transposable-elements

There are 8 repositories under transposable-elements topic.

• oushujun / EDTA

  Extensive de-novo TE Annotator

  benchmarkinggenome-annotationpipelinetransposable-elements
  Language:Perl 313
• EarlGrey

  TobyBaril / EarlGrey

  Earl Grey: A fully automated TE curation and annotation pipeline

  bioinformaticsgenomicstransposable-elementsgenome-annotationgenome-analysiste-annotations
  Language:Python 117

• parklab / xTea

  Comprehensive TE insertion identification with WGS/WES data from multiple sequencing technics

  transposable-elementslinked-readsilluminananoporepacbiomobile-element-insertion
  Language:Python 86

• hyunhwan-jeong / SalmonTE

  SalmonTE is an ultra-Fast and Scalable Quantification Pipeline of Transpose Element (TE) Abundances

  pipelinengs-analysistransposable-elementssalmon
  Language:Jupyter Notebook 79

• clemgoub / dnaPipeTE

  dnaPipeTE (for de-novo assembly & annotation Pipeline for Transposable Elements), is a pipeline designed to find, annotate and quantify Transposable Elements in small samples of NGS datasets. It is very useful to quantify the proportion of TEs in newly sequenced genomes since it does not require genome assembly and works on small datasets (< 1X).

  transposable-elementsannotationsassemblytrinityannotation-pipelinerepeatmaskerpipelinebioinformaticsgenomics
  Language:Dockerfile 46

• clemgoub / TE-Aid

  Annotation helper tool for the manual curation of transposable element consensus sequences

  transposonsblastdot-plotannotationproteintirltrstructurebioinformatics-tooltransposable-elements
  Language:R 38

• sestaton / Transposome

  A toolkit for annotation of transposable element families from unassembled sequence reads

  transposable-elementsgenome-annotationevolution
  Language:Perl 31

• sestaton / tephra

  A tool for discovering transposable elements and describing patterns of genome evolution

  transposable-elementstephraevolutiongenome-evolutiongenome-annotation
  Language:Perl 29

• sjteresi / TE_Density

  Python script calculating transposable element density for all genes in a genome. Publication: https://mobilednajournal.biomedcentral.com/articles/10.1186/s13100-022-00264-4

  transposable-elementsgenome
  Language:Python 28

• GonzalezLab / MCHelper

  MCHelper: An automatic tool to curate transposable element libraries

  annotationcurationgenomicstransposable-elements
  Language:Python 24

• egluckthaler / starfish

  starfish: a modular toolkit for giant mobile element annotation

  bioinformaticsgenomicsmobile-elementsstarshipstransposable-elements
  Language:Perl 22

• akiomiyao / tif

  Transposon Insertion Finder - Detection of new TE insertions in NGS data

  transposable-elementstransposonsngssomatic-mutationssomatic-indelssomatic-variants
  Language:Perl 19

• clemgoub / TypeTE

  Genotyping of segregating mobile elements insertions

  bioinformaticsvcfgenotypinggenotype-likelihoodstransposonsalushort-readstransposable-elements
  Language:Perl 19

• marieBvr / TEs_genes_relationship_pipeline

  Distribution of TEs and their relationship to genes in host genome

  bioinformatics-pipelinetransposable-elements
  Language:Python 19

• urgi-anagen / TE_finder

  A suite of C++ programs developed for transposable element search and their annotation in large eukaryotic genome sequence. A part of the REPET package.

  bioinformatics-tooltransposable-elements
  Language:C++ 18

• OliveiraDS-hub / ChimeraTE

  A pipeline to detect chimeric transcripts derived from genes and transposable elements.

  bioinformaticsilluminarna-seqtransposable-elements
  Language:Python 15

• robsyme / nf-repeatmasking

  Nextflow workflow for automatic repeat detection, classification and masking

  bioinformaticsnextflowtransposable-elementsgenomics
  Language:Perl 13

• akiomiyao / tef

  Transposable Element Finder - Detection of active transposable elements from NGS data

  transposable-elementstransposonssomatic-indelssomatic-mutationssomatic-variants
  Language:Perl 8

• bodegalab / irescue

  A tool to quantify transposable elements expression in scRNA-seq

  bioinformaticsscrna-seqscrnaseqsingle-cellsingle-cell-rna-seqtransposable-elements
  Language:Python 8
• DIGS-tool

  giffordlabcvr / DIGS-tool

  Database-Integrated Genome Screening (DIGS) tool. Explore genomes interactively using BLAST and a relational database.

  blast-searchescomparative-genomicsdata-miningevolutiongenome-annotationmolecular-geneticspaleovirologysequence-similaritysimilarity-searchtransposable-elements
  Language:Perl 8

• LKremer / TEcov

  A pipeline to to determine the repeat content of genes and their neighboring regions.

  genomicsgenometransposable-elementsrepeatmaskerbioinformatics-pipeline
  Language:Python 7

• CSU-KangHu / HiTE

  High-precision TE Annotator

  genome-annotationhigh-precisiontransposable-elementsprogressive-methods
  Language:Python 6

• ValentinaBoP / TransposableElements

  code to analyse RepeatMasker output

  evolutionrepeatmaskertransposable-elements
  Language:HTML 6

• bodegalab / tecount

  A package to count reads mapping on transposable elements subfamilies, families and classes.

  bioinformaticsngsrna-seqtransposable-elements
  Language:Python 5

• clbutler / RM_TRIPS

  RepeatMasker Trinity based Parse Script

  transcriptometrinitytransposable-elements
  Language:R 4

• danillo-alvarenga / tncomp_finder

  Composite Transposon Finder

  bioinformaticsmicrobiologygenomicsmobile-genetic-elementstransposable-elementscomposite-transposons
  Language:Python 4

• PlantDr430 / TransposableELMT

  Wrapper script to identify TEs and mask genome

  transposable-elements
  Language:Python 4

• stajichlab / REPET-slurm

  SLURM-ready bash scripts to run the complete REPET pipeline

  genome-annotationrepetslurmtransposonstransposable-elementsrepeatsde-novobioinformatics
  Language:Shell 4

• CSU-KangHu / NeuralTE

  TE Classifier Using CNN

  classificationsuperfamilytransposable-elementsconvolutional-neural-network
  Language:Python 2

• danillo-alvarenga / tn3-ta_finder

  Tn3 Transposon/Toxin Finder

  bioinformaticsmicrobiologygenomicsmobile-genetic-elementstransposable-elementstn3-transposasestype-ii-toxins
  Language:Python 2

• darcyabjones / pante

  A pipeline for predicting and masking transposable elements in multiple genomes.

  bioinformaticsgenomicsmasking-transposable-elementsmultiple-genomesnon-coding-rnarepeatmaskerrepeatmodelertransposable-elements
  Language:Groovy 2
• WashU_RepeatBrowser

  jamesc99 / WashU_RepeatBrowser

  Interactive Visualization Browser for Transposable Elements (TEs) community

  epigeneticsgenomics-visualizationtransposabletransposable-elementsvisualization
  2

• niekwit / rna-seq-star-tetranscripts

  Snakemake workflow for transposable element RNA-Seq using TEtranscripts

  ngs-pipelinerna-seq-pipelinesnakemake-workflowtransposable-elements
  Language:R 2

• boulardlab / 3t-seq

  A Snakemake workflow for single copy gene, transposable elements and tRNA expression analysis

  bioinformatics-pipelinerna-seq-analysissnakemaketransposable-elementstrna
  Language:Python 1

• MafaldaSFerreira / Atlherr_inversion_evol

  Evolutionary genomics of chromosomal inversions in Atlantic herring

  dnds-estimationdxyevolutionary-biologyfstgatk4genomicsgenotypeinversionslong-readsnucleotide-diversitypcaphylogenomicsrecombinationshort-readssite-frequency-spectrumtransposable-elementswhole-genome-alignment
  Language:R 1

• Tiago-Minuzzi / TEGym

  Build your own deep learning transposable elements classifier with ease.

  deep-learningneural-networkstransposable-elementsbioinformaticsomics
  Language:Python 1