A Free Newsletter for Quantitative and Algorithmic Trading, Portfolio Analysis, and Investing

An open, collaborative project to analyze data from the Single-cell Pediatric Cancer Atlas (ScPCA) Portal

Rust bindings to minimap2 library

Repo for student website

Collection of modular Cytoscape tutorials for online presentation using reveal.js

A growing collection of bioinformatics tutorials, project guides, tools, and articles I’ve developed to make bioinformatics more accessible.

GWAS Tutorial for Beginners

Automation of in silico vaccine design based on B-cells and T-cells epitopes

Detecting methylation using signal-level features from Nanopore sequencing reads of plants

Plotting tools for nanopore methylation data

Set of tools to manipulate and visualize modified base bam files

VirMake is a Snakemake based pipeline that offers viral metagenic data analysis on paired-end data. It offers taxonomic and functional annotation, supports offline running and support for HPC clust…

A workflow for methylation analysis using long-read (ONT) sequencing data.

add statistical significance annotations on seaborn plots. Further development of statannot, with bugfixes, new features, and a different API.

Create phylogenetic trees from Bracken/Kraken2 reports

Yet Another Chimeric Read Detector

General statistics of Glittr.org. Comes with the manuscript.

📚 Freely available programming books

Applied Computational Genomics Course at UU: Spring 2020

Genomics Workshop Overview

Creates stacked bar plots from Kracken and Bracken output.

Investigating the impact of database choice and confidence score on the performance of metagenomic taxonomic classification

Rapid & standardized annotation of bacterial genomes, MAGs & plasmids

hybrid assembly pipeline for bacterial genomes

An accurate and sensitive bacterial plasmid identification tool based on deep machine-learning of shared k-mers and genomic features.

A complete guide for analyzing bulk RNA-seq data. Go from raw FASTQ files to mapping reads using STAR and differential gene expression analysis using DESeq2, using example data from Guo et al. 2019.

Notes, exercises and assignments for the Coursera Bioinformatics Specialization

Collection of bioinformatics training materials

SIB course that introduces analysis of NGS data