CPAT (Coding Potential Assessment Tool)
Lift over genomics coordinates between assemblies
Evaluate Protein Activity with Gene Expression
Tools to analyze and visualize DNA methylation data
Epidaurus is a program to visualize the epigenomic landscape of genomic regions of interest (TF bindings, TSS, etc).
RNA-seq QC Package
A bioinformatics tool to visualize and evaluate *known* gene fusions
A program to assess DNA contamination level