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Anna Obenauf
2020-05-20T00:08:32+02:00
Shona Cronin
PhD Student
Shona Cronin
PhD Student
Databases and data analysis tools
cBioPortal: Visualization, analysis and download of large scale cancer genomics datasets
ICGC Cancer Genome Projects
Tumor Portal: Genes, Cancers, DNA Mutations & Annotations (Eric Lander and Gad Getz labs)
Mutation aligner: Somatic mutation hotspots in protein domains in cancer (Sander lab)
Cancer Rx: Genomics of drug sensitivity in cancer
Encode: Encyclopedia of DNA Elements
STRING: Protein-Protein Interaction networks
COSMIC: Catalogue of somatic mutations in cancer (Sanger Institute)
ENRICHR: Gene set enrichment analysis (Malayan lab)
WebGestalt: Gene set enrichment analysis (Zhang lab)
David Bioinformatics Resources
Primer-Tm Calculator
Gibson assembly primer design tool
Other helpful lists on NEB:
List of restriction enzyme sequence recognition motifs
Plasmid database and helpful information and guides cloning elements, viruses and other cool cloning technologies
CRISPR tools:
Great webpage for CRISPR-technology related info and updates + sgRNA&HDR-template design tools (free sign-up required)
Different sgRNA design and evaluation tools:
CRISPOR
CRISPRscan
E-CRISP
Database for mouse qPCR primers
Primer-Blast – primer design and genomic off-target evaluation:
Sequence alignments – Clustal Omega
Blast
Expasy – resource on bioinformatic analysis tools
Translate sequences
Analyse protein sequence parameters
General databases and resources
NCBI
UCSC
PDB
Uniprot
ATCC (cell lines)
Jackson lab (mouse strains)
BRB tools: Visualization and statistical analysis of Microarray gene expression,
copy number, methylation and RNA-Seq data
Heatmap generator
Venn Diagram tool (UGent)
Biostatistics and computational biology software and database resources (Shirley Liu Lab)
Tools, protocols, templates
Useful numbers for cell culture (Corning)
Templates for multi-well templates
Spectrum Viewer (BD)
Calculator (Biomath Promega)
Calculator (Chemical)
Communication
MIT CommKit
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Databases and data analysis tools
Tools, protocols, templates
Communication
Databases and data analysis tools
cBioPortal: Visualization, analysis and download of large scale cancer genomics datasets
ICGC Cancer Genome Projects
Tumor Portal: Genes, Cancers, DNA Mutations & Annotations (Eric Lander and Gad Getz labs)
Mutation aligner: Somatic mutation hotspots in protein domains in cancer (Sander lab)
Cancer Rx: Genomics of drug sensitivity in cancer
Encode: Encyclopedia of DNA Elements
STRING: Protein-Protein Interaction networks
COSMIC: Catalogue of somatic mutations in cancer (Sanger Institute)
ENRICHR: Gene set enrichment analysis (Malayan lab)
WebGestalt: Gene set enrichment analysis (Zhang lab)
David Bioinformatics Resources
BRB tools: Visualization and statistical analysis of Microarray gene expression, copy number, methylation and RNA-Seq data
Heatmap generator
Venn Diagram tool (UGent)
Biostatistics and computational biology software and database resources (Shirley Liu Lab)
Tools, protocols, templates
Useful numbers for cell culture (Corning)
Templates for multi-well templates
Spectrum Viewer (BD)
Calculator (Biomath Promega)
Calculator (Chemical)
Communication
MIT CommKit
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