Some useful resources and tools we use in our research and want to share with you.
cBioPortal – Visualization, analysis and download of large scale cancer genomics datasets
Cancer Therapy response Portal (Broad) – Links genetic, lineage, and other cellular features of cancer cell lines to small-molecule sensitivity
DepMap – Database showing the dependency of a gene of interest in different cancer types, based on published loss-of-function/RNAi screens; integrates Project Achilles and the Avana/Ceres datasets
Interactome Insider – Tool to assess protein-protein interactions, explore disease mutations and study mutation profiles
ICGC Cancer Genome Projects – Cancer genome database
Tumor Portal – Genes, Cancers, DNA Mutations & Annotations (Eric Lander and Gad Getz labs)
Mutation aligner – Enables exploration of somatic mutation hotspots in protein domains in cancer (Sander lab)
Cancer Rx – Database correlating drug sensitivity with genomic data in cancer
ENCODE – Interactive webface providing information on DNA elements in the human genome
STRING – Database of known and predicted protein-protein interaction networks
COSMIC – Catalogue of somatic mutations in cancer (Sanger Institute)
ENRICHR – Gene set enrichment analysis tool to analyse gene lists/data sets for enriched pathways or GO terms (Ma’ayan lab)
WebGestalt – Gene set enrichment analysis tool (Zhang lab)
DAVID – Functional annotation tool for gene lists
NEB restriction enzyme list and sequence recognition motifs
Addgene plasmid database and helpful information and guides cloning elements, viruses and other cool cloning technologies
Different sgRNA design and evaluation tools:
General databases and resources
BRB tools: Visualization and statistical analysis of Microarray gene expression,
copy number, methylation and RNA-Seq data
Venn Diagram tool (UGent)
CaTCH Addgene – Plasmids and maps are deposited here
CaTCH GitHub – Code for CaTCH experiment data analysis (Galaxy pipeline, …)
MIT CommKit – Communications guide from the Broad institute
iBiology – Instructive videos on different areas in biology.
Keep Science Going – A resource for online tutorials and webinars for home office.
Nature Online Resources
The PhD collection – Articles for future and current PhD students.
Scientific data collection – Articles on scientific data, collaboration and publishing.
Mentoring collection – Articles with advice for (future) mentors and mentees.
Science careers and mental health collection – Articles with a focus on mental health for PhD students and scientists in general.
Nature Masterclasses – Next to paid content also free resources, e.g. on Peer Review.
Comic relief: xkcd If things stop working altogether.
Hannes Zuber and Anna recently gave a lecture about “Current Trends in Cancer Research: Cancer Genomes, Genetic Tools and Immunotherapy”