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adaptive-biotech-portfolio

Collection of my data science projects from Adaptive Biotechnologies.

arpir

Automatic RNA-Seq Pipelines with Interactive Report

aws

A collection of bash shell scripts for automating various tasks with Amazon Web Services using the AWS CLI and jq.

bash_tutorial

basic-snakemake-pipeline

bio_610b

Course materials for Advanced Biological Statistics II, Bio 610B, at the University of Oregon.

bioinformatics

Compilation of R and Python programming codes on the Data Professor YouTube channel.

bisr-rnaseq

cancer-biomarker-prediction-pipeline-campp

The Cancer bioMarker Prediction Pipeline (CAMPP)

cancer_var_call

celldancer

changeseq

CHANGE-seq analysis pipeline

codespaces-jupyter

Explore machine learning and data science with Codespaces

community-notebooks_ml-in-python-and-r

Repository for Jupyter Notebooks

cookbook-rpolars

Cookbook to provide solutions to common tasks and problems in using Polars with R

data-analysis

Data Science Using Python

data-engineer-handbook

This is a repo with links to everything you'd ever want to learn about data engineering

data-science-interview-questions-answers

Curated list of data science interview questions and answers

deepsomatic

DeepSomatic is an analysis pipeline that uses a deep neural network to call somatic variants from tumor-normal sequencing data.

depmap_practice

This is code from a tutorial on how to use DepMap from genetic data in cancer to find selected genes for targeted cell lines.

devops-roadmap

DevOps Roadmap for 2024. with learning resources

dna_rchitect

A Shiny App for visualizing genomic data

fastq-to-bam

Optimised pipeline to process whole genome sequence data from fastq to BAM on NCI Gadi

fetchngs

Pipeline to fetch metadata and raw FastQ files from public databases

firebrowser

An R client for broads firehose pipeline, providing TCGA data sets

gatk4-jupyter-notebook-tutorials

This repository contains Jupyter Notebooks containing GATK Best Practices Workflows

genome-analysis-pipeline

Genome Analysis Pipeline

glmmseq

Gene-level general linear mixed model

gwas-pipeline

This is a general (somewhat comprehensive) description of the LNG GWAS pipeline which can be used to guide researchers on how-to run a GWAS.

immunotherapy_scrnaseq_papers

A collection of immunotherapy papers with scRNAseq