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autoeda-resources

A list of software and papers related to automatic and fast Exploratory Data Analysis

bowtie2

A fast and sensitive gapped read aligner

epimodel

Mathematical Modeling of Infectious Disease Dynamics

epimodelhiv

Network Models of HIV Transmission Dynamics among MSM and Heterosexuals

godata

Codebase and Community of Practice for Go.Data (https://www.who.int/tools/godata), an outbreak investigation tool developed by WHO in collaboration with Global Outbreak Alert and Response Network Partners.

individual

R Package for individual based epidemiological models

kleborate

kpneu_mic_prediction

Scripts and input files used for machine learning prediction of MIC in K. pneumoniae

mash

Fast genome and metagenome distance estimation using MinHash

ml-youtube-courses

📺 A place to discover the latest machine learning courses on YouTube.

modellingr_tmwr

Code and content for "Tidy Modeling with R"

ngs-book-dataset

panaroo

An updated pipeline for pangenome investigation

phandango

an interactive viewer for populations of bacterial genomes linked by a phylogeny

pod5-file-format

Pod5: a high performance file format for nanopore reads.

practical-statistics-for-data-scientists

Code repository for O'Reilly book

pyseer

SEER, reimplemented in python 🐍🔮

python-cheatsheet

All-inclusive Python cheatsheet

reddog

smith_etal_enterococcus

C. difficile metabolic modeling in co-culture with E. faecalis

srst2

Short Read Sequence Typing for Bacterial Pathogens

stability-sdk

SDK for interacting with stability.ai APIs (e.g. stable diffusion inference)

svm-r-markdown-templates

This is my (deprecated) suite of R Markdown templates for academic manuscripts, beamer presentations, and syllabi. DOWNLOAD {stevetemplates} INSTEAD.

tbprofiler

Profiling tool for Mycobacterium tuberculosis to detect ressistance and strain type from WGS data

treewas

treeWAS: A Phylogenetic Tree-Based Tool for Genome-Wide Association Studies in Microbes

unitig-caller

Methods to determine sequence element (unitig) presence/absence