Lab

R

The following Bioconductor packages will be used in class. We recommend that you visit the packages through the links below and explore their use.

1. Bioconductor is an open source and open development software projects for the analysis of high-throughput genomic and proteomic data. It uses the R statistical programming language. 
2. BioMart – genome annotations
3. Biostrings – manipulation of biological strings
4. BSgenome – full genomes and SNPs
5. GOexpress – gene ontology annotations
6. Limma – microarray data analysis
7. msa – multiple sequence alignment
8. rtracklayer – access to the UCSC Genome Browser
9. stringDB – interacting proteins database
10. systemPipeR – NGS workflows

UCSC GENOME BROWSER

1. Genome Browser
2. Table Browser
3. YouTube channel with training videos
4. FAQs
5. User guide