transposable-elements
There are 53 repositories under transposable-elements topic.
oushujun/EDTA
Extensive de-novo TE Annotator
TobyBaril/EarlGrey
Earl Grey: A fully automated TE curation and annotation pipeline
parklab/xTea
Comprehensive TE insertion identification with WGS/WES data from multiple sequencing technics
hyunhwan-jeong/SalmonTE
SalmonTE is an ultra-Fast and Scalable Quantification Pipeline of Transpose Element (TE) Abundances
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).
clemgoub/TE-Aid
Annotation helper tool for the manual curation of transposable element consensus sequences
sestaton/Transposome
A toolkit for annotation of transposable element families from unassembled sequence reads
sestaton/tephra
A tool for discovering transposable elements and describing patterns of genome evolution
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
GonzalezLab/MCHelper
MCHelper: An automatic tool to curate transposable element libraries
egluckthaler/starfish
starfish: a modular toolkit for giant mobile element annotation
marieBvr/TEs_genes_relationship_pipeline
Distribution of TEs and their relationship to genes in host genome
akiomiyao/tif
Transposon Insertion Finder - Detection of new TE insertions in NGS data
clemgoub/TypeTE
Genotyping of segregating mobile elements insertions
OliveiraDS-hub/ChimeraTE
A pipeline to detect chimeric transcripts derived from genes and transposable elements.
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.
robsyme/nf-repeatmasking
Nextflow workflow for automatic repeat detection, classification and masking
bodegalab/irescue
A tool to quantify transposable elements expression in scRNA-seq
akiomiyao/tef
Transposable Element Finder - Detection of active transposable elements from NGS data
LKremer/TEcov
A pipeline to to determine the repeat content of genes and their neighboring regions.
CSU-KangHu/HiTE
High-precision TE Annotator
ValentinaBoP/TransposableElements
code to analyse RepeatMasker output
bodegalab/tecount
A package to count reads mapping on transposable elements subfamilies, families and classes.
clbutler/RM_TRIPS
RepeatMasker Trinity based Parse Script
danillo-alvarenga/tncomp_finder
Composite Transposon Finder
PlantDr430/TransposableELMT
Wrapper script to identify TEs and mask genome
stajichlab/REPET-slurm
SLURM-ready bash scripts to run the complete REPET pipeline
CSU-KangHu/NeuralTE
TE Classifier Using CNN
darcyabjones/pante
A pipeline for predicting and masking transposable elements in multiple genomes.
niekwit/rna-seq-star-tetranscripts
Snakemake workflow for transposable element RNA-Seq using TEtranscripts
danillo-alvarenga/tn3-ta_finder
Tn3 Transposon/Toxin Finder
jamesc99/WashU_RepeatBrowser
Interactive Visualization Browser for Transposable Elements (TEs) community
Tiago-Minuzzi/TEGym
Build your own deep learning transposable elements classifier with ease.
boulardlab/3t-seq
A Snakemake workflow for single copy gene, transposable elements and tRNA expression analysis
MafaldaSFerreira/Atlherr_inversion_evol
Evolutionary genomics of chromosomal inversions in Atlantic herring
maxfieldk/RTE
Snakemake pipeline to analyze retrotransposable element 'omics data.