infectious-diseases
There are 124 repositories under infectious-diseases topic.
sanger-pathogens/Roary
Rapid large-scale prokaryote pan genome analysis
SORMAS-Foundation/SORMAS-Project
SORMAS (Surveillance, Outbreak Response Management and Analysis System) is an early warning and management system to fight the spread of infectious diseases.
EpiModel/EpiModel
Mathematical Modeling of Infectious Disease Dynamics
sanger-pathogens/snp-sites
Finds SNP sites from a multi-FASTA alignment file
sanger-pathogens/Artemis
Artemis is a free genome viewer and annotation tool that allows visualization of sequence features and the results of analyses within the context of the sequence, and its six-frame translation
sanger-pathogens/circlator
A tool to circularize genome assemblies
CSSEGISandData/COVID-19_Unified-Dataset
Unified COVID-19 Dataset
nickjcroucher/gubbins
Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins
sanger-pathogens/ariba
Antimicrobial Resistance Identification By Assembly
sanger-pathogens/assembly-stats
Get assembly statistics from FASTA and FASTQ files
chanzuckerberg/czid-web
Infectious Disease Sequencing Platform
jangevaare/Pathogen.jl
Simulation, visualization, and inference of individual level infectious disease models with Julia
sanger-pathogens/Fastaq
Python3 scripts to manipulate FASTA and FASTQ files
sanger-pathogens/assembly_improvement
Improve the quality of a denovo assembly by scaffolding and gap filling
antonin-lfv/simulation_virus_covid-19
Simulating epidemics using Python
sanger-pathogens/iva
de novo virus assembler of Illumina paired reads
KendrickOrg/kendrick
Domain-Specific Modeling for Epidemiology
andrewjpage/tiptoft
Predict plasmids from uncorrected long read data
mrc-ide/individual
R Package for individual based epidemiological models
sanger-pathogens/mlst_check
Multilocus sequence typing by blast using the schemes from PubMLST
sanger-pathogens/gff3toembl
Converts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI
sanger-pathogens/plasmidtron
Assembling the cause of phenotypes and genotypes from NGS data
chanzuckerberg/czid-dag
Please see https://github.com/chanzuckerberg/czid-workflows for the latest version of CZ ID workflows.
EnbinYang/tb_prediction_files
A multivariate multi-step LSTM forecasting model for tuberculosis incidence with model explanation
quadram-institute-bioscience/socru
Order and orientation of complete bacterial genomes
sanger-pathogens/saffrontree
SaffronTree: Reference free rapid phylogenetic tree construction from raw read data
sanger-pathogens/Bio-Tradis
A set of tools to analyse the output from TraDIS analyses
kpzoo/EpiFilter
Optimised estimates of reproduction numbers over time, which extract more information from an incidence curve than many conventional approaches
CIDO-ontology/cido
CIDO: Coronavirus Infectious Disease Ontology
cran-task-views/Epidemiology
CRAN Task View: Epidemiology
sanger-pathogens/seroba
k-mer based Pipeline to identify the Serotype from Illumina NGS reads
idem-lab/conmat
Create Contact Matrices from Population Data
Emergent-Epidemics/infectious_disease_predictability
Code and data for On the Predictability of Infectious Disease Outbreaks by SV Scarpino & G Petri
mhoehle/STA427_SM4IDE
Repo for the course Statistical Methods in Infectious Disease Epidemiology at UZH
epispot/epispot
A tool for modeling infectious diseases.