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aluminum_genes_classification

bioinformaticsalgorithmsbook

Repository for code of the book "Bioinformatics Algorithms" by Miguel Rocha and Pedro Ferreira. Editor: Elsevier

cancer-hallmarks

This repo is a collection of results obtained for cancer hallmark article

cancer_hallmarks_research

This repository includes a series of tools written in R and Python to compare cancer-related genes to cancer hallmarks and their respective orthologue genes in A. thaliana

climate-change

This repository compiles a set of R Scripts to do a climate change analysis using 5 algorithms of Species Distribution Models through sdm R package platform and using multivariate analyses

cluster_mun

These scripts allow make a Hierachical Cluster of Principal Components. boxplots and summmary statistics for the new groups found. Also, you will able to perform a PCA3D of the results using a modified version of prcomp function structure

compare_geo_datasets

This dataset allows compare different georeferenced coordinates using three criteria (Distance, Uncertainty, ISO2)

composition

SDMs spatial SDM composition using an automatic R Script

cwr_northamerica

This is a repository of R Scripts used to improve Ramirez-Villegas 2010 gap analysis methodology using variable selection, background creation and using several ensemble methodologies

dada2-pipeline

This repository is a set of R scripts to run DADA2 pipeline and microbial diversity analysis using a regular laptop

diffusion-coefficient

This repository contains a set of R scripts designed to get queries of compounds using webchem clasifyer services

distance-from-conflict-to-deforestation

This repository was made to perform an analysis using georeferenced data from Uppsala conflict database and deforestation forecasts come from Terra-i

edger_nf-core-rnaseq

This repository consists of a set of functions to use an edgeR pipeline which obtains differential expressed genes automatically and using CPU-parallelized computing

egad

Gene network analysis

fao_graphics

The objective of this repository is create line graphics to explore sheep datasets from FAOSTAT

garcia-merchan-et-al-chapter-2020

This repository is a supplementary information repository from García-Merchán et al... 2020 publication.

genetics

These scripts allow perform analysis using polyploids and find genetic structure using R packages adegenet, ggplot, pegas, polysat...

geographic_overlap

This Repository perform a geographic overlap pairwise among species distribution models thresholded rasters according to Kantar et al., (2015)

gh-pages-template

Fork this to start your own site or template for free hosting on GitHub Pages

gis_analysis

Miscellaneous R Scripts to perform GIS analysis and data analysis

gocompare

This is an R package designed to analyze functional enrichment results between two species (A list of genes and their orthologues)

gocompare_interactive_graphs

huanuco

Huanuco survey data analysis

iso-3166-countries-with-regional-codes

ISO 3166-1 country lists merged with their UN Geoscheme regional codes in ready-to-use JSON, XML, CSV data sets

lisa_rcode

This is a repo to perform LISA using R programming language

methylated-position-script

This repository is a set of Python scripts used to count methylated positions in all the three contexts (CG, CGH, CHH) using a gene list containing a start and end position and a file in a plain format where each line represents a methylated cytosine

noisymputer_python

This is a repository of the implementation of NOISYmputer algorithm in Python programming language

occurrences

R Scripts to perform species distribution models previous steps like create Native areas, get occurrences from GBIF and count occurences per species for each USA county information

pecanpy

A fast, parallelized, memory efficient, and cache-optimized Python implementation of node2vec

penetrologger

This repository includes three codes to convert raw penetrologger text file to csv files using R.