Mark Renton (indexofire)

indexofire

Geek Repo

Company:HZCDC

Location:Zhejiang, Hangzhou

Home Page:https://indexofire.github.io/pathongs/

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Mark Renton's starred repositories

ComfyUI

The most powerful and modular stable diffusion GUI, api and backend with a graph/nodes interface.

Language:PythonLicense:GPL-3.0Stargazers:43312Issues:342Issues:2571

appwrite

Your backend, minus the hassle.

Language:TypeScriptLicense:BSD-3-ClauseStargazers:42686Issues:378Issues:3536

awesome-genome-visualization

A list of interesting genome browser or genome-browser-like implementations

MetaPhlAn

MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data

Language:PythonLicense:MITStargazers:283Issues:19Issues:205

fastq-dl

Download FASTQ files from SRA or ENA repositories.

Language:PythonLicense:MITStargazers:268Issues:5Issues:13

awk-hack-the-planet

Source code repo for Ben Porter (FreedomBen)'s free course on Awk (originally a talk at Linux Fest Northwest 2019 and 2020)

Language:RubyLicense:MITStargazers:232Issues:8Issues:1

awesome-nanopore

A curated list of awesome nanopore analysis tools.

genomad

geNomad: Identification of mobile genetic elements

Language:PythonLicense:NOASSERTIONStargazers:174Issues:5Issues:110

dragonflye

:dragon: :fly: Assemble bacterial isolate genomes from Nanopore reads

Language:PerlLicense:GPL-3.0Stargazers:109Issues:4Issues:33

rerio

Research release basecalling models and configurations

Language:PythonLicense:NOASSERTIONStargazers:98Issues:33Issues:62

gravis

Interactive graph visualizations with Python and HTML/CSS/JS.

Language:HTMLLicense:NOASSERTIONStargazers:90Issues:1Issues:12

dnaapler

Reorients assembled microbial sequences

Language:PythonLicense:MITStargazers:89Issues:3Issues:23

ExpansionHunterDenovo

A suite of tools for detecting expansions of short tandem repeats

Language:C++License:NOASSERTIONStargazers:77Issues:15Issues:45

AllTheBacteria

Follow up to Grace Blackwell's 661k dataset, for 2023

Language:PythonLicense:MITStargazers:68Issues:19Issues:24

fujiplot

:mount_fuji: Fuji plot—a circos representation of multiple GWAS results— :mount_fuji:

Language:RLicense:GPL-3.0Stargazers:68Issues:3Issues:7

ecoli_serotyping

In silico prediction of E. coli serotype

Language:PythonLicense:Apache-2.0Stargazers:46Issues:8Issues:19

pairsnp

A set of scripts for calculating pairwise SNP distance

assembly_accuracy

tools for assessing the accuracy of genome assemblies

Language:PythonLicense:MITStargazers:34Issues:4Issues:3

public_health_bioinformatics

Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of pathogens of public health concern.

Language:WDLLicense:GPL-3.0Stargazers:34Issues:4Issues:247

genomics_adventure

Workshop on Genomics - Genomics Adventure

pca-book

Source files for a book on Principal component analysis

Grandeur

UPHL's Reference Free Pipeline

Language:NextflowLicense:GPL-3.0Stargazers:23Issues:4Issues:153
Language:PythonStargazers:21Issues:0Issues:0

SyntenyFinder

SyntenyFinder contains a collection of scripts to easily perform and visualize macrosynteny analysis when provided with the accessions of annotated chromosome-level genome assemblies from NCBI.

Language:Jupyter NotebookStargazers:9Issues:0Issues:0

VPsero

rapid serotyping of Vibrio parahaemolyticus from whole genome sequencing data using serogroup-specific genes

ShigaPass

An in silico tool to predict Shigella serotypes

Language:ShellLicense:GPL-3.0Stargazers:5Issues:3Issues:3

vista

The Pathogenwatch Vibrio cholerae genotyping tool

Language:PythonLicense:MITStargazers:5Issues:1Issues:0

PhyloTrace

PhyloTrace is a GUI platform for a fully controllable cgMLST analysis workflow.

Language:RLicense:GPL-3.0Stargazers:4Issues:3Issues:1

nfvibrio

Nextflow pipeline to run metagenomic sequence analysis of Vibrio Parahaemolyticus, based on nf-core template, by John Palmer & Zohaib Anwar

Language:Jupyter NotebookLicense:MITStargazers:1Issues:0Issues:0