Alma Hernández de Rojas's repositories
course_2021_radboud
Radboud Summer Course 7/2021 https://www.ru.nl/radboudsummerschool/courses/2021/brain-bacteria-behaviour/
ampvis2
Tools for visualising amplicon data
qiime2
Official repository for the QIIME 2 framework.
metagenomics
Metagenomica
Keemei
Validate tabular bioinformatics file formats in Google Sheets
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.
bookdown
Authoring Books and Technical Documents with R Markdown
MicrobiotaProcessWorkshop
The workshop of microbiome datasets analysis using MicrobiotaProcess
training-material
A collection of Galaxy-related training material
microbiomeutilities
The is mostly a wrapper tool using phyloseq and microbiome R packages.
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.
swirl_courses
:mortar_board: A collection of interactive courses for the swirl R package.
labs
Rmd source files for the HarvardX series PH525x
mothur.github.io
wiki for the mothur software package
megan-ce
MEGAN Community Edition
docs.qiime2.org
https://docs.qiime2.org live site
burrito
A visualization tool for exploratory data analysis of metagenomic data
metagenomeSeq
Statistical analysis for sparse high-throughput sequencing
pema
PEMA: a flexible Pipeline for Environmental DNA Metabarcoding Analysis of the 16S/18S rRNA, ITS and COI marker genes
cytoscape
Cytoscape: an open source platform for network analysis and visualization
NMIT
An R package for Microbial Temporal Dependency Comparison
dada2
Accurate sample inference from amplicon data with single nucleotide resolution
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:
taxa
taxonomic classes for R
iMAP
iMAP v1.0 (Pre-release): Integrated Microbiome Analysis Pipeline
siamcat
R package for Statistical Inference of Associations between Microbial Communities And host phenoType
CoDaSeq
Functions for compositional analysis of high throughput sequencing
book
Compiled and pretty version of labs