MATHIEU LUPIEN RESEARCH LABORATORY

TOOLS



Variant Set Enrichment (VSE) - click to link to GitHub

Used to reveal the genomic features most significantly targeted by genetic predispositions to a given disease.



IntraGenomic Replicates (IGR) - click to link to reference

Used to reveal if a particular single nucleotide variant can alter the chromatin binding affinity for a transcription factor.



Allele-specific Binding from ChIP-seq (ABC) - click to link to GitHub

Used to identify Single Nucleotide Variants (either SNPs or mutations) that alter the binding affinity of transcription factors based on ChIP-seq data.


ERR022033.sorted.sam.gz compressed SAM file

ABC_SNPs.txt compressed text file



Cross Cell-type Correlation in DNA accessibility (C3D) - click to link to GitHub

Used to delineate correlation between two distinct genomic coordinates, inferring physical and or functional interaction.



Clustering of genomic REgions Analysis Method (CREAM) - click to link to CRAN

CREAM is a method for identification of clusters of genomic regions within chromosomes, including of "Cluster of Regulatory Elements/Super-enhancers, Large Organized Chromatin Lysine (K) modification domains (LOCKs), etc) .