GitHub topics: transposable-elements
Rowena-h/StarshipTrees
Scripts for Hill et al. (2025) doi:10.1093/g3journal/jkaf082 🚀
Language: R - Size: 8.39 MB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 1 - Forks: 0
TobyBaril/EarlGrey
Earl Grey: A fully automated TE curation and annotation pipeline
Language: Python - Size: 5.5 MB - Last synced at: 9 days ago - Pushed at: 10 days ago - Stars: 165 - Forks: 20
GonzalezLab/MCHelper
MCHelper: An automatic tool to curate transposable element libraries
Language: Python - Size: 348 MB - Last synced at: 11 days ago - Pushed at: 11 days ago - Stars: 36 - Forks: 3
niekwit/rna-seq-star-tetranscripts
Snakemake workflow for transposable element RNA-Seq using TEtranscripts
Language: R - Size: 95.3 MB - Last synced at: 11 days ago - Pushed at: 11 days ago - Stars: 3 - Forks: 0
CSU-KangHu/HiTE
High-precision TE Annotator
Language: Python - Size: 206 MB - Last synced at: 11 days ago - Pushed at: 11 days ago - Stars: 108 - Forks: 5
oushujun/EDTA
Extensive de-novo TE Annotator
Language: Perl - Size: 228 MB - Last synced at: 6 days ago - Pushed at: 17 days ago - Stars: 373 - Forks: 78
parklab/xTea
Comprehensive TE insertion identification with WGS/WES data from multiple sequencing technics
Language: Python - Size: 7.8 MB - Last synced at: 3 days ago - Pushed at: 4 days ago - Stars: 108 - Forks: 23
islandevolution/islandevolution.github.io
Source code for the Island biology, diversification, genome evolution lab
Language: HTML - Size: 44.9 MB - Last synced at: 9 days ago - Pushed at: about 1 month ago - Stars: 0 - Forks: 0
akiomiyao/tef
Transposable Element Finder - Detection of active transposable elements from NGS data
Language: Perl - Size: 634 KB - Last synced at: 26 days ago - Pushed at: 26 days ago - Stars: 9 - Forks: 0
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
Language: Python - Size: 7.5 MB - Last synced at: 3 days ago - Pushed at: 7 months ago - Stars: 31 - Forks: 4
clemgoub/TE-Aid
Annotation helper tool for the manual curation of transposable element consensus sequences
Language: R - Size: 2.13 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 47 - Forks: 7
bradyfullerton/TE_Genome_ABM_NetLogo
A NetLogo agent based model of transposable element "behaviour" in the genome.
Language: HTML - Size: 3.13 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 0 - Forks: 0
Marcos-Fernando/AnnoTEP_v1
AnnoTEP - a platform for the annotation of transposable elements in plants
Language: Perl - Size: 123 MB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 2 - Forks: 0
egluckthaler/starfish
starfish: a modular toolkit for giant mobile element annotation
Language: Perl - Size: 69.4 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 27 - Forks: 5
boulardlab/3t-seq
A Snakemake workflow for single copy gene, transposable elements and tRNA expression analysis
Language: Python - Size: 28.4 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 5 - Forks: 1
NMoralesD/IDENTAM
This repository provides the code for identifying potential LTR retrotransposon tandem loci.
Language: Python - Size: 41 KB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 0 - Forks: 0
bodegalab/tecount
A package to count reads mapping on transposable elements subfamilies, families and classes.
Language: Python - Size: 3.49 MB - Last synced at: 7 days ago - Pushed at: about 2 years ago - Stars: 7 - Forks: 0
mptrsen/mobilome
TE annotation pipeline and analysis scripts for the insect mobilome publication by Petersen et al.
Language: Perl - Size: 33.2 KB - Last synced at: about 2 months ago - Pushed at: about 4 years ago - Stars: 2 - Forks: 3
raphaelrubrice/TELLAM
Pipeline for Transposable Elements Locus Level Analysis.
Language: Python - Size: 2.35 MB - Last synced at: 6 months ago - Pushed at: 7 months ago - Stars: 0 - Forks: 0
maxfieldk/TE-Seq
Snakemake pipeline to analyze retrotransposable element 'omics data.
Language: R - Size: 67 MB - Last synced at: 9 months ago - Pushed at: 9 months ago - Stars: 1 - Forks: 0
bodegalab/irescue
A tool to quantify transposable elements expression in scRNA-seq
Language: Python - Size: 16.7 MB - Last synced at: 12 months ago - Pushed at: about 1 year ago - Stars: 7 - Forks: 1
hyunhwan-jeong/SalmonTE
SalmonTE is an ultra-Fast and Scalable Quantification Pipeline of Transpose Element (TE) Abundances
Language: Jupyter Notebook - Size: 258 MB - Last synced at: 6 months ago - Pushed at: about 2 years ago - Stars: 81 - Forks: 23
CSU-KangHu/NeuralTE
TE Classifier Using CNN
Language: Python - Size: 160 MB - Last synced at: 10 months ago - Pushed at: 10 months ago - Stars: 3 - Forks: 0
OliveiraDS-hub/ChimeraTE
A pipeline to detect chimeric transcripts derived from genes and transposable elements.
Language: Python - Size: 24.8 MB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 16 - Forks: 4
giffordlabcvr/DIGS-tool
Database-Integrated Genome Screening (DIGS) tool. Explore the dark genome using BLAST and a relational database.
Language: Perl - Size: 49.1 MB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 8 - Forks: 6
robsyme/nf-repeatmasking
Nextflow workflow for automatic repeat detection, classification and masking
Language: Perl - Size: 390 KB - Last synced at: 7 days ago - Pushed at: about 7 years ago - Stars: 13 - Forks: 6
GReD-Clermont/sRNAPipe-cli
CLI tool for bioinformatic in-depth exploration of small RNA-seq data
Language: Perl - Size: 161 KB - Last synced at: 12 months ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0
MafaldaSFerreira/Atlherr_inversion_evol
Evolutionary genomics of chromosomal inversions in Atlantic herring
Language: R - Size: 639 KB - Last synced at: 12 months ago - Pushed at: 12 months ago - Stars: 1 - Forks: 0
Public-Health-Bioinformatics/irida-plugin-tetyper
Determine the sequence type of specific transposable elements in bacterial isolates.
Language: Java - Size: 343 KB - Last synced at: about 1 year ago - Pushed at: over 4 years ago - Stars: 0 - Forks: 0
lydia-holley/Wyeomyia-smithii-project
Scripts I wrote as a graduate research assistant while working on the Wyeomyia smithii Genome project for Dr. Elizabeth Cooper's Lab at UNC Charlotte
Language: Python - Size: 7.81 KB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0
lydia-holley/Cooper-Lab
Scripts I have written as a graduate research assistant
Language: Python - Size: 12.7 KB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0
Tiago-Minuzzi/HamleTE
Find and classify transposable elements using convolutional neural networks.
Language: Python - Size: 167 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 1 - Forks: 0
Tiago-Minuzzi/TEGym
Build your own deep learning transposable elements classifier with ease.
Language: Python - Size: 336 KB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 1 - Forks: 0
dwarriaz/overwriTE
Interrogating the influence of Transposable Element insertions on transcriptional dynamics
Language: Python - Size: 2.18 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0
marieBvr/TEs_genes_relationship_pipeline
Distribution of TEs and their relationship to genes in host genome
Language: Python - Size: 20.1 MB - Last synced at: about 1 year ago - Pushed at: almost 2 years ago - Stars: 19 - Forks: 4
clbutler/RM_TRIPS
RepeatMasker Trinity based Parse Script
Language: R - Size: 78.1 KB - Last synced at: over 1 year ago - Pushed at: over 3 years ago - Stars: 4 - Forks: 1
danillo-alvarenga/tncomp_finder
Composite Transposon Finder
Language: Python - Size: 2.09 MB - Last synced at: over 1 year ago - Pushed at: almost 4 years ago - Stars: 2 - Forks: 1
danillo-alvarenga/tn3-ta_finder
Tn3 Transposon/Toxin Finder
Language: Python - Size: 186 KB - Last synced at: over 1 year ago - Pushed at: almost 5 years ago - Stars: 2 - Forks: 1
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).
Language: Dockerfile - Size: 381 MB - Last synced at: over 1 year ago - Pushed at: about 2 years ago - Stars: 41 - Forks: 10
sestaton/Transposome
A toolkit for annotation of transposable element families from unassembled sequence reads
Language: Perl - Size: 33.4 MB - Last synced at: over 1 year ago - Pushed at: almost 2 years ago - Stars: 31 - Forks: 6
darcyabjones/pante
A pipeline for predicting and masking transposable elements in multiple genomes.
Language: Groovy - Size: 4.53 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 2 - Forks: 9
roblehmann/umbridae_genome_expansion
Supplementary to publication "DNA Transposon Expansion is Associated with Genome Size Increase in Mudminnows"
Size: 2.57 MB - Last synced at: over 1 year ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0
jacopoM28/Python_Scripts
Useful python scripts for genomic analyses
Language: Python - Size: 105 KB - Last synced at: almost 2 years ago - Pushed at: about 2 years ago - Stars: 1 - Forks: 0
jamesc99/WashU_RepeatBrowser
Interactive Visualization Browser for Transposable Elements (TEs) community
Size: 782 MB - Last synced at: about 1 year ago - Pushed at: about 2 years ago - Stars: 2 - Forks: 0
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.
Language: C++ - Size: 91.4 MB - Last synced at: almost 2 years ago - Pushed at: about 2 years ago - Stars: 16 - Forks: 2
retrogenomics/bs-ATLAS-seq
bs-ATLAS-seq analysis scripts
Language: Shell - Size: 10.8 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 1 - Forks: 0
sestaton/tephra
A tool for discovering transposable elements and describing patterns of genome evolution
Language: Perl - Size: 215 MB - Last synced at: about 2 years ago - Pushed at: about 3 years ago - Stars: 26 - Forks: 3
akiomiyao/tif
Transposon Insertion Finder - Detection of new TE insertions in NGS data
Language: Perl - Size: 229 MB - Last synced at: over 1 year ago - Pushed at: over 2 years ago - Stars: 16 - Forks: 4
GReD-Clermont/sRNAPipe
a GALAXY-based pipeline for bioinformatic in-depth exploration of small RNA-seq data
Language: HTML - Size: 16.3 MB - Last synced at: 12 months ago - Pushed at: about 1 year ago - Stars: 1 - Forks: 3
clemgoub/TypeTE
Genotyping of segregating mobile elements insertions
Language: Perl - Size: 62.5 MB - Last synced at: about 2 years ago - Pushed at: over 3 years ago - Stars: 18 - Forks: 1
TommasoBarberis/polishTE
A simple bash pipeline for extension and edge polishing of transposable elements consensi.
Language: Shell - Size: 98.6 KB - Last synced at: about 2 years ago - Pushed at: almost 3 years ago - Stars: 0 - Forks: 0
TommasoBarberis/PASTEC-singularity
Singularity image for PASTEC (transposable elements classification tool).
Language: Singularity - Size: 1.41 MB - Last synced at: about 2 years ago - Pushed at: about 3 years ago - Stars: 0 - Forks: 0
LKremer/TEcov
A pipeline to to determine the repeat content of genes and their neighboring regions.
Language: Python - Size: 6.84 KB - Last synced at: 21 days ago - Pushed at: almost 8 years ago - Stars: 7 - Forks: 1
Manu-1512/Matt_et_al_2021
Simultaneous analysis of genes and transposable elements (TEs) from 10X scRNAseq datasets derived from CD and NIBD samples using Alevin.
Language: R - Size: 58.6 KB - Last synced at: almost 2 years ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 0
RawalTeam/MeX-Pipeline
A pipeline for identification and annotation of transposable element (TE) insertions using next generation sequencing (NGS) data.
Language: Python - Size: 53.7 KB - Last synced at: about 2 years ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 1
stajichlab/REPET-slurm
SLURM-ready bash scripts to run the complete REPET pipeline
Language: Shell - Size: 40 KB - Last synced at: almost 2 years ago - Pushed at: almost 6 years ago - Stars: 4 - Forks: 2
PlantDr430/TransposableELMT
Wrapper script to identify TEs and mask genome
Language: Python - Size: 894 KB - Last synced at: over 1 year ago - Pushed at: about 5 years ago - Stars: 2 - Forks: 1
k8hertweck/REpipe
characterization of TEs from low-coverage genomic sequence data
Language: Shell - Size: 77.1 KB - Last synced at: about 2 months ago - Pushed at: almost 7 years ago - Stars: 0 - Forks: 1
k8hertweck/flyPopGenomics
transposon and LD analysis for replicated experimental evolution fruit fly populations
Language: R - Size: 3.75 MB - Last synced at: about 2 months ago - Pushed at: almost 8 years ago - Stars: 0 - Forks: 0