Resources

Private (lab members only)

Tools

Sets – http://lichtlab.cancer.ufl.edu/tools/sets/sets.py

A web-based tool to evaluate the significance of intersections between sets. Also produces Venn diagrams.

Useful sites

• Addgene – The non-profit plasmid repository.
• Bits of DNA – Lior Pachter’s computational biology blog
• Cancerrxgene – Genomics of Drug Sensitivity in Cancer.
• cBioPortal – Visualization, analysis and download of large-scale cancer genomics data sets.
• ChIP-Enrich and Broad-enrich – Gene set enrichment testing.
• ChromHMM – Chromatin state discovery and characterization.
• CistromeCancer – Predicted transcription factor targets and enhancer profiles in cancers.
• CiteAb – The Antibody Search Engine.
• DAVID – Database for Annotation, Visualization and Integrated Discovery.
• DeepBlue – Epigenomic Data Server.
• Deskgen – CRISPR/Cas9 guide RNA design software.
• Enrichr – Interactive and collaborative gene list enrichment analysis tool.
• IHEC – International Human Epigenome Consortium.
• LincsCloud – Catalog of gene-expression data collected from human cells treated with chemical compounds and genetic reagents.
• NCBI Probe – An online compendium of previously published probes including shRNA.
• Pan-Cancer Atlas – From the TCGA consortium.
• Reactome Icon Library and Servier SMART – Icons and graphical elements.
• RNA-Seqlopedia – Everything about RNA-Seq.
• UALCAN – Cancer transcriptome web portal.