cmcshou

cmcshou's Stars

• tk2/RetroSeq

  RetroSeq is a bioinformatics tool that searches for mobile element insertions from aligned reads in a BAM file and a library of reference transposable elements. Please read the wiki page (link below) for usage instructions. Also, there is a page on the wiki describing how the 1000 genomes CEU trio was carried out with the files and parameters used for the various steps.

  Language:Perl6525

• LeileiCui/Dominance_3Stocks

  Language:R31

• Jwindler/AutoHiC

  A novel genome assembly pipeline based on deep learning

  Language:Python345

• shangshanzhizhe/Work_flow_of_population_genetics

  整理常用的群体遗传学分析流程和脚本

  Language:Perl8728

• Illumina/paragraph

  Graph realignment tools for structural variants

  Language:C++14828

• PapenfussLab/sv_benchmark

  Comprehensive benchmark of structural variant callers

  Language:R416

• jianlin-cheng/GenomeFlow

  GenomeFlow: A Graphical Tool for Modeling and Analyzing 3D Genome Structure

  Language:Java214

• DecodeGenetics/svimmer

  Structural variant merging tool

  Language:Python439

• pblischak/HyDe

  Hybridization detection using phylogenetic invariants

  Language:Python4115

• TheFraserLab/ASEr

  Get ASE counts from BAMs or raw fastq data -- repackage of pipeline by Carlo Artieri

  Language:Python63

• shohei-kojima/MEGAnE

  MEGAnE

  Language:Python242

• PhyloSofS-Team/thoraxe

  Use Thor's Axe to cut exons into their evolutionary building blocks :zap:

  Language:Python103

• fritzsedlazeck/SURVIVOR

  Toolset for SV simulation, comparison and filtering

  Language:C++34546

• millanek/Dsuite

  Fast calculation of Patterson's D (ABBA-BABA) and the f4-ratio statistics across many populations/species

  Language:C++16026

• starskyzheng/panpop

  Application of pan-genome for population

  Language:Perl878

• simonhmartin/genomics_general

  General tools for genomic analyses.

  Language:Python32792

• ndierckx/NOVOPlasty

  NOVOPlasty - The organelle assembler and heteroplasmy caller

  Language:Perl17362

• bejerano-lab/percomorphCONDELs

  Language:Python31

• ANGSD/angsd

  Program for analysing NGS data.

  Language:C++22451

• baoxingsong/AnchorWave

  Sensitive alignment of genomes with high sequence diversity, extensive structural polymorphism and whole-genome duplication variation

  Language:C++14519

• zeeev/smartie-sv

  calling SVs from Blasr contig level alignments

  Language:C++5323

• MareesAT/GWA_tutorial

  A comprehensive tutorial about GWAS and PRS

  807323

• qiao-xin/DupGen_finder

  A pipeline used to identify different modes of duplicated gene pairs

  Language:C++9029

• esayyari/DiscoVista

  Language:Python3613

• griffithlab/rnaseq_tutorial

  Informatics for RNA-seq: A web resource for analysis on the cloud. Educational tutorials and working pipelines for RNA-seq analysis including an introduction to: cloud computing, critical file formats, reference genomes, gene annotation, expression, differential expression, alternative splicing, data visualization, and interpretation.

  Language:R1.3k619