microbialman

RNAPath

Self-supervised representation learning combining GTEx histology, RNA-seq and WGS

lazypredict

Lazy Predict help build a lot of basic models without much code and helps understand which models works better without any parameter tuning

lupus_1M_cells_clean

rmarkdown

Dynamic Documents for R

iSEE

R/shiny interface for interactive visualization of data in SummarizedExperiment objects

BrachioGraph

BrachioGraph is an ultra-cheap (total cost of materials: €14) plotter that can be built with minimal skills.

awsmegatests

CloudFormation templates to setup the aws megatests necessary cloud infrastructure

mlr3

mlr3: Machine Learning in R - next generation

coronastatus

Anonymous crowd sourcing of COVID-19 symptoms all over the world (with public data sets)!

cgat-core

Core functionality of the CGAT code

cgat-flow

cgat-flow repository

urbit

An operating function

snakemake

This is the development home of the workflow management system Snakemake. For general information, see

centrifuge

Classifier for metagenomic sequences

spades

SPAdes Genome Assembler

processing

Source code for the Processing Core and Development Environment (PDE)

megahit

Ultra-fast and memory-efficient (meta-)genome assembler

kraken2

The second version of the Kraken taxonomic sequence classification system

Prodigal

Prodigal Gene Prediction Software

eggnog-mapper

Fast genome-wide functional annotation through orthology assignment

prokka

:zap: :aquarius: Rapid prokaryotic genome annotation

earlham-sherlock.github.io

an open source data platform, developed in the Korcsmaros Group to store, analyze and integrate bioinformatics data

HLA-LA

Fast HLA type inference from whole-genome data

slurmpy

submit jobs to slurm with quick-and-dirty python

reference-frames

songbird

Vanilla regression methods for microbiome differential abundance analysis

cgat-apps

cgat-apps repository

cgat

Do not use - please refer to our newest code: https://github.com/cgat-developers/cgat-apps

awesome-multi-omics

List of software packages for multi-omics analysis

micRowave