R/zzz.R

In mglR: Master Gene List

.onAttach <- function(libname = '/Volumes/STORAGE/mgl', pkgname = 'mglpkg'){
	packageStartupMessage('Please cite and acknowledge as appropriate: \n
	Elements 1:5 - biomaRt:\n
(1) Durinck S, Spellman P, Birney E and Huber W (2009). "Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt." Nature Protocols, 4, pp. 1184-1191. \n
(2) Durinck S, Moreau Y, Kasprzyk A, Davis S, De Moor B, Brazma A and Huber W (2005). "BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis." Bioinformatics, 21, pp. 3439-3440. \n
	Element 6 - NCBI2R: \n
Scott Melville (2015). NCBI2R: Queries and Annotates SNPs, Genes and Pathway from NCBI. R package version 1.4.7. https://CRAN.R-project.org/package=NCBI2R \n
	Elements 7:11, 13:17, and 20 - GTEx:\n
The Genotype-Tissue Expression (GTEx) Project was supported by the Common Fund http://commonfund.nih.gov/GTEx/index of the Office of the Director of the National Institutes of Health, and by the NCI, NHGRI, NHLBI, NIDA, NIMH, and NINDS.  The data used for the analyses described in this manuscript were version 6p obtained from the GTEx Portal http://www.gtexportal.org/ on 01/03/2017.\n
	Element 12 - DNAse: \n
Maurano, Matthew T, Eric Haugen, Richard Sandstrom, Jeff Vierstra, Anthony Shafer, Rajinder Kaul, and John A Stamatoyannopoulos. 2015. "Large-Scale Identification of Sequence Variants Influencing Human Transcription Factor Occupancy in Vivo." Nature genetics 47 (12): 1393-1401. doi:10.1038/ng.3432. \n
	Element 15 - sqtlSeek: \n
(1) Monlong, J. et. al. Identification of genetic variants associated with alternative splicing using sQTLseekeR. Nat. Commun. 5:4698 doi:10.1038/ncomms5698 (2014) \n
(2) GTEx Consortium. (2015). The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans. Science (New York, NY) 348(6235), 648-660. http://doi.org/10.1126/science.1262110 \n 
	Element 16 - sqtlAltrans: \n
(1) Ongen, H. and Dermitzakis, E.T. (2015). Alternative Splicing QTLs in European and African Populations. American Journal of Human Genetics, 97(4), 567-575. http://doi.org/10.1016/j.ajhg.2015.09.004 \n
(2) GTEx Consortium. (2015). The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans. Science (New York, NY) 348(6235), 648-660. http://doi.org/10.1126/science.1262110\n
	Element 17 - pqtl: \n
Rivas MA, Pirinen M, Conrad DF, et. al. Impact of predicted protein-truncating genetic variants on the human transcriptome. Science (New York, NY). 2015; 348(6235):666-669. doi.10.1126/science.1261877. \n
	Element 18 - NHGRI-EBI GWAS Catalog: \n
Welter D, MacArthur J, Morales J, Burdett T, Hall P, Junkins H, Klemm A, Flicek P, Manolio T, Hindorff L, Parkinson H. The NHGRI GWAS Catalog, a curated resource of SNP-trait associations. Nucleic Acids Research, 2014, Vol. 42 (Database issue): D1001-D1006 \n
	Element 19 - GRASP: \n
(1)Leslie R, ODonnell CJ, Johnson AD (2014) GRASP: analysis of genotype-phenotype results from 1390 genome-wide association studies and corresponding open access database. Bioinformatics 30(12), i185-94. GRASP Build 2.0.0.0 \n
(2) Carey V (2016). grasp2db: grasp2db, sqlite wrap of GRASP 2.0. R package version 0.1.14. \n')
}