National Institute of General Medical Sciences

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33 repositories

Consensus-Pathway-Analysis-in-the-Cloud
Public
Consensus pathway analysis module developed by the University of Nevada at Reno
aws gcp gene-expression meta-analysis pathway-analysis r-programming enrichment-analysis differential-expression-analysis omics-data high-throughput-data
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•8•2•0•0•Updated Jan 6, 2026Jan 6, 2026
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 Googl…
machine-learning random-forest structural-biology protein-data-bank protein-structure gcp molecular-dynamics computational-biology biochemistry pymol
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Creative Commons Zero v1.0 Universal
•1•1•0•0•Updated Aug 21, 2025Aug 21, 2025
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
aws rna-seq nextflow gcp transcriptomics high-throughput-sequencing aws-batch transcriptome-assembly functional-annotation google-batch
Jupyter Notebook
•4•0•0•0•Updated Jun 9, 2025Jun 9, 2025
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
aws rna-seq azure gcp transcriptomics r-programming differential-gene-expression
Jupyter Notebook
•2•6•0•0•Updated Jun 9, 2025Jun 9, 2025
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, mode…
machine-learning random-forest structural-biology gcp molecular-dynamics computational-biology pymol drug-discovery logistic-regression protein-protein-interaction
Jupyter Notebook
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Creative Commons Zero v1.0 Universal
•1•0•0•1•Updated Jun 9, 2025Jun 9, 2025
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 bas…
github python aws data-science bioinformatics programming anaconda azure numpy jupyter-notebook
Jupyter Notebook
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Creative Commons Zero v1.0 Universal
•2•1•0•0•Updated Jun 9, 2025Jun 9, 2025
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…
docker conda next-generation-sequencing genome-annotation microbial-genomics comparative-genomics genome-sequencing genome-assembly whole-genome-sequencing illumina-sequencing
Jupyter Notebook
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Creative Commons Zero v1.0 Universal
•1•1•0•1•Updated Jun 9, 2025Jun 9, 2025
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 methylati…
python aws bioinformatics nextflow differential-methylation high-throughput-sequencing cancer-research r-programming sagemaker functional-enrichment-analysis
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Creative Commons Zero v1.0 Universal
•0•0•0•0•Updated Jun 6, 2025Jun 6, 2025
Intro-to-Pangenomics
Public
This repository provides a comprehensive module on graphical pangenomics, guiding users through building, indexing, mapping, and visualizing pangenome graphs. T…
bioinformatics gcp computational-biology population-genomics variant-calling high-throughput-sequencing genome-analysis genome-assembly illumina-sequencing read-mapping
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Other
•0•0•0•0•Updated Jun 6, 2025Jun 6, 2025
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.
aws bioinformatics jupyter-notebook gcp data-visualization cloud-computing proteomics mass-spectrometry data-preprocessing r-programming
Jupyter Notebook
•5•1•0•0•Updated Jun 6, 2025Jun 6, 2025
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
aws rna-seq gcp epigenetics transcriptomics dna-methylation multi-omics differential-expression-analysis reduced-representation-bisulfite-sequencing
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•2•11•0•0•Updated Jun 6, 2025Jun 6, 2025
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 Nextfl…
next-generation-sequencing epigenetics dna-methylation nf-core whole-genome-bisulfite-sequencing methylation-calling differentially-methylated-regions methylseq
Jupyter Notebook
•4•16•0•0•Updated Jun 6, 2025Jun 6, 2025
Fundamentals-of-Bioinformatics
Public
Introduction to bioinformatics command line tools on the cloud, developed by Dartmouth College
bash aws bioinformatics genomics command-line gcp cloud-computing genome-annotation google-cloud-platform introduction
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•6•9•0•0•Updated Jun 6, 2025Jun 6, 2025
Bulk-and-Single-Cell-RNAseq
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In this module, you will take a deeper look at RNA-sequencing using single-cell approaches and miRNA sequencing, and investigate their impacts on gene regulatio…
bioinformatics rna-seq aws-s3 deseq2 scrna-seq high-throughput-sequencing differential-gene-expression microrna-sequence single-cell-rna-seq gene-expression-omnibus
Jupyter Notebook
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Creative Commons Zero v1.0 Universal
•0•0•0•0•Updated Jun 6, 2025Jun 6, 2025
Analysis-of-Biomedical-Data-for-Biomarker-Discovery
Public
R-based module that uses machine learning in biomarker discovery
aws bioinformatics linear-regression gcp cloud-computing logistic-regression proteomics r-programming biomarker-discovery nih-nigms-sandbox
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•8•5•0•0•Updated Jun 6, 2025Jun 6, 2025
Introduction-to-Data-Science-for-Biology
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Python-based machine learning and data science module from SFSU developed for the NIGMS Sandbox project
aws data-science machine-learning bioinformatics gcp cloud-computing decision-trees model-evaluation health-data-analysis covid-19-data
Jupyter Notebook
•8•11•0•0•Updated Jun 6, 2025Jun 6, 2025
ATAC-Seq-and-Single-Cell-ATAC-Seq-Analysis
Public
ATAC-seq and scATAC-seq module developed by the University of Nebraska Medical Center
aws azure gcp genome-annotation atac-seq differential-peak-calling single-cell-analysis scatac-seq transcription-factor-footprinting
Jupyter Notebook
•5•10•0•0•Updated Jun 6, 2025Jun 6, 2025
Metagenomics-Analysis-of-Biofilm-Microbiome
Public
In this module, you will learn how to use a Docker container to analyze amplicon sequencing metagenomics data with common tools such as qiime2 and PICRUSt2
docker aws nextflow gcp metagenomics aws-batch biomarker-discovery microbiome-analysis quorum-sensing biofilm
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GNU General Public License v3.0
•4•8•0•0•Updated Jun 6, 2025Jun 6, 2025
Biomedical-Imaging-Analysis-using-AI-ML-Approaches
Public
Machine Learning module for cloud-based analyses developed as part of the NIGMS Sandbox Project
aws machine-learning computer-vision deep-learning gcp image-processing artificial-intelligence neural-networks cloud-computing data-analysis
Jupyter Notebook
•6•17•0•0•Updated Jun 6, 2025Jun 6, 2025
X-Ray-Crystallography-and-Molecular-Energies
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In this module, you will learn to solve protein structure from crystallography data. This course will cover detailed aspects of protein structures, from primary…
aws numpy protein-structure computational-biology scipy quantum-chemistry matplotlib biophysics phenix xray-crystallography
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Creative Commons Zero v1.0 Universal
•1•0•0•0•Updated Jun 6, 2025Jun 6, 2025
Population-Genomics-and-Phylogenetics-with-RADseq
Public
This repository provides a comprehensive tutorial for phylogenetic analysis, covering data collection, sequence alignment, tree construction, and interpretation…
python bioinformatics gcp computational-biology phylogenetic-trees phylogenetics population-genetics high-throughput-sequencing genome-assembly r-programming
Jupyter Notebook
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Creative Commons Zero v1.0 Universal
•0•1•0•0•Updated Jun 6, 2025Jun 6, 2025
16SrRNA-Microbial-Analysis
Public
This repository provides a cloud-based learning module for microbial analysis of 16S rRNA sequencing data. It covers principles, data preprocessing, taxonomic c…
ggplot2 bioinformatics docker-container computational-biology microbiome high-throughput-sequencing r-programming genomic-data-analysis phyloseq taxonomic-classification
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Creative Commons Zero v1.0 Universal
•0•0•0•0•Updated Jun 6, 2025Jun 6, 2025
NIGMS-Sandbox-Repository-Template
Public template
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MIT License
•2•0•0•1•Updated Jun 6, 2025Jun 6, 2025
Data-Science-Foundations-in-R
Public
This repository offers an introductory data science module using R and cloud computing on Google Cloud Platform (GCP). Key topics include R programming, Tidyver…
data-science ggplot2 rna-seq dplyr linear-regression gcp tidyverse deseq2 anova r-programming
Jupyter Notebook
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Creative Commons Zero v1.0 Universal
•1•1•0•0•Updated Jun 6, 2025Jun 6, 2025
Introduction-to-Phylogenetics
Public
This repository offers a tutorial for assembling RADseq data and performing basic population genetic and phylogenetic analyses. It runs on Google Cloud Platform…
aws phylogenetic-trees phylogenetics comparative-genomics nih evolutionary-biology sagemaker sars-cov-2 disease-dynamics phylogenetic-reconstruction
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Creative Commons Zero v1.0 Universal
•0•1•0•0•Updated Jun 6, 2025Jun 6, 2025
NIGMS-Sandbox
Public
Collection of cloud-based biomedical data science learning modules funded by the National Institute of General Medical Sciences at the NIH
bioinformatics google-cloud-platform life-sciences nih
Shell
•25•84•0•0•Updated Jun 6, 2025Jun 6, 2025
Chromatin-Occupancy
Public
In this module, you will learn how to perform the bioinformatics analysis of differential chromatin occupancy using data generated by three well-known high-thro…
bioinformatics transcription-factors gcp next-generation-sequencing epigenetics chip-seq atac-seq histone-modifications high-throughput-sequencing differential-gene-expression
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Creative Commons Zero v1.0 Universal
•1•1•0•0•Updated Jun 4, 2025Jun 4, 2025
AI-ML-For-Biomedical-Researchers
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This repository provides a practical, data-centric AI/ML module for biomedical researchers. It covers R programming, data preparation, model building, and AI/ML…
python aws machine-learning ai deep-learning tensorflow keras artificial-intelligence feature-engineering model-interpretation
Jupyter Notebook
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Creative Commons Zero v1.0 Universal
•0•1•0•0•Updated Jun 4, 2025Jun 4, 2025
Workshop-Tutorials
Public
Jupyter Notebook
•1•0•0•0•Updated Nov 18, 2024Nov 18, 2024
AWS-HealthOmics-Module-Template
Public
Template repo for NIGMS Sandbox modules that use AWS HealthOmics
MIT License
•1•0•0•0•Updated Nov 12, 2024Nov 12, 2024