Nextflow training material

This is a collection of tutorials for learning how to use Docker with various tools. Contributions welcome.

resources for bioinformatics education

Curated list of project-based tutorials

A Python package to make publication-ready but customizable coefficient plots.

Scripts and lab notebooks for characterising the variant landscape of CYP2D6 in the SG10K_Health cohort

Allelic decomposition and exact genotyping of highly polymorphic and structurally variant genes

Install GISTIC2 by one line code; GISTIC2 docker image

Copy number variant detection from targeted DNA sequencing

MutSig2CV from Lawrence et al. 2014

resources for learning bioinformatics

A minimap2 frontend for PacBio native data formats

A centralized location for storing curated data from cBioPortal

An opinionated list of awesome Python frameworks, libraries, software and resources.

Using classification techniques (logistic regression model and random forest) to predict the diagnosis of breast tumor tissues as either malignant or benign based on ten cytological features.

Presentation-Ready Data Summary and Analytic Result Tables

Applied Computational Genomics Course at UU: Spring 2020

Allelic decomposition and exact genotyping of highly polymorphic and structurally variant genes

This is GWAS pipeline based on plink including QC, Imputation and Association analysis

A pipeline for Human GWAS analysis that accomodates both Affymetrix (raw .CEL files) and Illumina (Plink binaries) data

Calling star alleles in highly polymorphic pharmacogenes (e.g. CYP450 genes) by leveraging genome graph-based variant detection.

DeepSurv is a deep learning approach to survival analysis.

This has a shiny app that implements the rms package.