Private (lab members only)
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).
A web-based tool to evaluate the significance of intersections between sets. Also produces Venn diagrams.
- 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.