R Package for specific expression analysis: pSI_1.1.tar
This package includes:
1) Streamlined functions for calculating the specificity index statistic from any gene expression dataset
2) Functions for statistical comparison of your candidate gene lists to pSI values
This package is also hosted at CRAN.
R Package containing all data from CSEA publication: pSI.data_1.0.tar
This package includes precalculated specificity index p-values (pSI) indicating specific and enriched transcripts for currently published bacTRAP cell types (as of Oct 2013).
Please reference PMID:20308160 and the CSEA publication (PMID: 24453331), when using these tools.
Installation
To install these packages, after downloading type the following commands into R (updating the path “~/Downloads” to the appropriate directory on your machine).
install.packages('~/Downloads/pSI_1.1.tar_.gz', repos = NULL, type="source")
install.packages('~/Downloads/pSI.data_1.0.tar_.gz', repos = NULL, type="source")
Note that pSI depends on the gdata package, which can be installed from CRAN.
Data for Tissue Specific Expression Analysis
These are also the data used in the article “The anatomical distribution of genetic association” in Nucleic Acids Research, available through PubMed Central. Table S1 is supplemental table 1 from the above paper and contains the mean summarized RPKM values for each coding gene in each tissue. Table S3 is supplemental table 3 from the above paper and contains the pSI values for each coding gene in each tissue. If you are interested in identifying sets of transcripts enriched in a particular tissue you can use the pSI value to filter for genes from Table S3.
tables1_nar_dougherty_tissue_rpkm_mean_summary_v3
tables3_nar_dougherty_tissue_gene_psi_v3-1
Example Script: TSEA_brain_filter_example_R_script
Questions or comments? Email: jdougherty_at_genetics.wustl.edu
Edited 04/15/16