Zhenlisme

Zhenlisme's Stars

• NBISweden/AGAT

  Another Gtf/Gff Analysis Toolkit

  Language:Perl44254

• egluckthaler/starfish

  starfish: a modular toolkit for giant mobile element annotation

  Language:Perl265

• cgroza/GraffiTE

  GraffiTE is a pipeline that finds polymorphic transposable elements in genome assemblies and/or long reads, and genotypes the discovered polymorphisms in read sets using genome-graphs.

  Language:R1064

• mlbendall/telescope

  Quantification of transposable element expression using RNA-seq

  Language:Python6015

• evotools/nf-LO

  A Nextflow workflow to generate lift over files for any pair of genomes

  Language:Nextflow5110

• zhangrengang/SubPhaser

  Phase, partition and visualize subgenomes of a neoallopolyploid or hybrid based on the subgenome-specific repetitive kmers.

  Language:Python5312

• lh3/miniprot

  Align proteins to genomes with splicing and frameshift

  Language:C31517

• qjiangzhao/TEtrimmer

  TEtrimmer: a novel tool to automate manual curation of transposable elements

  Language:Python582

• neurogenomics/orthogene

  🧬 o r t h o g e n e 🧬✨✨✨✨✨✨✨ Interspecies gene mapping✨✨✨✨✨ 🦠 🔁 🌱 🔁 🌳 🔁 🍎 🔁 🍊 🔁 🪱 🔁 🪰 🔁 🐟 🔁 🦎 🔁 🐓 🔁 🦇 🔁 🐄 🔁 🐖 🔁 🐐 🔁 🐎 🔁 🐈 🔁 🐕 🔁 🐁 🔁 🐒 🔁 🦧 🔁 🦍 🔁 🏃‍♀️

  Language:R394

• weng-lab/TEMP2

  Algorithm to detect germline and de novo transposon insertions

  Language:Shell266

• shohei-kojima/MEGAnE

  MEGAnE

  Language:Python242

• hms-dbmi/hic-data-analysis-bootcamp

  Workshop on measuring, analyzing, and visualizing the 3D genome with Hi-C data.

  Language:Jupyter Notebook18749

• elzbth/jitterbug

  Jitterbug is a bioinformatic software that predicts insertion sites of transposable elements in a sample sequenced by short paired-end reads with respect to an assembled reference.

  Language:Python178

• parklab/xTea

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

  Language:Python9522

• fmenardo/Treemmer

  Python tool to reduce size and redundancy of phylogenetic datasets

  Language:Python248

• ablab/quast

  Genome assembly evaluation tool

  Language:AMPL39276

• DecodeGenetics/Ratatosk

  Hybrid error correction of long reads using colored de Bruijn graphs

  Language:C++937

• vibansal/HapCUT2

  software tools for haplotype assembly from sequence data

  Language:C19935

• malonge/RagTag

  Tools for fast and flexible genome assembly scaffolding and improvement

  Language:Python46047

• malonge/RaGOO

  RaGOO is no longer supported. Please use RagTag instead: https://github.com/malonge/RagTag

  Language:Python16928

• moeinzadeh/Ranbow

  Language:Python91

• zengxiaofei/HapHiC

  HapHiC: a fast, reference-independent, allele-aware scaffolding tool based on Hi-C data

  Language:Python1248

• IOB-Muenster/denovoTE-eval

  Supporting repository for article "Software Evaluation for 'de novo' Detection of Transposons"

  Language:Python55

• inab/trimal

  A tool for automated alignment trimming in large-scale phylogenetic analyses. Development version: 2.0

  Language:C++16741

• Zhenlisme/SeqFindpy

  This script can be used for searching a sequence in a fasta-format file.

  Language:Python1

• crazyhottommy/RNA-seq-analysis

  RNAseq analysis notes from Ming Tang

  Language:Python867293