liaoherui/StrainAMR

A learning-based tool to predict antimicrobial resistance and identify AMR-related genomic features with bacterial strain genomes

Size: 2.93 KB - Last synced: 13 days ago - Pushed: 13 days ago - Stars: 0 - Forks: 0

liaoherui/AnnoSINE_v2 Fork of oushujun/AnnoSINE_v2

Accelerating de novo SINE annotation in plant and animal genomes

Language: Python - Size: 39.7 MB - Last synced: 17 days ago - Pushed: 17 days ago - Stars: 1 - Forks: 0

liaoherui/VirStrain

An RNA virus strain-level identification tool for short reads.

Language: Python - Size: 6.82 MB - Last synced: 15 days ago - Pushed: 3 months ago - Stars: 19 - Forks: 1

liaoherui/StrainScan

High-resolution strain-level microbiome composition analysis tool based on reference genomes and k-mers

Language: Python - Size: 56.7 MB - Last synced: 19 days ago - Pushed: about 2 months ago - Stars: 31 - Forks: 4

liaoherui/bioconda-recipes Fork of bioconda/bioconda-recipes

Conda recipes for the bioconda channel.

Language: Shell - Size: 371 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 0 - Forks: 0

liaoherui/GDmicro

GDmicro - Use GCN and Deep adaptation network to classify host disease status based on human gut microbiome data.

Language: Python - Size: 3.57 MB - Last synced: 4 days ago - Pushed: 2 months ago - Stars: 7 - Forks: 0

liaoherui/MetaComp

MAEP(Metagenomics Assebly Evaluation Pipeline).This pipeline is a new version of LAEP.

Language: HTML - Size: 2 MB - Last synced: about 1 year ago - Pushed: over 2 years ago - Stars: 3 - Forks: 1

liaoherui/StrainKmer

StrainKmer- an efficient and user-friendly tool for extracting viral strains' k-mers from raw sequencing data

Language: Python - Size: 13.4 MB - Last synced: 11 months ago - Pushed: 11 months ago - Stars: 2 - Forks: 0

liaoherui/AssemblyEvaluator Fork of snayfach/AssemblyEvaluator

A simple tool for evaluating a metagenomic assembly

Size: 28.7 MB - Last synced: about 1 year ago - Pushed: over 8 years ago - Stars: 0 - Forks: 0

liaoherui/fastq_phred Fork of jiewencai/fastq_phred

Perl script for judge the fastq's encoding, whether it is phred33 or phred64.

Language: Perl - Size: 148 KB - Last synced: about 1 year ago - Pushed: over 9 years ago - Stars: 0 - Forks: 0

liaoherui/StrainAnalyze

StrainAnalyze: a user-friendly bioinformatics pipeline used to analyze given identified bacterial strains in short reads.

Language: Python - Size: 14.6 KB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

liaoherui/StrainDetect

StrainDetect is an online viral strain-level analysis tool based on VirStrain.

Language: Vue - Size: 9.98 MB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 1 - Forks: 0

liaoherui/HOTSPOT Fork of Orin-beep/HOTSPOT

HOTSPOT is a hierarchical host prediction tool for plasmid contigs using Transformer.

Size: 160 KB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

liaoherui/LRTK Fork of ericcombiolab/LRTK

A unified and versatile toolkit for analyzing Linked-Read sequencing data

Size: 241 MB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

liaoherui/RNA_virus_detector Fork of GreyGuoweiChen/RNA_virus_detector

VirBot: a protein-based RNA virus detector for metagenomic data

Size: 9.33 MB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

liaoherui/PlantBind Fork of wenkaiyan-kevin/PlantBind

A tool for predicting transcription factor binding sites in plants

Size: 32.1 MB - Last synced: about 1 year ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 0

liaoherui/GraphV

GraphV - An RNA virus strain-level identification tool using long reads and genome graph.

Language: Python - Size: 1.08 MB - Last synced: about 1 year ago - Pushed: almost 4 years ago - Stars: 1 - Forks: 0

liaoherui/CHERRY Fork of KennthShang/CHERRY

Host prediction

Size: 399 MB - Last synced: about 1 year ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0

liaoherui/PhaGCN Fork of KennthShang/PhaGCN

GCN classifier for phage taxanomy classification

Size: 54.3 MB - Last synced: about 1 year ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0

liaoherui/IDMIL Fork of mrahma23/IDMIL

IDMIL: An alignment-free interpretable deep multiple instance learning (MIL) for predicting disease from whole-metagenomic data

Size: 235 KB - Last synced: about 1 year ago - Pushed: over 3 years ago - Stars: 0 - Forks: 0

liaoherui/ToolsCommandLines

All command lines running tools in VirStrain paper.

Size: 65.4 KB - Last synced: about 1 year ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0

liaoherui/SibeliaZ Fork of medvedevgroup/SibeliaZ

A fast whole-genome aligner based on de Bruijn graphs

Size: 37.2 MB - Last synced: about 1 year ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0

liaoherui/flask-vue-microblog

Language: Python - Size: 111 KB - Last synced: about 1 year ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0

liaoherui/flask_microblog

flask_microblog

Language: Python - Size: 116 KB - Last synced: about 1 year ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0

liaoherui/quast Fork of ablab/quast

Genome assembly evaluation tool

Size: 1020 MB - Last synced: about 1 year ago - Pushed: about 3 years ago - Stars: 0 - Forks: 0

liaoherui/PStrain Fork of wshuai294/PStrain

An Iterative Microbial Strains Profiling Algorithm for Shotgun Metagenomic Sequencing Data.

Size: 33.4 MB - Last synced: about 1 year ago - Pushed: over 3 years ago - Stars: 0 - Forks: 0

liaoherui/strainest Fork of compmetagen/strainest

StrainEst - abundance estimation of strains

Size: 2.96 MB - Last synced: about 1 year ago - Pushed: over 4 years ago - Stars: 0 - Forks: 0

liaoherui/liaoherui.github.io

My blog - 2020 version

Language: HTML - Size: 289 KB - Last synced: about 1 year ago - Pushed: over 3 years ago - Stars: 0 - Forks: 0

liaoherui/kraken2 Fork of DerrickWood/kraken2

The second version of the Kraken taxonomic sequence classification system

Size: 401 KB - Last synced: about 1 year ago - Pushed: over 3 years ago - Stars: 0 - Forks: 0

liaoherui/README Fork of guodongxiaren/README

README文件语法解读，即Github Flavored Markdown语法介绍

Size: 594 KB - Last synced: about 1 year ago - Pushed: over 3 years ago - Stars: 0 - Forks: 0

liaoherui/GFA-spec Fork of GFA-spec/GFA-spec

Graphical Fragment Assembly (GFA) Format Specification

Size: 1.08 MB - Last synced: about 1 year ago - Pushed: over 4 years ago - Stars: 0 - Forks: 0

liaoherui/vg Fork of vgteam/vg

tools for working with genome variation graphs

Size: 70.8 MB - Last synced: about 1 year ago - Pushed: over 4 years ago - Stars: 0 - Forks: 0

liaoherui/GenGraph Fork of jambler24/GenGraph

A repository for the GenGraph toolkit for the creation and manipulation of graph genomes

Size: 49.5 MB - Last synced: about 1 year ago - Pushed: over 4 years ago - Stars: 0 - Forks: 0

liaoherui/science_flask Fork of danielhomola/science_flask

ScienceFlask: an open-source template for scientific web-app development

Size: 1.32 MB - Last synced: about 1 year ago - Pushed: over 5 years ago - Stars: 0 - Forks: 0

liaoherui/pavian Fork of fbreitwieser/pavian

🌈 Interactive analysis of metagenomics data

Size: 13.3 MB - Last synced: about 1 year ago - Pushed: over 4 years ago - Stars: 0 - Forks: 0

liaoherui/metaWRAP Fork of bxlab/metaWRAP

MetaWRAP - a flexible pipeline for genome-resolved metagenomic data analysis

Size: 38.3 MB - Last synced: about 1 year ago - Pushed: over 4 years ago - Stars: 0 - Forks: 0

liaoherui/NCBI-GenBank-file-parser Fork of dewshr/NCBI-GenBank-file-parser

This program can be used to parse the NCBI GenBank file to create a tabulated csv file.

Size: 10.7 KB - Last synced: about 1 year ago - Pushed: about 5 years ago - Stars: 0 - Forks: 0

liaoherui/MAEP-Python

MAEP(Metagenomics Assebly Evaluation Pipeline).This pipeline is a new version of LAEP.

Language: HTML - Size: 3.97 MB - Last synced: about 1 year ago - Pushed: about 5 years ago - Stars: 0 - Forks: 0

liaoherui/MAGpurify Fork of snayfach/MAGpurify

Improvement of metagenome-assembled genomes

Language: Python - Size: 26.8 MB - Last synced: about 1 year ago - Pushed: about 5 years ago - Stars: 0 - Forks: 0

liaoherui/MSV-Python

宏基因数据统计可视化自动分析流程(Metagenomics Stat and Visual)

Language: Python - Size: 416 KB - Last synced: about 1 year ago - Pushed: over 5 years ago - Stars: 1 - Forks: 0

liaoherui/Flye Fork of fenderglass/Flye

Fast and accurate de novo assembler for single molecule sequencing reads

Language: C++ - Size: 9.12 MB - Last synced: about 1 year ago - Pushed: over 5 years ago - Stars: 0 - Forks: 0

liaoherui/LAEP-python

LAEP(linked-read assembly evaluation pipeline)

Language: Shell - Size: 148 KB - Last synced: about 1 year ago - Pushed: over 5 years ago - Stars: 0 - Forks: 0

liaoherui/CMTW-python

宏基因数据转换为网站需求数据流程(Convert Metagenomics data to web data)

Language: Python - Size: 2.93 KB - Last synced: about 1 year ago - Pushed: over 5 years ago - Stars: 0 - Forks: 0