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basset

Convolutional neural network analysis for predicting DNA sequence activity.

bgeedb

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

biocadvanced

Advanced R / Bioconductor training material

bioinfo_pipelines

Pipelines for RNAseq, Chipseq, ...

chip-seq-pipeline2

ENCODE ChIP-seq pipeline

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

epigenomicstutorial-ismb2017

Repository for the Epigenomics Tutorial hold at ISMB 2017 in Prague

feather

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

giotto

Spatial omics analysis toolbox

gviz_visualizations

Collection of the scripts for the integrative sequencing visualizations

gwas-stats-genetics

resources when working with GWAS summary stats

integrative

Software Pipeline for Integrative Genetic Association Analysis: Probabilistic Assessment of Enrichment and Colocalization

itaconate_paper

Code to analyze human samples

lifespan-paper-collaboration

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

milor

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

ogb

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

omicsplayground

Visual self-service analytics platform for big omics data.

oncogenesis-paper-

Code to analyze Epigenetic silencing of monoallelically methylated miRNA loci in precancerous colorectal lesions.

phd_thesis_markdown

Template for writing a PhD thesis in Markdown

python-machine-learning-book

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

regression_survival_analysis_r

collection of the R scripts for the clinical datasets

remake

Make-like declarative workflows in R

scqc

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

sequence-a-genome

Source files of materials for practicals of sequence a genome, spring 2016.

spatial_atac-seq

spatialbook

Book on Spatial Omics Analysis with Bioconductor

spatialdata

An open and universal framework for processing spatial omics data

spatialexperiment

starting_with_docker

docker pipelines