Package: GeoTcgaData 2.13.0

Erqiang Hu

GeoTcgaData: Processing Various Types of Data on GEO and TCGA

Gene Expression Omnibus(GEO) and The Cancer Genome Atlas (TCGA) provide us with a wealth of data, such as RNA-seq, DNA Methylation, SNP and Copy number variation data. It's easy to download data from TCGA using the gdc tool, but processing these data into a format suitable for bioinformatics analysis requires more work. This R package was developed to handle these data.

Authors:Erqiang Hu [aut, cre]

GeoTcgaData_2.13.0.tar.gz
GeoTcgaData_2.13.0.zip(r-4.7)GeoTcgaData_2.13.0.zip(r-4.6)GeoTcgaData_2.13.0.zip(r-4.5)
GeoTcgaData_2.13.0.tgz(r-4.6-any)GeoTcgaData_2.13.0.tgz(r-4.5-any)
GeoTcgaData_2.13.0.tar.gz(r-4.7-any)GeoTcgaData_2.13.0.tar.gz(r-4.6-any)
GeoTcgaData_2.13.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
GeoTcgaData/json (API)

# Install 'GeoTcgaData' in R:

install.packages('GeoTcgaData', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/yulab-smu/geotcgadata/issues

Datasets:

gene_cov - A data.frame of gene length and GC content
geneExpress - A data.frame of gene expression data
GSE66705_sample2 - A matrix of gene expression data in GEO
kegg_liver - A matrix of gene expression data in TCGA
module - A matrix of module name, gene symbols, and the number of gene symbols
profile - A matrix of gene expression data in TCGA
ventricle - A matrix of gene expression data in GEO

On BioConductor:GeoTcgaData-2.13.0(bioc 3.24)GeoTcgaData-2.12.0(bioc 3.23)

geneexpression differentialexpression rnaseq copynumbervariation microarray software dnamethylation differentialmethylation snp atacseq methylationarray

5.88 score 28 stars 27 scripts 23 exports 47 dependencies

Last updated from:9ffceb9e2f. Checks:1 NOTE, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	1368
linux-devel-x86_64	OK	1423
source / vignettes	OK	1456
linux-release-x86_64	OK	1439
macos-release-arm64	OK	1056
macos-oldrel-arm64	OK	1028
windows-devel	OK	1336
windows-release	OK	1186
windows-oldrel	OK	1191
wasm-release	OK	1300

Exports:array_preprocess cal_mean_module cluster_array combine_pvalue countToFpkm countToTpm differential_array differential_CNV differential_limma differential_methy differential_RNA differential_SNP differential_SNP_GEO differential_SNP_tcga fpkmToTpm gene_ave get_geo_array id_conversion_TCGA Merge_methy_tcga prepare_chi repAssign repRemove SNP_QC

Dependencies:abind assertthat Biobase BiocGenerics cli cpp11 cqn data.table DelayedArray farver generics GenomicRanges ggplot2 glue gtable IRanges isoband labeling lattice lifecycle MASS Matrix MatrixGenerics MatrixModels matrixStats mclust nor1mix plyr quantreg R6 RColorBrewer Rcpp rlang S4Arrays S4Vectors S7 scales Seqinfo SparseArray SparseM SummarizedExperiment survival topconfects vctrs viridisLite withr XVector

GeoTcgaData

Rendered fromGeoTcgaData.Rmdusingknitr::rmarkdown

Last update: 2023-02-20
Started: 2019-09-04

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Preprocess of Microarray data	array_preprocess
Find the mean value of the gene in each module	cal_mean_module
cluster probes of Microarray data	cluster_array
combine pvalues of SNP difference analysis result	combine_pvalue
Convert count to FPKM	countToFpkm
Convert count to Tpm	countToTpm
Differential analysis of Microarray data	differential_array
Do difference analysis of gene level copy number variation data	differential_CNV
differential_limma	differential_limma
differential_methy	differential_methy
differential_RNA	differential_RNA
Do difference analysis of SNP data	differential_SNP
Do difference analysis of SNP data downloaded from GEO	differential_SNP_GEO
Do difference analysis of SNP data downloaded from TCGAbiolinks	differential_SNP_tcga
Convert fpkm to Tpm	fpkmToTpm
Average the values of same genes in gene expression profile	gene_ave
a data.frame of gene length and GC content	gene_cov
a data.frame of gene expression data	geneExpress
Get Microarray matrix data from GEO	get_geo_array
a matrix of gene expression data in GEO	GSE66705_sample2
Convert ENSEMBL gene id to gene Symbol in TCGA	id_conversion_TCGA
a matrix of gene expression data in TCGA	kegg_liver
Merge methylation data downloaded from TCGA	Merge_methy_tcga
a matrix of module name, gene symbols, and the number of gene symbols	module
Preparer file for chi-square test	prepare_chi
a matrix of gene expression data in TCGA	profile
Handle the case where one id corresponds to multiple genes	repAssign
Handle the case where one id corresponds to multiple genes	repRemove
Do quality control of SNP data downloaded from TCGAbiolinks	SNP_QC
a matrix of gene expression data in GEO	ventricle