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16s-qiime2

Analysis of microbiome samples in CWL using QIIME2

16s_rrna_bacterial_communities_analysis

The set of scripts for programming language R for analyzing genetic and taxonomic diversity of bacterial communities received by metagenomic data of 16S rRNA

a-microbiologist-wants-to-compute

This repo collects the list of learning online resources related to microbiome computational science and tools.

adv-r

Advanced R: a book

advancedr

SIOB-296 Advanced R Programming

ampvis2

Tools for visualising amplicon data

an-introduction-to-applied-bioinformatics

Interactive lessons in bioinformatics.

analysis-of-community-composition

A set of scripts for analyzing the composition of a community of organisms using a package of vegan for the programming language R

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/

apuntesmaster

Apuntes estadística Master

art-culo-ngs-malaga

Scripts for the manuscript Assessment of short-term spatio-temporal variability in mesozooplankton communities’ structure integrating microscopy and multigene high-throughput sequencing

awesome-nanopore

A curated list of awesome nanopore analysis tools.

blogdown

Create Blogs and Websites with R Markdown

book

Compiled and pretty version of labs

bookdown

Authoring Books and Technical Documents with R Markdown

burrito

A visualization tool for exploratory data analysis of metagenomic data

calffecalmicrobiome

The study focused on a longitudinal study of the calf fecal microbiome from their arrival to the farm until 112 days. During this period, the 60 animals were treated divided in two treatment groups probiotic (SCFP) and control. Fecal samples were collected on the days 0, 28, 56, 84 and 112 for the microbiome analysis.

cgview_comparison_tool

The CGView Comparison Tool (CCT) is a package for visually comparing bacterial, plasmid, chloroplast, and mitochondrial sequences.

classifier

RDP extensible sequence classifier for fungal lsu, bacterial and archaeal 16s

codaseq

Functions for compositional analysis of high throughput sequencing

comparison_of_da_microbiome_methods

corrzidf

CorrZIDF: A distribution-free model for detection of significantly differentially abundant features for longitudinal metagenomic data

course_2021_radboud

Radboud Summer Course 7/2021 https://www.ru.nl/radboudsummerschool/courses/2021/brain-bacteria-behaviour/

cura

3D printer / slicing GUI built on top of the Uranium framework

curaengine

Powerful, fast and robust engine for converting 3D models into g-code instructions for 3D printers. It is part of the larger open source project Cura.

cursogenomicaryc

cutadapt

Cutadapt removes adapter sequences from sequencing reads

cytoscape

Cytoscape: an open source platform for network analysis and visualization

dada2

Accurate sample inference from amplicon data with single nucleotide resolution

dada2_guidelines

A repository with a general dada2 pipeline for amplicon processing