Charlie Pauvert's repositories
in-phi-luence
Automatic fetch of Philosophers influence from Wikipedia and InPho and visualised as a network in Shiny app
Assembly-stats
Provides some of the common assembly statistics used to identify how good a metagenomic assembly is.
biolink-model
Schema and generated objects for biolink data model and upper ontology
md5sum-in-gz
Bash scripts to compute/verify md5sums in gz-compressed files
consortm
ConsortM: MALDI-based consortia monitoring
cpauvert.github.io
Personal website powered with Pelican
DataHarmonizer
A standardized browser-based spreadsheet editor and validator that can be run offline and locally, and which includes templates for SARS-CoV-2 and Monkeypox sampling data. This project, created by the Centre for Infectious Disease Genomics and One Health (CIDGOH), at Simon Fraser University, is now an open-source collaboration with contributions fr
iMGMC
Repository of the integrated mouse gut metagenomic catalog
linkml-project-cookiecutter
A cookiecutter for linkml projects. An equivalent of `linkml-ws new project-name`.
mdmcleaner
MDMcleaner the assessment, classification and refinement tool for microbial dark matter SAGs and MAGs
MetadataStandards
The primary objective of this GitHub page is to serve as a centralized repository for existing (meta)data standards.
MIntO
Pipeline for Reproducible and Scalable Integration of Metagenomic and Metatranscriptomic Data
nfdi4microbiota-knowledge-base
The NFDI4Microbiota Knowledge Base
PLNnetwork-workflow
Infer network from count data within Snakemake using a sparse Poisson lognormal model (PLNnetwork)
postman-cli
A client software for dataset request and download from openBIS
prepare-for-cran
A Collaborative list of things to know before submitting to CRAN
Protologger
Protologgger is a tool for the description of novel taxa by providing taxonomic, functional and ecological insights
quarto-legendary-giggle
Testing Quarto presentations and index pages via Github pages
RforMassSpectrometry
The R for Mass Spectrometry meta-package
shell-genomics
Introduction to the Command Line for Genomics
shinyFiles
A shiny extension for server side file access
snakemake
This is the development home of the workflow management system Snakemake. For general information, see
snakemake-wrappers
This is the development home of the Snakemake wrapper repository, see
SPeDE
A python application for MALDI-TOF MS dereplication
targets-shiny
Example Shiny app containing a targets pipeline.
taxize
A taxonomic toolbelt for R