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16s

R and bash scripts for sequence processing and analysis of 16S amplicon sequencing data

16s-snapp-py3

16S SNAPP on Python 3

2020-bioinformatics_prerequisites_workshop

An introduction to the basics of bioinformatics for biologists. No data analysis experience necessary.

a-practice-awesome-nextflow

A curated list of nextflow based pipelines

anaconda

Anaconda turns your Sublime Text 3 in a full featured Python development IDE including autocompletion, code linting, IDE features, autopep8 formating, McCabe complexity checker Vagrant and Docker support for Sublime Text 3 using Jedi, PyFlakes, pep8, MyPy, PyLint, pep257 and McCabe that will never freeze your Sublime Text 3

analysis_of_microbiome_community_data_in_r

This is the source code for the "Analysis of Microbiome Community Data in R" ICPP 2018 workshop. The website is available at: https://grunwaldlab.github.io/analysis_of_microbiome_community_data_in_r/

ansible

Ansible is a radically simple IT automation platform that makes your applications and systems easier to deploy and maintain. Automate everything from code deployment to network configuration to cloud management, in a language that approaches plain English, using SSH, with no agents to install on remote systems. https://docs.ansible.com.

ansible-role-laniakea-irida

Ansible role to install IRIDA using Galaxy in a docker.

ansible-role-micromamba

Install micromamba, and optionally create a base conda environment.

awesome-galaxy

Awesome resources related to Galaxy project

basecalling-comparison

A comparison of different Oxford Nanopore basecallers

bio-ansible

Proof of concept to use ansible + Lmod to deploy a bioinformatics server

bioinformatica

Pipelines e scripts para análises em Bioinformática

biopython

Official git repository for Biopython (originally converted from CVS)

blast-tutorial

bonito

A PyTorch Basecaller for Oxford Nanopore Reads

bookchapter-rna-seq-analyses

Best practice RNA-Seq analysis pipeline for reference-based RNA-Seq analysis

business-machine-learning

A curated list of practical business machine learning (BML) and business data science (BDS) applications for Accounting, Customer, Employee, Legal, Management and Operations (by @firmai)

callings-nf

GATK RNA-Seq Variant Calling in Nextflow

consensus-assembly-and-variant-calling-workflow.

Consensus assembly and variant calling workflow.

controllingcontaminants16s

coral-basecaller

dada2hpcpipe

:ocean: 16S rRNA microbiome data analysis workflow using DADA2 and R on a high performance cluster using SLURM

daniel_its-anslysis

DAnIEL: a user-friendly web server for fungal ITS amplicon sequencing data

data-science-from-scratch

code for Data Science From Scratch book

data-science-template

Template for a data science project

dataharmonizer-a-standardized-browser-based-spreadsheet-editor-and-validator-

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 from the National Microbiome Data Collaborative (NMDC), the LinkML development team, and others.

deepsimulator

The first deep learning based Nanopore simulator which can simulate the process of Nanopore sequencing.

dmptool---data-management-planning-tools

DMPTool version of the DMPRoadmap codebase

docker-galaxy-stable-reference

:whale::bar_chart::books: Docker Images tracking the stable Galaxy releases.