandem elements of transposable elements (TE). ConTExt intends to establish the repeat-family from which the read…

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TEcandidates
Desktop

TEcandidates

Reports candidate transposable elements (TEs) to be considered in downstream…

Reports candidate transposable elements (TEs) to be considered in downstream expression analysis. TEcandidates is a pipeline based on de novo transcriptome assembly. It also includes a modified…

ERVcaller
Desktop

Endogenous RetroViruses ERVcaller

Locates and genotypes transposable elements (TEs) in the human genome with a…

Locates and genotypes transposable elements (TEs) in the human genome with a focus on non-reference unfixed endogenous retroviruses (ERVs). ERVcaller is able to pinpoint TE insertions of various…

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Telescope
Desktop

Telescope

Provides an estimation of transposable elements (TE) expression resolved to…

Provides an estimation of transposable elements (TE) expression resolved to specific genomic locations. Telescope addresses uncertainty in fragment assignment by reassigning ambiguously mapped…