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agora

The aim of this repository is to maintain, refine, and expand the AGORA collection of genome-scale metabolic reconstructions for human gut microbes through the use of issues. Please note that pull requests will be automatically closed.

antibiotic-resistance

An analysis of antibiotic resistance in the infant gut microbiome using genome-resolved metagenomics data.

causal_microbiome_tutorial

Causal inference framework for environment-microbiome data applied to American Gut data.

deepmicrobes

DeepMicrobes: taxonomic classification for metagenomics with deep learning

dislncrf

Inferring disease-associated lncRNAs using tissue expression profiles

eunapius_lncrna

R and bash code for the Master's Thesis "Computational analysis of long non-coding RNA in endemic cave sponge (Eunapius subterraneus)", K. Bodulić, 2020

expressionlncr

ExpressionLncr: a pipeline to find overlap between lncRNAs and GEO expression information

fungal_metagenomics

Shell and python scripts for clinical fungal metagenomics

getting-started-with-genomics-tools-and-resources

Unix, R and python tools for genomics and data science

gwas_scripts

Codebook from my GWAS cookbook

gwastutorial

Genome-wide association studies tutorial 🧬

human_metagenomes_analysis

A Metagenomic Meta-Analysis Reveals Functional Signatures of Health and Disease in the Human Gut Microbiome

jialab-ucr.github.io

lipidr

Data Mining and Analysis of Lipidomics datasets in R

lncrna_bc

It is a repository that contains information about my master's project. The main topic is lincRNA as biomarkers in breast cancer. The main objective is to identificate lincRNA biomarkers by transcriptome analysis

metagenomecourse2019

Course material for the metagenomics course

micop

MiCoP is a method for high-accuracy profiling of viral and fungal metagenomic communities.

primates-gutmicrobiome-16s

Plasticity in the Human Gut Microbiome Defies Evolutionary Constraints

rcode

resequencingmetaanalysis

Our aim is to compile a large database of publicly available GWAS data related to the genetic architecture of obesity, type-II diabetes and kidney function. From this reference data set, we aim to extract candidate SNPs / genes that are highly associated with these diseases which we will specifically target in a similar study of Polynesian populations.

rgi

Resistance Gene Identifier (RGI). Software to predict resistomes from protein or nucleotide data, including metagenomics data, based on homology and SNP models.

sz-lncrna-mrna-wgcna-in-human-pmgs

lncRNA-mRNA co-expression networks in human primary microglia analyzed on schizophrenia-associated lncRNAs and mRNAs.

tcga-rnaseq-tutorial

tcga_rnaseq

TCGA_RNAseq_Count_Limma_Log2FC_Log2TPM_Analysis

tcga_rnaseq-1

tcgabiolinks_examples

repository with the scripts to run examples of the publications with new functionalities of TCGAbiolinks

tcgasurvival

Scripts to analyze TCGA data

tcgaworkflow

TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages

tools-metabolomics

Galaxy tools for metabolomics maintained by Workflow4Metabolomics

topic-metagenomics

A repository for the lessons and notebooks used for Binder tutorials