Márcio Fernandes Alves Leite's repositories
DMG-symposium
In this repository, you will find the references used in my presentation for the DMG symposium “Practical applications of metagenomics towards typing”. The title of my presentation is You must choose, but choose wisely: Model-based approaches for microbial community analysis and data integration.
ZIPPCAlnm
Zero-Inflated Probabilistic PCA framework with logistical normal multinomial distribution (ZIPPCA-LNM), that extends probabilistic PCA from the Gaussian setting to multivariate abundance data, and an empirical Bayes approach was proposed for inferring microbial compositions. An efficient VA algorithm, classification VA, has been developed for fitting this model.
2022-09-26-ds-dl-intro
Introduction to Deep Learning workshop
AFS_Microbiome
This repository contain the scripts used to the paper: Microbiome resilience of Amazonian forests: secondary succession convergence to fungi and agroforest divergence to bacteria
CBFM
Spatio-temporal joint species distribution modeling using community-level basis functions
DAA
Code and Data in manuscript: A comprehensive evaluation of microbial differential abundance analysis methods: current status and potential solutions
dataumbrella22-intro-pytorch
Code for Data Umbrella Talk "Intro to PyTorch and LightningLite
DTMM
Dirichlet-tree Multinomial Mixtures
Microbiome-Friday-2023-09-08
In this repository, you will find the references used in my presentation for the Microbiome Friday. The title of my presentation is The data essence is not invisible to the eyes: exploring microbiome data through the lens of model-based approaches.
differential-abundance-theory
A manuscript exploring the effects of taxonomic bias on microbiome differential-abundance analysis.
GDM_script
Script for performing GDM analysis
GJAM-PROMISE
A repository of the GJAM analysis performed for the PROMISE project.
gllvm
Generalized Linear Latent Variable Models
glmms_workflow
This space will be used to maintain the script and functions file associated with the paper "A versatile workflow for linear modelling in R" published in Frontiers of Ecology and Evolution.
GraphBio
GraphBio: a shiny web app to easily perform popular visualization analysis for omics data
GromovMatcher
Automated Alignment of Untargeted Metabolic Datasets with Optimal Transport
intro_spatialR
Introduction to GIS and mapping in R with the sf package
JuliaProgrammingForNervousBeginners
A course for people who are hesitant but curious about learning to write code in Julia.
leitemfa.github.io
My personal website
mvgam
Bayesian Generalised Additive Models for discrete time series
nifHdada2
dada2 formatted nifH database
picrust2_ML
Code, unit tests, and tutorials for running PICRUSt2
PySR
High-Performance Symbolic Regression in Python
smartfarming
This website is for the project Soil microbial farming to increase plant productivity: reducing nutrient inputs to increase plant-microbe interactions and managing soil microbial diversity
snake_gtdbtk
A snakemake for GTDB-tk
Statistical-Methods-Seminar-Series
Repository for code shared be presenters in the EFI hosted Statistical Methods Seminar Series
Tutorial_Atlas
A tutorial for Metagenome-Atlas given at ECCB. Edited for my own purposes. Here I want to include the model-based approaches