Alma Hernández de Rojas's repositories
A-microbiologist-wants-to-compute
This repo collects the list of learning online resources related to microbiome computational science and tools.
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
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.
CorrZIDF
CorrZIDF: A distribution-free model for detection of significantly differentially abundant features for longitudinal metagenomic data
cutadapt
Cutadapt removes adapter sequences from sequencing reads
dryad-app
Codebase for the collaboration of Dryad and Dash data publication and curation services.
emmeans
Estimated marginal means
ggvegan
ggplot-based plots for vegan
jmodeltest2
Automatically exported from code.google.com/p/jmodeltest2
LDM
Linear Decomposition Model
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"
libro-sig
Libro libre sobre Sistemas de Información Geográfica
LongRead_tutorials
Workflows and tutorials for LongRead analysis with specific focus on Oxford Nanopore data
microbiomeMarker
R package for microbiome biomarker discovery
MitoFinder
MitoFinder: efficient automated large-scale extraction of mitogenomic data from high throughput sequencing data
modeltest
Best-fit model selection
ph525x
ph525x. functions only, no data
poretools
a toolkit for working with Oxford nanopore data
quast
Genome assembly evaluation tool
R-ebook
R programming ebooks
readytowear
Ready-made Taxonomic Weights Repository
stamps2022
Materials for the STAMPS 2022 course at the MBL in Woods Hole, MA, USA
stats-in-r
Statistical Analysis of Biological Data
tidyMicro
tidyMicro GitHup Repository
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.
WRS
Wilcox' Robust Statistics