SNPsea protocols

View SNPsea computational protocol

SNPsea statistics

To access cutting-edge analytics on consensus tools, life science contexts and associated fields, you will need to subscribe to our premium service.

Subscribe
info

Citations per year

Citations chart
info

Popular tool citations

chevron_left Pathway analysis chevron_right
Popular tools chart
info

Tool usage distribution map

Tool usage distribution map
info

Associated diseases

Associated diseases

SNPsea specifications

Information


Unique identifier OMICS_18197
Name SNPsea
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data A list of SNP identifiers and a matrix of genes and conditions.
Input format TXT
Operating system Unix/Linux, Mac OS, Windows
Programming languages C++
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.0.3
Stability Stable
Source code URL https://codeload.github.com/slowkow/snpsea/tar.gz/v1.0.3
Maintained Yes

Download


Versioning


Add your version

Documentation


Maintainer


  • person_outline Soumya Raychaudhuri <>

Publication for SNPsea

SNPsea in pipeline

2016
PMCID: 4767573
PMID: 26808113
DOI: 10.1038/ng.3496

[…] enrichr: http://amp.pharm.mssm.edu/enrichr/, geneatlas: http://biogps.gnf.org, immgen, http://www.immgen.org/, fantom5: http://fantom.gsc.riken.jp/5/, snpsea: http://www.broadinstitute.org/mpg/snpsea/, r version 3.0.0: http://www.r-project.org/, proc: http://web.expasy.org/proc/, haplotter: http://haplotter.uchicago.edu/, hgdp selection browser: […]


To access a full list of citations, you will need to upgrade to our premium service.

SNPsea in publications

 (4)
PMCID: 5852557
PMID: 29370075
DOI: 10.3390/genes9020061

[…] database is a powerful resource where the link between gene and the tissue that is affected is investigated []. similarly, for many ocular traits, an ocular tissues database has been utilized []. snpsea is a tool developed at the broad institute (cambridge, ma, usa) to help prioritize the genetic associations to identify tissues and pathways that are affected by the expression of specific […]

PMCID: 5192301
PMID: 28070503
DOI: 10.1155/2016/7983236

[…] is to determine which pathways are affected by these mutations. common pathway resources and tools used for these types of analysis include kegg [], david [], string [], berex [], dapple [], and snpsea []., kegg represents one of the most popular databases for pathway analysis. david is a popular online tool for performing functional enrichment analysis based on user defined gene lists. […]

PMCID: 4889647
PMID: 27172182
DOI: 10.1534/g3.116.027326

[…] we aimed to elucidate the cell types, tissues, and pathways influenced by common variants in systemic lupus erythematosus (sle). we applied a nonparameter enrichment statistical approach, termed snpsea, in 181 single nucleotide polymorphisms (snps) that have been identified to be associated with the risk of sle through genome-wide association studies (gwas) in eastern asian and caucasian […]

PMCID: 4767573
PMID: 26808113
DOI: 10.1038/ng.3496

[…] identify which cell types significantly express sle candidate genes. specificity p-values were estimated based on the permutation of ranked expression levels for each locus (1010 permutations) using snpsea (, ). p-values (blue bars) that passed the multiple testing threshold (black line) show significant enrichment in sle loci. threshold lines are dependent on the number of categories present […]


To access a full list of publications, you will need to upgrade to our premium service.

SNPsea institution(s)
Bioinformatics and Integrative Genomics, Harvard University, Cambridge, MA, USA; Harvard-MIT Division of Health Sciences and Technology, Harvard Medical School, Boston, MA, USA; Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA; Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
SNPsea funding source(s)
Supported by the National Institutes of Health (5K08AR055688, 1R01AR062886-01, 1U01HG0070033, T32 HG002295/HG/ NHGRI, 7T32HG002295-10), the Arthritis Foundation and the Doris Duke Foundation.

SNPsea reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review SNPsea