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  1. deep-learning-long-read-sequencing deep-learning-long-read-sequencing Public

    variant calling followed by deep learning modeling (MLP, CNN, RNN, LSTM) of sequencing artifacts in Oxford Nanopore Technologies (ONT) WGS data

    Jupyter Notebook

  2. RNA-seq RNA-seq Public

    Nextflow pipeline for Salmon quantification of HSC bulk RNA-seq data followed by R/Bioconductor analysis

    Jupyter Notebook

  3. scRNA-seq scRNA-seq Public

    Seurat R/Bioconductor scRNA-seq analysis of non-small-cell lung cancer (NSCLC) cells compared to normal lung cells

    Jupyter Notebook

  4. scATAC-seq scATAC-seq Public

    Signac R/Bioconductor scATAC-seq analysis comparing chromatin accessibility in hematopoietic stem cells (HSCs) of young vs aged mice

    Jupyter Notebook

  5. exome-sequencing exome-sequencing Public

    SLURM bash pipeline/workflow for downloading and analyzing exome sequencing NGS data from the SRA database on HPC cluster

    Shell

  6. whole-genome-sequencing-cloud whole-genome-sequencing-cloud Public

    WDL/Cromwell GATK WGS workflow running on Google Cloud Platform (GCP) preemptible spot instances using Docker containers

    WDL