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2020_global_nematode_dataset

Global Nematode Dataset

acadie_16s

Analysis of the phyllosphere and soil bacterial communities (16S amplicon sequencing)

acadie_18s

Analysis of the soil nematode communities and nematode-bacteria co-occurrence networks

astrobiomike.github.io

Site to help biologists wade their way into bioinformatics.

biome

BIOinformatics for MEtabarcoding

dada2

Accurate sample inference from amplicon data with single nucleotide resolution

elevationassembly

friendsdontletfriends

Friends don't let friends make certain types of data visualization - What are they and why are they bad.

git_tutorial

graphlan

Tools for visualization phylogenetic trees and annotations from a Bitbucket repository: https://bitbucket.org/nsegata/graphlan/wiki/Home

lab_scripts

useful scripts for lab members

metaphlan

MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data

metaphlan-plot-by-taxa

Python script to convert the metagenomic profile txt file to taxa level plots in python's bokeh and R's phyloseq

metatranscriptomics

microbiome

microbiome R package

microbiome_helper

A repository of bioinformatic scripts, SOPs, and tutorials for analyzing microbiome data.

microbiomebioinformaticsanalysisworkshop2023

Oswaldo Cruz Foundation - Rio de Janeiro, Brazil (April 2023)

miseq-test

nextflow

A DSL for data-driven computational pipelines

planetes

les planetes

plateplanner

rna-secondary-structure

Bioinformatics class project

samsa2

SAMSA pipeline, version 2.0. This version supports use on a local cluster using DIAMOND for annotations.

shell_intro_for_bioinformatics_stg

Intro to Shell for Bioinformatics - with STG examples

sra_upload

template-elsevier-cas-dc

A template repository for quickly setting up papers to be submitted to Elsevier Journals

tools-microbiome-analysis

A list of R environment based tools for microbiome data exploration, statistical analysis and visualization

uofcmicrobiomeworkshop2018

wesanderson

A Wes Anderson color palette for R