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2019-winter-bioinformatics_command_line_and_r_prerequisites_workshop

An introduction to the basics of bioinformatics for biologists. No data analysis experience necessary.

2021-march-introduction-to-r-for-bioinformatics

An introduction to the basic R programming for biologists. No data analysis experience necessary! Participants will gain skills necessary to run basic statistical analyses and generate figures in R.

2021-march-introduction-to-the-command-line-for-bioinformatics

An introduction to command line basics for bioinformatics. Aimed at giving biologists with little-to-no data analysis experience the tools to successfully run bioinformatics workflows on the command line.

2021-march-single-cell-rna-seq-analysis

A workshop for biologists preparing to run their first single-cell RNA Seq experiment. Participants should have some command line and R experience to participate successfully. We recommend our introductory courses for beginners!

2022_qupath_scripts

Assorted collection of QuPath scripts, likely between 2022 and 2023

2024_isb_workshop_practical_methods_in_spatial-omics

aaopto-aotf

python driver to control MPDSnCxx AOTF devices

abdiv

Alpha and beta diversity measures for community ecology

adv_scrnaseq_2020

Material for lectures and exercises of the SIB course "Advanced topics in single-cell transcriptomics" (May 2020)

advancedheatmaptutorial

for YouTube Channel

akoya_webinar_0622

alevin-fry

🐟 🔬🦀 alevin-fry is an efficient and flexible tool for processing single-cell sequencing data, currently focused on single-cell transcriptomics and feature barcoding.

alphadev

annotationhub

Client for the Bioconductor AnnotationHub web resource

applied-computational-genomics

Applied Computational Genomics Course at UU: Spring 2020

ashlar

ASHLAR: Alignment by Simultaneous Harmonization of Layer/Adjacency Registration

avillachlab-jenkins-dev-release-control

aware

AWARE: Contextualizing protein representations using deep learning on interactomes and single-cell experiments

awesome-deepbio

A curated list of awesome deep learning applications in the field of computational biology

bart

BART risk predictor (experimental)

bds-files

Supplementary files for my book, "Bioinformatics Data Skills"

be-view_app

bedtools2

bedtools - the swiss army knife for genome arithmetic

benchmarking-tools

Repository for the GA4GH Benchmarking Team work developing standardized benchmarking methods for germline small variant calls

beng469

best-of-ml-python

🏆 A ranked list of awesome machine learning Python libraries. Updated weekly.

bicseq2

BICSEQ2 pipeline for processing CPTAC3 somatic WGS CNA

bioawk

BWK awk modified for biological data

biocypher

A unifying framework for biomedical research knowledge graphs

biofx_python

Code for Mastering Python for Bioinformatics (O'Reilly, 2021, ISBN 9781098100889)