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2023-09-27_multiomics_practical

2023-mer_metagenomics

Tutorial and assignments for the course Marine Genomics at IMBRSEA, Plentzia

2023-mer_metagenomics_exercises

Exercises for the metabarcoding part of the Marine Genomic Resources class

2024-mer_metabarcoding-exercises

2024-mer_metagenomics

Tutorial and assignments for the course Marine Genomics at IMBRSEA, Plentzia

ansible-role-slurm

For installing and configuring SLURM - Simple Linux Utility for Resource Management

bioconda-recipes

Conda recipes for the bioconda channel.

biopython.github.io

Source of biopython.org website, migrated from MediaWiki

bioservices

Access to Biological Web Services from Python.

cache

Cache dependencies and build outputs in GitHub Actions

comp-genomics-class

Code and examples for JHU Computational Genomics class

cookiecutter-empty

cookiecutter template completely empty + readme

cookiecutter-exfi-validation

Cookiecutter template to validate exfi

cookiecutter-smsk

cookiecutter boilerplate for smsk

docker-kollector

Docker container for kollector

docker-orthofinder

Dockerfile for OrthoFinder tool

exfi

Get exons from a transcriptome and raw genomic reads using abyss-bloom and bedtools

exfi-docker

Build a Docker container with all the tools to execute exfi

exfi_validation

Snakemake pipeline to validate exfi's performance

gatb_core_examples

gatb-core set of snippets

guide_to_scientific_computing_in_cpp_solutions

Solutions to the exercises of the book Guide to Scientific Computing in C++

hillr

An R pakage to calculate diversity through Hill Numbers

ht_quant

Repository containing bioinformatic code for macro-scale host transcriptomic data processing

khmer_trinity_snakemake

A Snakemake pipeline for Illumina Transcriptome Assembly: trimmomatic + dignorm+ trinity

lintr-cli

Bash wrapper for lintr: lint your code outside of R, not inside

md_paper

md_paper is a skeleton of a paper to be writen in Markdown and compiled into a pdf or docx with pandoc

mofa2

Multi-Omics Factor Analysis

mpuma-galaxy

A Galaxy implementation of the mPuma pipeline

ngs16

oari_paper

Selection sweep scan of _Ovis aries_ populations. Version for paper.