Package: GeoTcgaData 2.7.0

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_2.7.0.tar.gz
GeoTcgaData_2.7.0.zip(r-4.5)GeoTcgaData_2.7.0.zip(r-4.4)GeoTcgaData_2.7.0.zip(r-4.3)
GeoTcgaData_2.7.0.tgz(r-4.4-any)GeoTcgaData_2.7.0.tgz(r-4.3-any)
GeoTcgaData_2.7.0.tar.gz(r-4.5-noble)GeoTcgaData_2.7.0.tar.gz(r-4.4-noble)
GeoTcgaData_2.7.0.tgz(r-4.4-emscripten)GeoTcgaData_2.7.0.tgz(r-4.3-emscripten)
GeoTcgaData.pdf |GeoTcgaData.html✨
GeoTcgaData/json (API)

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

Peer review:

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

Datasets:
  • GSE66705_sample2 - A matrix of gene expression data in GEO
  • geneExpress - A data.frame of gene expression data
  • gene_cov - A data.frame of gene length and GC content
  • 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-2.5.0(bioc 3.20)GeoTcgaData-2.4.0(bioc 3.19)

geneexpressiondifferentialexpressionrnaseqcopynumbervariationmicroarraysoftwarednamethylationdifferentialmethylationsnpatacseqmethylationarray

6.06 score 23 stars 25 scripts 354 downloads 23 exports 65 dependencies

Last updated 23 days agofrom:49ac154cac. Checks:OK: 2 ERROR: 5. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 30 2024
R-4.5-winERROROct 31 2024
R-4.5-linuxOKOct 30 2024
R-4.4-winERROROct 31 2024
R-4.4-macERROROct 31 2024
R-4.3-winERROROct 31 2024
R-4.3-macERROROct 31 2024

Exports:array_preprocesscal_mean_modulecluster_arraycombine_pvaluecountToFpkmcountToTpmdifferential_arraydifferential_CNVdifferential_limmadifferential_methydifferential_RNAdifferential_SNPdifferential_SNP_GEOdifferential_SNP_tcgafpkmToTpmgene_aveget_geo_arrayid_conversion_TCGAMerge_methy_tcgaprepare_chirepAssignrepRemoveSNP_QC

Dependencies:abindaskpassassertthatBiobaseBiocGenericsclicolorspacecqncrayoncurldata.tableDelayedArrayfansifarverGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegtablehttrIRangesisobandjsonlitelabelinglatticelifecyclemagrittrMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmclustmgcvmimemunsellnlmenor1mixopensslpillarpkgconfigplyrquantregR6RColorBrewerRcpprlangS4ArraysS4VectorsscalesSparseArraySparseMSummarizedExperimentsurvivalsystibbletopconfectsUCSC.utilsutf8vctrsviridisLitewithrXVectorzlibbioc

GeoTcgaData

Rendered fromGeoTcgaData.Rmdusingknitr::rmarkdownon Oct 30 2024.

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

Readme and manuals

Help Manual

Help pageTopics
Preprocess of Microarray dataarray_preprocess
Find the mean value of the gene in each modulecal_mean_module
cluster probes of Microarray datacluster_array
combine pvalues of SNP difference analysis resultcombine_pvalue
Convert count to FPKMcountToFpkm
Convert count to TpmcountToTpm
Differential analysis of Microarray datadifferential_array
Do difference analysis of gene level copy number variation datadifferential_CNV
differential_limmadifferential_limma
differential_methydifferential_methy
differential_RNAdifferential_RNA
Do difference analysis of SNP datadifferential_SNP
Do difference analysis of SNP data downloaded from GEOdifferential_SNP_GEO
Do difference analysis of SNP data downloaded from TCGAbiolinksdifferential_SNP_tcga
Convert fpkm to TpmfpkmToTpm
Average the values of same genes in gene expression profilegene_ave
a data.frame of gene length and GC contentgene_cov
a data.frame of gene expression datageneExpress
Get Microarray matrix data from GEOget_geo_array
a matrix of gene expression data in GEOGSE66705_sample2
Convert ENSEMBL gene id to gene Symbol in TCGAid_conversion_TCGA
a matrix of gene expression data in TCGAkegg_liver
Merge methylation data downloaded from TCGAMerge_methy_tcga
a matrix of module name, gene symbols, and the number of gene symbolsmodule
Preparer file for chi-square testprepare_chi
a matrix of gene expression data in TCGAprofile
Handle the case where one id corresponds to multiple genesrepAssign
Handle the case where one id corresponds to multiple genesrepRemove
Do quality control of SNP data downloaded from TCGAbiolinksSNP_QC
a matrix of gene expression data in GEOventricle