Pinned Repositories
au-bootcamp-git-intro
Git introduction for Auburn University Bioinformatics Bootcamp
bacterial-genomics-tutorial
barcode-constrained-phylogeny
Pipeline for building topologically-constrained phylogenies from DNA barcode data
Bioinformatic_algorithms_coding_challenges
Scripts for the coding challenges of the course "Bioinformatic algorithms: an active learning approach"
Bioinformatics-pipeline
Courses, tutorials and books that facilitate bioinformatics.
Bioinformatics-Training
Bioinformatics training resources
Biopython-cn
Biopython Tutorial Chinese Translation
bold_identification
To identify taxa of given sequences via BOLD system (http://www.boldsystems.org/index.php)
C-C-
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CandiHap
A haplotype analysis toolkit for natural variation study.
deyuanyang's Repositories
deyuanyang/bacterial-genomics-tutorial
deyuanyang/barcode-constrained-phylogeny
Pipeline for building topologically-constrained phylogenies from DNA barcode data
deyuanyang/bold_identification
To identify taxa of given sequences via BOLD system (http://www.boldsystems.org/index.php)
deyuanyang/CandiHap
A haplotype analysis toolkit for natural variation study.
deyuanyang/delineate
Package for species delimitation analysis
deyuanyang/FastaChar
A tool to determine molecular diagnostic characters for species from sequences in fasta format
deyuanyang/fastHaN
fastHaN is a fast and scalable program for constructing haplotype networks for large samples
deyuanyang/genome_skimming_LAB
A set of scripts to analyze Illumina sequencing data to find whole mitochondrial genomes using Smithsonian's Hydra HPC
deyuanyang/gnfinder
GNfinder finds scientific names in UTF8 texts, PDF files, MS Word/Excel documents, URLs etc.
deyuanyang/graphphylo
visualization of phylogenetic output files
deyuanyang/jcvi
Python library to facilitate genome assembly, annotation, and comparative genomics
deyuanyang/KARAJ
deyuanyang/MAVR
various bioinformatic instruments
deyuanyang/mito
The mitosheet package, trymito.io, and other public Mito code.
deyuanyang/Mito-AssemblyViz
Mitochondrial Genome Assembly Assessment Visualization
deyuanyang/Mitochondrial-ORFans
This repository serves as a resource for the scripts and data associated with our research article "ORFans in Mitochondrial Genomes of Marine Polychaete Polydora"
deyuanyang/Mitochondrial_Benchmarking_study
This repository contains the codes and additional data utilized in the benchmark study of short read based mitochondrial assemblers for human datasets
deyuanyang/MitochondrialGeneAnalysis
deyuanyang/mtGrasp
mtGrasp: Snakemake pipeline for de novo reference-grade mitochondrial genome assembly and standardization
deyuanyang/orthoflow
Orthoflow is a workflow for phylogenetic inference of genome-scale datasets of protein-coding genes.
deyuanyang/Polychate_mt
deyuanyang/pyGenomeViz
A genome visualization python package for comparative genomics
deyuanyang/ray
Ray is a unified framework for scaling AI and Python applications. Ray consists of a core distributed runtime and a toolkit of libraries (Ray AIR) for accelerating ML workloads.
deyuanyang/RyanLabShortReadAssembly
Our pipeline for assembling short reads
deyuanyang/samtools
Tools (written in C using htslib) for manipulating next-generation sequencing data
deyuanyang/skim2phylo
A snakemake pipeline for the batch assembly, annotation, and phylogenetic analysis of mitochondrial genomes and ribosomal genes from genome skims
deyuanyang/SPdel
Comparing species delimitation methods and statistics for DNA Barcoding data sets
deyuanyang/taxonworks
Workbench for biodiversity informatics.
deyuanyang/teaching
Tutorials written for my Spring 2015 class on the basics of computing for biologists
deyuanyang/ugene
UGENE is free open-source cross-platform bioinformatics software