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

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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.

Author
Xinan Yang <xyang2@uchicago.edu>; Bin Wang <binw@uchicago.edu>
Date of publication
None
Maintainer
Xinan Yang <xyang2@uchicago.edu> with contribution from Lorenzo Pesce <lpesce@uchicago.edu> and Ana Marija Sokovic <anamarija@uchicago.edu>
License
GPL-2
Version
1.6.0

View on Bioconductor

Man pages

addDescription
Retrieve "gene description" attributes for gene symbol.
Chipseq_Peak_demo
chip seq loci 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).

Files in this package

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