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This repo contains source code for the paper "Controlling bias and inflation in epigenome- and transcriptomewide association studies using the empirical null distribution" by Maarten van Iterson, Erik W. van Zwet and Bastiaan T. Heijmans.
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This repository gather all genomics data and analysis we performed on Zbtb24 in mouse embryonic stem cells.
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Generate and Annotate DNAse-seq footprint with Transcription factor binding sites.
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Mirrors / mutalyzer
Creative Commons Attribution Share Alike 4.0 InternationalMirror of https://github.com/LUMC/mutalyzer.git
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R scripts that could be useful for analysis in RP3. For example, extracting information from the metaDb, calculating GC content and length based on the exons files, RNAseq normalization e.g. cqn, ...
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anatomy / WebGL Viewer
Apache License 2.0Public repository containing the code for the open source WebGL viewer based on BabylonJS
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Sam Nooij / FECBUD functional analysis-HUMAnN
BSD 3-Clause "New" or "Revised" LicenseFunctional metagenomics analysis using the HUMAnN tool version 3
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This pipeline takes paired-end fastq files, does a quick genome assembly on them (via Velvet + kmergenie), and predicts antibiotic resistance via abricate.
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Scripts used for differential gene expression analysis and its reporting (currently for RNA-seq data)
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