Pinned Repositories
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/
POGO_ML_workshop_genomics
POGO 2019 Workshop on Machine Learning and Artificial Intelligence in Biological Oceanographic Observations
AHdeRojas's Repositories
AHdeRojas/ampvis2
Tools for visualising amplicon data
AHdeRojas/book
Compiled and pretty version of labs
AHdeRojas/bookdown
Authoring Books and Technical Documents with R Markdown
AHdeRojas/burrito
A visualization tool for exploratory data analysis of metagenomic data
AHdeRojas/CoDaSeq
Functions for compositional analysis of high throughput sequencing
AHdeRojas/course_2021_radboud
Radboud Summer Course 7/2021 https://www.ru.nl/radboudsummerschool/courses/2021/brain-bacteria-behaviour/
AHdeRojas/Cura
3D printer / slicing GUI built on top of the Uranium framework
AHdeRojas/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.
AHdeRojas/cytoscape
Cytoscape: an open source platform for network analysis and visualization
AHdeRojas/dada2
Accurate sample inference from amplicon data with single nucleotide resolution
AHdeRojas/docs.qiime2.org
https://docs.qiime2.org live site
AHdeRojas/Experimental-Design-and-Biometry-R-
The repository is about the basic statistical concepts and procedures that are necessary to conduct statistical analyses in biological research. The codes are about probabilistic foundations, experimental designs and their analyses, summarizing and visualizing data, and inferential statistics.
AHdeRojas/iMAP
iMAP v1.0 (Pre-release): Integrated Microbiome Analysis Pipeline
AHdeRojas/Keemei
Validate tabular bioinformatics file formats in Google Sheets
AHdeRojas/labs
Rmd source files for the HarvardX series PH525x
AHdeRojas/megan-ce
MEGAN Community Edition
AHdeRojas/metagenomeSeq
Statistical analysis for sparse high-throughput sequencing
AHdeRojas/metagenomics
Metagenomica
AHdeRojas/microbiomeutilities
The is mostly a wrapper tool using phyloseq and microbiome R packages.
AHdeRojas/MicrobiotaProcessWorkshop
The workshop of microbiome datasets analysis using MicrobiotaProcess
AHdeRojas/mothur.github.io
wiki for the mothur software package
AHdeRojas/NMIT
An R package for Microbial Temporal Dependency Comparison
AHdeRojas/pema
PEMA: a flexible Pipeline for Environmental DNA Metabarcoding Analysis of the 16S/18S rRNA, ITS and COI marker genes
AHdeRojas/phyloseq
phyloseq is a set of classes, wrappers, and tools (in R) to make it easier to import, store, and analyze phylogenetic sequencing data; and to reproducibly share that data and analysis with others. See the phyloseq front page:
AHdeRojas/qiime2
Official repository for the QIIME 2 framework.
AHdeRojas/siamcat
R package for Statistical Inference of Associations between Microbial Communities And host phenoType
AHdeRojas/swirl_courses
:mortar_board: A collection of interactive courses for the swirl R package.
AHdeRojas/taxa
taxonomic classes for R
AHdeRojas/themetagenomics
AHdeRojas/training-material
A collection of Galaxy-related training material