National Institute of General Medical Sciences
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NIGMS-Sandbox
NIGMS-Sandbox PublicCollection of cloud-based biomedical data science learning modules funded by the National Institute of General Medical Sciences at the NIH
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DNA-Methylation-Sequencing-Analysis-with-WGBS
DNA-Methylation-Sequencing-Analysis-with-WGBS PublicIn 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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Biomedical-Imaging-Analysis-using-AI-ML-Approaches
Biomedical-Imaging-Analysis-using-AI-ML-Approaches PublicMachine Learning module for cloud-based analyses developed as part of the NIGMS Sandbox Project
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Integrating-Multi-Omics-Datasets
Integrating-Multi-Omics-Datasets PublicMulti-omics module that includes RNAseq, Epigenetics, and integrated multi-omics analyses developed as part of the NIGMS Sandbox project
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Metagenomics-Analysis-of-Biofilm-Microbiome
Metagenomics-Analysis-of-Biofilm-Microbiome PublicIn 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
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Introduction-to-Data-Science-for-Biology
Introduction-to-Data-Science-for-Biology PublicPython-based machine learning and data science module from SFSU developed for the NIGMS Sandbox project
Repositories
- 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
- NIGMS-Sandbox Public
Collection of cloud-based biomedical data science learning modules funded by the National Institute of General Medical Sciences at the NIH
- NIGMS-Sandbox-Repository-Template Public template
- Fundamentals-of-Bioinformatics Public
Introduction to bioinformatics command line tools on the cloud, developed by Dartmouth College
- 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
- RNA-Seq-Differential-Expression-Analysis Public
RNAseq workflow run using Snakemake on Google Cloud Platform, developed as part of the NIH NIGMS Sandbox
- ATAC-Seq-and-Single-Cell-ATAC-Seq-Analysis Public
ATAC-seq and scATAC-seq module developed by the University of Nebraska Medical Center
- 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
- Consensus-Pathway-Analysis-in-the-Cloud Public
Consensus pathway analysis module developed by the University of Nevada at Reno
- Analysis-of-Biomedical-Data-for-Biomarker-Discovery Public
R-based module that uses machine learning in biomarker discovery
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