Resources

Private (lab members only)

Tools

Gene Set Manager – https://lichtlab.cancer.ufl.edu/tools/gs/

Create and combine sets of genes (integrated with RNA-Seq reports).

Region Set Manager – https://lichtlab.cancer.ufl.edu/tools/rs/

Create and combine sets of genomic regions (integrated with ChIP-Seq reports).

Sets – https://lichtlab.cancer.ufl.edu/tools/sets/

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.