FunciSNP: Integrating Functional Non-coding Datasets with Genetic Association Studies to Identify Candidate Regulatory SNPs

FunciSNP integrates information from GWAS, 1000genomes and chromatin feature to identify functional SNP in coding or non-coding regions.

Author
Simon G. Coetzee <simon@simoncoetzee.com> and Houtan Noushmehr, PhD <houtan@usp.br>
Date of publication
None
Maintainer
Simon G. Coetzee <simon@simoncoetzee.com>
License
GPL-3
Version
1.16.0
URLs

View on Bioconductor

Man pages

CorrelatedSNPs-class
Class '"CorrelatedSNPs"'
FunciSNPAnnotateSummary
Genomic Annotation of YAFSNPs.
FunciSNPbed
Creates a BED file to view YAFSNPs in your favorite genome...
FunciSNPidsFromSummary
coming soon.
FunciSNP-package
Functional Identification of SNPs with Phenotype by...
FunciSNPplot
FunciSNPplot to visualize YAFSNP summary.
FunciSNPsummaryOverlaps
Summarizes FunciSNP results by overlaps
FunciSNPtable
Will output a summary report from FunciSNP at specified...
getFSNPs
Functional Identification of SNPs with Phenotype by...
TagSNP-class
Class '"TagSNP"'
TSList-class
Class '"TSList"'

Files in this package

FunciSNP/DESCRIPTION
FunciSNP/NAMESPACE
FunciSNP/R
FunciSNP/R/classes.R
FunciSNP/R/funcisnp.R
FunciSNP/build
FunciSNP/build/vignette.rds
FunciSNP/data
FunciSNP/data/datalist
FunciSNP/data/glioma.rda
FunciSNP/inst
FunciSNP/inst/CITATION
FunciSNP/inst/NEWS
FunciSNP/inst/doc
FunciSNP/inst/doc/FunciSNP_vignette.R
FunciSNP/inst/doc/FunciSNP_vignette.Rnw
FunciSNP/inst/doc/FunciSNP_vignette.pdf
FunciSNP/inst/extdata
FunciSNP/inst/extdata/TFBS_Nrsf_U87.bed
FunciSNP/inst/extdata/TFBS_Pol2_U87.bed
FunciSNP/inst/extdata/glioma.snp
FunciSNP/man
FunciSNP/man/CorrelatedSNPs-class.Rd
FunciSNP/man/FunciSNP-package.Rd
FunciSNP/man/FunciSNPAnnotateSummary.Rd
FunciSNP/man/FunciSNPbed.Rd
FunciSNP/man/FunciSNPidsFromSummary.Rd
FunciSNP/man/FunciSNPplot.Rd
FunciSNP/man/FunciSNPsummaryOverlaps.Rd
FunciSNP/man/FunciSNPtable.Rd
FunciSNP/man/TSList-class.Rd
FunciSNP/man/TagSNP-class.Rd
FunciSNP/man/getFSNPs.Rd
FunciSNP/vignettes
FunciSNP/vignettes/FunciSNP_vignette.Rnw
FunciSNP/vignettes/UCSC_genomeviewer_glioma.pdf