ucsc-browser

Generate IGV style locus tracks from bigWig files in R

An R package designed to integrate and visualize various levels of epigenomic information, including but not limited to: ChIP, Histone, ATAC, and RNA sequencing. epiRomics is also designed to identify enhancer and enhanceosome regions from these data.

Create UCSC Track Hubs with ease

Process UCSC multiple alignment database, e.g. extract metadata, choose subset of species.

An install script for the UCSC Genome Browser

Python tool for assessing genomic coordinate liftOver results using exact alignment geometry, UCSC comparative evidence, reverse liftOver and flanking-context checks, and provenance-aware interpretation.

Biplots, Volcano plots, PCA plots, Heatmaps and more Computational Genomics data created and visualized during University of Pittsburgh course, Computational Biology (BIOSC1540), with Dr. Miler Lee

Variant pathogenicity analysis using ClinVar, OMIM, UCSC, ACMG, and VCF annotation (GRCh38).

Sequencing data preprocessing

An introductory activity for epigenetics, or the idea of "nature versus nurture" in genetics. Learners use the UCSC Genome Browser.

This folder contains R scripts for differential expression analysis and analyses of tissue-specific expression, inter-species conservation, and genetic variations of the CAPN10 gene in a bioinformatics project on PCOS and insulin resistance.

Permutation-based spatial association analysis of transposable elements and pathogenic SNPs in the human genome (hg38) — MSc Dissertation, University of Edinburgh

An easy to use tool to generate heatmap like tracks for the UCSC Genome Browser