Links for Genomic Research
The links below are good starting points for genomic research*
*The core does not support these applications, it does not recommend these in place of proper graduate training.
Data Analysis
While raw data are always provided to the expert user, the core facility offers advanced data analysis and bioinformatics services. In genomics, transformation, filtering, analysis and presentation of large amounts of biological data for biological interpretation is a science called bioinformatics.
For those who like to manipulate their data, we recommend several graduate applications and classes in the Los Angeles Area. For example the R (Manual and classes, BioConductor, and BioPerl.
General Sites
- UCSC genome browser and Ensembl are biologist-friendly whole genome databases with easy access to tools for genes, sequence, regulation, polymorphisms, and expression data.
- EurExpress is a whole genome RNA in situ hybridization database.
- Linux is often the operating system of choice. The command line interface, 64 bit processing, and multiple languages enable programmers to transform, filter, and program these large datasets without limitations.
Microarray Specific Software
- dChip is biologist-friendly software for basic normalization, filtering, transformation, basic statistical analysis, and heat map generation.
- Stanford Microarray Database (SMD) was the first public set of biologist-friendly microarray databases and tools that can be used to upload raw or normalized data. It can be used to filter, build correlations, gene lists, and heat maps.
- Gene Expression Omnibus (GEO), Celcius, and Array Express are the largest public microarray databases in the world.
- UGET and Prospector are biologist-friendly tools to query the genome for similar expression or disease genes in linkage intervals.
- Affymetrix Expression Console Software is a basic tool for quality assessments and normalization of raw data.
