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/A-microbiologist-wants-to-compute
This repo collects the list of learning online resources related to microbiome computational science and tools.
AHdeRojas/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
AHdeRojas/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.
AHdeRojas/cgview_comparison_tool
The CGView Comparison Tool (CCT) is a package for visually comparing bacterial, plasmid, chloroplast, and mitochondrial sequences.
AHdeRojas/CorrZIDF
CorrZIDF: A distribution-free model for detection of significantly differentially abundant features for longitudinal metagenomic data
AHdeRojas/cutadapt
Cutadapt removes adapter sequences from sequencing reads
AHdeRojas/dryad-app
Codebase for the collaboration of Dryad and Dash data publication and curation services.
AHdeRojas/emmeans
Estimated marginal means
AHdeRojas/ggvegan
ggplot-based plots for vegan
AHdeRojas/gp_growth_phenotype
AHdeRojas/jmodeltest2
Automatically exported from code.google.com/p/jmodeltest2
AHdeRojas/LDM
Linear Decomposition Model
AHdeRojas/Li_AqFl1-Microbiota_2021
Code for reproducing results published in the paper: "Consistent changes in the intestinal microbiota of Atlantic salmon fed insect meal diets"
AHdeRojas/libro-sig
Libro libre sobre Sistemas de Información Geográfica
AHdeRojas/LongRead_tutorials
Workflows and tutorials for LongRead analysis with specific focus on Oxford Nanopore data
AHdeRojas/microbiomeMarker
R package for microbiome biomarker discovery
AHdeRojas/MitoFinder
MitoFinder: efficient automated large-scale extraction of mitogenomic data from high throughput sequencing data
AHdeRojas/MLRepo
AHdeRojas/modeltest
Best-fit model selection
AHdeRojas/ph525x
ph525x. functions only, no data
AHdeRojas/poretools
a toolkit for working with Oxford nanopore data
AHdeRojas/quast
Genome assembly evaluation tool
AHdeRojas/R-ebook
R programming ebooks
AHdeRojas/readytowear
Ready-made Taxonomic Weights Repository
AHdeRojas/stamps2022
Materials for the STAMPS 2022 course at the MBL in Woods Hole, MA, USA
AHdeRojas/stats-in-r
Statistical Analysis of Biological Data
AHdeRojas/tidyMicro
tidyMicro GitHup Repository
AHdeRojas/Tree-Root-Microbiome-Project
The scripts contained in this repository relate directly to the work conducted by the Tree Root Microbiome Project (TRMP) led by Dr Steve Wakelin.
AHdeRojas/workflow-qc-of-radseq-reads
AHdeRojas/WRS
Wilcox' Robust Statistics