fbeghini

WSL

Issues found on WSL

awesome-wsl

Awesome list dedicated to Windows Subsystem for Linux

esquisse

RStudio add-in to make plots interactively with ggplot2

hrbrthemes

:lock_with_ink_pen: Opinionated, typographic-centric ggplot2 themes and theme components

covid19-opendata-vaccini

Open Data su consegna e somministrazione dei vaccini anti COVID-19 in Italia - Commissario straordinario per l'emergenza Covid-19

Online_R_learning

Online R learning for applied statistics

BI-BE-CS-183-2023

Introduction to Computational Biology and Bioinformatics Course at Caltech, 2023

CoverM

Read coverage calculator for metagenomics

EIG

Eigen tools by Nick Patterson and Alkes Price lab

CheckM2

Assessing the quality of metagenome-derived genome bins using machine learning

NetCoMi

Network construction, analysis, and comparison for microbial compositional data

parsnp

Parsnp was designed to align the core genome of hundreds to thousands of bacterial genomes within a few minutes to few hours. Input can be both draft assemblies and finished genomes, and output includes variant (SNP) calls, core genome phylogeny and multi-alignments. Parsnp leverages contextual information provided by multi-alignments surrounding SNP sites for filtration/cleaning, in addition to existing tools for recombination detection/filtration and phylogenetic reconstruction.

mob-suite

MOB-suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies

platon

Identification & characterization of bacterial plasmid-borne contigs from short-read draft assemblies.

corncob

Count Regression for Correlated Observations with the Beta-binomial

AMR

Functions to simplify and standardise antimicrobial resistance (AMR) data analysis and to work with microbial and antimicrobial properties by using evidence-based methods, as described in https://doi.org/10.18637/jss.v104.i03.

kraken2_classification

Snakemake workflow for metagenomic classification with Kraken2

MGV

Supporting code for uncultivated gut virus manuscript

vclust

Fast and accurate tool for calculating Average Nucleotide Identity (ANI) and clustering virus genomes and metagenomes

Microbiome-conferences-c

This repo collects the list of conferences/meetings/workshops etc. related to microbiome science and tools.

ycrc.github.io

documentation repo for the YCRC, see src branch for more info

mobileOG-db

code repo for mobileOG-db

EukHeist

imputation_accuracy_calculator

microbiomeGWAS

lvm4net-Workshop

nf-core-cmgd

hail-utils

misc. hail utils

netglm

General linear regression framework for network data. Multi-group Quadratic Assignment Proccedure

HondurasTools.jl

Tools for cleaning, analyzing the Honduras data.