seq2pathway: a novel tool for functional gene-set (or termed as pathway) analysis of next-generation sequencing data
Version 1.8.0

Seq2pathway is a novel tool for functional gene-set (or termed as pathway) analysis of next-generation sequencing data, consisting of "seq2gene" and "gene2path" components. The seq2gene links sequence-level measurements of genomic regions (including SNPs or point mutation coordinates) to gene-level scores, and the gene2pathway summarizes gene scores to pathway-scores for each sample. The seq2gene has the feasibility to assign both coding and non-exon regions to a broader range of neighboring genes than only the nearest one, thus facilitating the study of functional non-coding regions. The gene2pathway takes into account the quantity of significance for gene members within a pathway compared those outside a pathway. The output of seq2pathway is a general structure of quantitative pathway-level scores, thus allowing one to functional interpret such datasets as RNA-seq, ChIP-seq, GWAS, and derived from other next generational sequencing experiments.

Browse man pages Browse package API and functions Browse package files

AuthorXinan Yang <xyang2@uchicago.edu>; Bin Wang <binw@uchicago.edu>
Bioconductor views Software
Date of publicationNone
MaintainerXinan Yang <xyang2@uchicago.edu> with contribution from Lorenzo Pesce <lpesce@uchicago.edu> and Ana Marija Sokovic <anamarija@uchicago.edu>
LicenseGPL-2
Version1.8.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("seq2pathway")

Man pages

addDescription: Retrieve "gene description" attributes for gene symbol.
Chipseq_Peak_demo: chip seq loci data example
dat_chip: chip seq data example
dat_RNA: RNA sequence data example
FisherTest_GO_BP_MF_CC: A wrapper function to perform the Fisher's exact test, using...
FisherTest_MsigDB: A wrapper function to perform conditional Fisher's exact...
gene2pathway_test: A wrapper function to perform gene2pathway test.
GRanges_demo: loci information with GRanges format
runseq2gene: R wrapped python function to map genomic regions on the...
runseq2pathway: An function to perform the runseq2pathway algorithm(s).

Functions

Chipseq_Peak_demo Man page
FAIME Source code
FAIME_EmpiricalP Source code
FisherTest_GO_BP_MF_CC Man page Source code
FisherTest_MsigDB Man page Source code
GRanges_demo Man page
KSrank Source code
KSrank_EmpiricalP Source code
Normalize_F Source code
Peak_Gene_Collapse Source code
addDescription Man page Source code
cumulativerank Source code
cumulativerank_EmpiricalP Source code
dat_RNA Man page
dat_chip Man page
gene2pathway_test Man page Source code
rungene2pathway Source code
rungene2pathway_EmpiricalP Source code
runseq2gene Man page Source code
runseq2pathway Man page Source code

Files

DESCRIPTION
NAMESPACE
R
R/seq2pathway-internal.r
build
build/vignette.rds
data
data/Chipseq_Peak_demo.rda
data/GRanges_demo.rda
data/dat_RNA.rda
data/dat_chip.rda
data/datalist
inst
inst/CITATION
inst/NEWS
inst/doc
inst/doc/seq2pathwaypackage.R
inst/doc/seq2pathwaypackage.Rnw
inst/doc/seq2pathwaypackage.pdf
inst/extexample
inst/extexample/Chipseq_peak_annotation.txt
inst/scripts
inst/scripts/Function_PeakMutationAnnotation_GENCODE_05182015.py
inst/seq2pathwaypackage.pdf
man
man/Chipseq_Peak_demo.Rd
man/FisherTest_GO_BP_MF_CC.Rd
man/FisherTest_MsigDB.Rd
man/GRanges_demo.Rd
man/addDescription.Rd
man/dat_RNA.rd
man/dat_chip.rd
man/gene2pathway_test.Rd
man/runseq2gene.Rd
man/runseq2pathway.Rd
vignettes
vignettes/Fig1_seq2gene.png
vignettes/Fig2_pseudo_scripts_bin_07102014_xy_v2.png
vignettes/Fig3_search_radius_xy.png
vignettes/Fig4_promoter_radius.jpg
vignettes/Fig5_PeakMtoStart_V4.png
vignettes/Fig6_type_xy.png
vignettes/Fig7_BidirectionalRegion.jpg
vignettes/Fig8_gene2pathway_flowchart_xy.png
vignettes/Fig9_Fisher_v2.png
vignettes/seq2pathwaypackage.Rnw
seq2pathway documentation built on May 20, 2017, 10:34 p.m.