This is a non-comprehensive list of free software and sites used in my research.
Image analysis software
- Cell Profiler/Cell Analyst. An open-source software designed to enable biologists without training in programming to quantitatively measure phenotypes from thousands of images automatically, developed and maintained by the Broad Institute.
- Fiji-ImageJ. Hugely popular and versatile open source image processing package.
Functional genomic analysis software
- R2: Genomics analysis and visualization platform.
- The human Protein Atlas. Information on localization and expression of the majority of all human protein-coding genes. Includes the Pathology Atlas, with mRNA and protein expression data for the most common forms of human cancer.
- The Cell Image Library. A collection of freely available images of cells and organelles.
- PedcBioPortal: childhood cancer genomics portal
- St Jude cloud PeCAN: Pediatric cancer data portal.
Cancer data resources
- Geo: curated gene expression datasets.
- TCGA: Cancer Genome atlas from the NIH.
- Array Express: European archive of Functional Genomics Data from high-throughput functional genomics experiments.
- Cancer Cell Line Encyclopedia (CCLE): genetic characterization of a large panel of human cancer cell lines.
- The Resistant Cancer Cell Line (RCCL) collection from the University of Kent.
- PedcBioPortal: childhood cancer genomics
Please email for specific lab protocols.