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1. DNABert2-RNAseq-classification-model DNABert2-RNAseq-classification-model Public

   Python scripts that are used to train and apply DNABert2 models to classify RNASeq reads to detect coinfections of IAV, IBV, RSV and SARS-CoV-2

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2. Observations-of-COVID-19-vaccine-coverage-and-hesitancy Observations-of-COVID-19-vaccine-coverage-and-hesitancy Public

   Git Repository for Observations of COVID-19 vaccine coverage and vaccine hesitancy on COVID-19 outbreak: An American ecological study

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3. SARS-CoV-2-RNAseq SARS-CoV-2-RNAseq Public

   Python scripts for SARS-CoV-2 bulk RNAseq

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4. SARS-CoV-2-transformer-based-model-training-dataset SARS-CoV-2-transformer-based-model-training-dataset Public

   Python scripts that allow user to locally subset any given large corpus dataset to pretrain and finetune transformer-based model by filtering out ambiguous sequences, and convert to model readable …

   Jupyter Notebook

5. kraken2_metagenomic kraken2_metagenomic Public

   Python scripts that download, trim, align SRA files to host genome, extract unaligned reads and detect pathogens using Kraken2

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6. Nextflow_bulk_RNAseq Nextflow_bulk_RNAseq Public

   Nextflow pipeline to trim, QC, align and quantify bulk RNA-seq fastq files

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