National Institute of General Medical Sciences
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NIGMS-Sandbox NIGMS-Sandbox Public
Collection of cloud-based biomedical data science learning modules funded by the National Institute of General Medical Sciences at the NIH
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Biomedical-Imaging-Analysis-using-AI-ML-Approaches Biomedical-Imaging-Analysis-using-AI-ML-Approaches Public
Machine Learning module for cloud-based analyses developed as part of the NIGMS Sandbox Project
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DNA-Methylation-Sequencing-Analysis-with-WGBS DNA-Methylation-Sequencing-Analysis-with-WGBS Public
In this module, you will learn how to download raw sequence data, calculate differentially methylated regions, and run a canonical methyl-seq pipeline in Nextflow
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Integrating-Multi-Omics-Datasets Integrating-Multi-Omics-Datasets Public
Multi-omics module that includes RNAseq, Epigenetics, and integrated multi-omics analyses developed as part of the NIGMS Sandbox project
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Introduction-to-Data-Science-for-Biology Introduction-to-Data-Science-for-Biology Public
Python-based machine learning and data science module from SFSU developed for the NIGMS Sandbox project
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ATAC-Seq-and-Single-Cell-ATAC-Seq-Analysis ATAC-Seq-and-Single-Cell-ATAC-Seq-Analysis Public
ATAC-seq and scATAC-seq module developed by the University of Nebraska Medical Center
Repositories
- Protein-Protein-Interactions-using-ML Public
In this module, you will harness novel machine learning techniques to investigate how proteins behave. A special focus will be given to data preprocessing, model training, and evaluation techniques to uncover complex biological relationships
- Consensus-Pathway-Analysis-in-the-Cloud Public
Consensus pathway analysis module developed by the University of Nevada at Reno
- Structural-Biology-and-Drug-Discovery Public
This repository provides a comprehensive module on structural biology and drug discovery, covering protein structure, docking, and drug design. It runs on Google Cloud Platform using Jupyter notebooks and includes tools like PyMOL and AutoDock.
- Transcriptome-Assembly-Refinement-and-Applications Public
In this module, you will learn how to use a Nextflow pipeline to assemble and annotate a novel transcriptome using RNA-seq data
- RNA-Seq-Differential-Expression-Analysis Public
RNAseq workflow run using BASH, Nextflow, and Snakemake on AWS and GCP, developed as part of the NIH NIGMS Sandbox
- Foundations-of-Python-for-Data-Science Public
This repository offers an introductory Python module for bioinformatics, emphasizing practical coding techniques for biological scientists. It covers Python basics, data handling with NumPy and Pandas, and cloud computing on Azure.
- Comparative-Microbial-Genomics Public
In this module, you will learn how sequencing data is generated and go through a detailed guide on assembling, assessing, and annotating a bacterial genome. You will then automate the workflow and perform a large-scale comparative genomic analysis.
- RNA-Methylation-with-MeRIP-seq Public
The MeRIP-seq data analysis tutorial is structured into four submodules, designed to comprehensively guide users through the complete workflow for RNA methylation analysis
- Intro-to-Pangenomics Public
This repository provides a comprehensive module on graphical pangenomics, guiding users through building, indexing, mapping, and visualizing pangenome graphs. The module runs on Google Cloud Platform using Jupyter notebooks and includes tools like PGGB, vg, BLAST, and Bandage.
- Proteome-Quantification Public
Secondary analysis of Proteomics data in R, developed by the University of Arkansas for Medical Sciences for the NIH NIGMS Sandbox project.
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