What is Goldmine?

Goldmine is an R package that integrates information to help biologists interpret the genomic ranges that result from epigenome-wide sequencing experiments. The package takes as input any set of genomic ranges (defined by chromosome, start, end) and will annotate these ranges with respect to known genes and features.

Key Features:

• Annotates genomic context for sets of genomic ranges (promoter, gene 3' end, exon, intron, intergenic)
• Detailed accounting of specific gene model and feature overlaps (including CpG islands/shores/shelves, COSMIC mutations, GWAS catalog loci, and ENCODE DNaseI sites)
• Downloads and caches the most up-to-date data from the UCSC Genome Browser (including gene sets: UCSC, RefSeq, ENSEMBL; feature sets: ENCODE ChIP-seq supertracks, ENCODE DNaseI supertrack, CpG islands; and all other tables available from UCSC.)
• Works for any species with an assembled and annotated genome available from UCSC

How to Use Goldmine

We have created a step-by-step how to for new users to learn the essential functions of the R package and perform an analysis on example data.

Step-by-Step How To:

• View Online
• Download PDF
• Download DOCX

For more advanced options, please refer to the function manual. This information is also available from within R using the "?" command.

Function Reference Manual:

• Download PDF

Citation

Please refer to our open access manuscript to learn more about Goldmine. Please cite this work if Goldmine is useful in your research.

Bhasin, JM and Ting, AH. (2016). Goldmine integrates information placing genomic ranges into meaningful biological contexts. Nucleic Acids Res. PMID: 26673711. PMCID: PMC4705678.

Contact and Help

Please open an issue on the Goldmine GitHub Issues page for questions, bug reports, or enhancement requests.

You may also contact the package author with questions or feedback: