iGC: An integrated analysis package of Gene expression and Copy number alteration

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This package is intended to identify differentially expressed genes driven by Copy Number Alterations from samples with both gene expression and CNA data.

Author
Yi-Pin Lai [aut], Liang-Bo Wang [aut, cre], Tzu-Pin Lu [aut], Eric Y. Chuang [aut]
Date of publication
None
Maintainer
Liang-Bo Wang <r02945054@ntu.edu.tw>
License
GPL-2
Version
1.4.0
URLs

View on Bioconductor

Man pages

create_gene_cna
Load and map CNA gain/loss onto human gene location by genome...
create_gene_exp
Create an joint gene expression table of all samples
create_sample_desc
Create sample description table containing all required...
direct_gene_cna
Load the existed CNA gain/loss based on gene location.
find_cna_driven_gene
Perform an integrated analysis of gene expression (GE) and...
hg19DBNM
hg19-RefSeq
iGC
iGC: an integrated analysis package of gene expression and...

Files in this package

iGC/DESCRIPTION
iGC/NAMESPACE
iGC/R
iGC/R/create_gene_exp.R
iGC/R/create_sample_desc.R
iGC/R/data_hg19DBNM.R
iGC/R/direct_gene_cna.R
iGC/R/faster_gene_cna.R
iGC/R/find_cna_driven_gene.R
iGC/R/iGC.R
iGC/build
iGC/build/vignette.rds
iGC/data
iGC/data/hg19DBNM.rda
iGC/inst
iGC/inst/CITATION
iGC/inst/NEWS.Rd
iGC/inst/doc
iGC/inst/doc/Introduction.R
iGC/inst/doc/Introduction.Rmd
iGC/inst/doc/Introduction.html
iGC/inst/extdata
iGC/inst/extdata/CNA
iGC/inst/extdata/CNA/A04_697150.hg19.txt
iGC/inst/extdata/CNA/A05_697032.hg19.txt
iGC/inst/extdata/CNA/A07_697200.hg19.txt
iGC/inst/extdata/CNA/A09_697146.hg19.txt
iGC/inst/extdata/CNA/B01_697160.hg19.txt
iGC/inst/extdata/CNA/B03_697186.hg19.txt
iGC/inst/extdata/CNA/B05_697036.hg19.txt
iGC/inst/extdata/CNA/B07_697190.hg19.txt
iGC/inst/extdata/CNA/B08_697166.hg19.txt
iGC/inst/extdata/CNA/B10_697116.hg19.txt
iGC/inst/extdata/CNA/B11_697062.hg19.txt
iGC/inst/extdata/CNA/C01_697154.hg19.txt
iGC/inst/extdata/CNA/C02_697152.hg19.txt
iGC/inst/extdata/CNA/C03_707088.hg19.txt
iGC/inst/extdata/CNA/C04_697074.hg19.txt
iGC/inst/extdata/CNA/C06_697142.hg19.txt
iGC/inst/extdata/GE
iGC/inst/extdata/GE/US82800149_251976012154_S01.tcga_level3.txt
iGC/inst/extdata/GE/US82800149_251976012155_S01.tcga_level3.txt
iGC/inst/extdata/GE/US82800149_251976012200_S01.tcga_level3.txt
iGC/inst/extdata/GE/US82800149_251976012204_S01.tcga_level3.txt
iGC/inst/extdata/GE/US82800149_251976012205_S01.tcga_level3.txt
iGC/inst/extdata/GE/US82800149_251976012210_S01.tcga_level3.txt
iGC/inst/extdata/GE/US82800149_251976012261_S01.tcga_level3.txt
iGC/inst/extdata/GE/US82800149_251976012263_S01.tcga_level3.txt
iGC/inst/extdata/GE/US82800149_251976012264_S01.tcga_level3.txt
iGC/inst/extdata/GE/US82800149_251976012483_S01.tcga_level3.txt
iGC/inst/extdata/GE/US82800149_251976012487_S01.tcga_level3.txt
iGC/inst/extdata/GE/US82800149_251976012503_S01.tcga_level3.txt
iGC/inst/extdata/GE/US82800149_251976012504_S01.tcga_level3.txt
iGC/inst/extdata/GE/US82800149_251976012510_S01.tcga_level3.txt
iGC/inst/extdata/GE/US82800149_251976012512_S01.tcga_level3.txt
iGC/inst/extdata/GE/US82800149_251976012517_S01.tcga_level3.txt
iGC/inst/extdata/sample_desc.csv
iGC/man
iGC/man/create_gene_cna.Rd
iGC/man/create_gene_exp.Rd
iGC/man/create_sample_desc.Rd
iGC/man/direct_gene_cna.Rd
iGC/man/find_cna_driven_gene.Rd
iGC/man/hg19DBNM.Rd
iGC/man/iGC.Rd
iGC/vignettes
iGC/vignettes/Introduction.Rmd
iGC/vignettes/pics
iGC/vignettes/pics/analysis_workflow.png