wirawara

itaconate_paper

Code to analyze human samples

targetedmetabolomics_paper

Code to analyze targeted metabolomics, RNAseq, scRNAseq and other miscellaneous in vitro metabolomics data

SpatialBook

Book on Spatial Omics Analysis with Bioconductor

spatialdata

An open and universal framework for processing spatial omics data

starting_with_docker

docker pipelines

GWAS-stats-genetics

resources when working with GWAS summary stats

Giotto

Spatial omics analysis toolbox

BgeeDB

an R package for retrieval of curated expression datasets and for gene list expression localization enrichment tests, Komljenovic et al. f1000Research

versatile-genomics-scripts

wirawara.github.io

Andrea's github pages

Lifespan-paper-collaboration

code to analyze RNA-seq and microarrays, for lifespan paper

SpatialExperiment

Spatial_ATAC-seq

Bioinfo_Pipelines

Pipelines for RNAseq, Chipseq, ...

ogb

Benchmark datasets, data loaders, and evaluators for graph machine learning

Gviz_visualizations

Collection of the scripts for the integrative sequencing visualizations

cromwell

Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments

Cross_species_integration

Code to analyze cross-species functional modules link proteostasis to human normal aging, Komljenovic et al. Plos Comp Bio

scQC

an R package; a method for multivariate QC for large-scale single-cell RNA-seq datasets.

regression_survival_analysis_R

collection of the R scripts for the clinical datasets

miloR

R package implementation of Milo for testing for differential abundance in KNN graphs

chip-seq-pipeline2

ENCODE ChIP-seq pipeline

omicsplayground

Visual self-service analytics platform for big omics data.

feather

Feather: fast, interoperable binary data frame storage for Python, R, and more powered by Apache Arrow

Basset

Convolutional neural network analysis for predicting DNA sequence activity.

remake

Make-like declarative workflows in R

EpigenomicsTutorial-ISMB2017

Repository for the Epigenomics Tutorial hold at ISMB 2017 in Prague

python-machine-learning-book

The "Python Machine Learning" book code repository and info resource

BiocAdvanced

Advanced R / Bioconductor training material

phd_thesis_markdown

Template for writing a PhD thesis in Markdown