{ "_id": "6a494db6f6c47c4419499dce", "Package": "GeoTcgaData", "Type": "Package", "Title": "Processing Various Types of Data on GEO and TCGA", "Version": "2.13.0", "Authors@R": "person(given = \"Erqiang\", family = \"Hu\", email = \"13766876214@163.com\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-1798-7513\"))", "Description": "Gene Expression Omnibus(GEO) and The Cancer Genome Atlas\n(TCGA) provide us with a wealth of data, such as RNA-seq, DNA\nMethylation, SNP and Copy number variation data. It's easy to\ndownload data from TCGA using the gdc tool, but processing\nthese data into a format suitable for bioinformatics analysis\nrequires more work. This R package was developed to handle\nthese data.", "License": "Artistic-2.0", "Encoding": "UTF-8", "RoxygenNote": "7.2.3", "VignetteBuilder": "knitr", "Language": "en-US", "URL": "https://github.com/YuLab-SMU/GeoTcgaData", "BugReports": "https://github.com/YuLab-SMU/GeoTcgaData/issues", "biocViews": "GeneExpression, DifferentialExpression, RNASeq,\nCopyNumberVariation, Microarray, Software, DNAMethylation,\nDifferentialMethylation, SNP, ATACSeq, MethylationArray", "Config/testthat/edition": "3", "Config/pak/sysreqs": "zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 13:00:16 UTC", "RemoteUrl": "https://github.com/bioc/GeoTcgaData", "RemoteRef": "HEAD", "RemoteSha": "9ffceb9e2fdfcd89ec52afabb14f510a85a1c583", "NeedsCompilation": "no", "Packaged": { "Date": "2026-07-03 21:47:32 UTC", "User": "root" }, "Author": "Erqiang Hu [aut, cre] (ORCID: )", "Maintainer": "Erqiang Hu <13766876214@163.com>", "_user": "bioc", "_type": "src", "_file": "GeoTcgaData_2.13.0.tar.gz", "_fileid": "https://r2.ropensci.org/bb3cb7efb5e2b808ba881300e0a04d1092acffc58f5deda6532731b3ccc700a4", "_filesize": 3636153, "_sha256": "bb3cb7efb5e2b808ba881300e0a04d1092acffc58f5deda6532731b3ccc700a4", "_expires": "2026-10-12T18:15:16.000Z", "_created": "2026-07-03T21:47:32.000Z", "_published": "2026-07-04T18:15:18.829Z", "_bioccheck": { "error": 0, "warning": 0, "note": 7 }, "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/28683963949", "_status": "success", "_upstream": "https://github.com/bioc/GeoTcgaData", "_commit": { "id": "9ffceb9e2fdfcd89ec52afabb14f510a85a1c583", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777381216 }, "_maintainer": { "name": "Erqiang Hu", "email": "13766876214@163.com", "login": "huerqiang", "description": "", "uuid": 48857018, "orcid": "0000-0002-1798-7513" }, "_distro": "resolute", "_jobs": [ { "job": 85155411498, "time": 1368, "config": "bioc-checks", "r": "4.6.1", "check": "NOTE", "artifact": "8075430934" }, { "job": 85155411362, "time": 1423, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "8075439200" }, { "job": 85155411552, "time": 1439, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "8075441444" }, { "job": 85155411391, "time": 1028, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "8075377511" }, { "job": 85155411400, "time": 1056, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "8075382031" }, { "job": 85155411249, "time": 1456, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "8075205959" }, { "job": 85155411319, "time": 1300, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "8075420509" }, { "job": 85155411397, "time": 1336, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "8075426292" }, { "job": 85155411418, "time": 1191, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "8075403439" }, { "job": 85155411493, "time": 1186, "config": "windows-release", "r": "4.6.1", "check": "OK", "artifact": "8075402642" } ], "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.2.0", "role": "Depends" }, { "package": "utils", "role": "Imports" }, { "package": "data.table", "role": "Imports" }, { "package": "plyr", "role": "Imports" }, { "package": "cqn", "role": "Imports" }, { "package": "topconfects", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "SummarizedExperiment", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "DESeq2", "role": "Suggests" }, { "package": "S4Vectors", "role": "Suggests" }, { "package": "ChAMP", "role": "Suggests" }, { "package": "impute", "role": "Suggests" }, { "package": "tidyr", "role": "Suggests" }, { "package": "clusterProfiler", "role": "Suggests" }, { "package": "org.Hs.eg.db", "role": "Suggests" }, { "package": "edgeR", "role": "Suggests" }, { "package": "limma", "role": "Suggests" }, { "package": "quantreg", "role": "Suggests" }, { "package": "minfi", "role": "Suggests" }, { "package": "IlluminaHumanMethylation450kanno.ilmn12.hg19", "role": "Suggests" }, { "package": "dearseq", "role": "Suggests" }, { "package": "NOISeq", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" }, { "package": "CATT", "role": "Suggests" }, { "package": "TCGAbiolinks", "role": "Suggests" }, { "package": "enrichplot", "role": "Suggests" }, { "package": "GEOquery", "role": "Suggests" }, { "package": "BiocGenerics", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "2.13.0", "bioc": "3.24" }, { "branch": "release", "version": "2.12.0", "bioc": "3.23" } ], "_topics": [ "geneexpression", "differentialexpression", "rnaseq", "copynumbervariation", "microarray", "software", "dnamethylation", "differentialmethylation", "snp", "atacseq", "methylationarray" ], "_stars": 28, "_contributors": [ { "user": "huerqiang", "count": 143, "uuid": 48857018 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 445, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_devurl": "https://github.com/yulab-smu/geotcgadata", "_searchresults": 27, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/GeoTcgaData.html", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/yulab-smu/geotcgadata", "_realowner": "bioc", "_cranurl": false, "_releases": [ { "version": "0.1.0", "date": "2019-09-16" }, { "version": "0.2.0", "date": "2019-09-23" }, { "version": "0.2.2", "date": "2020-01-07" }, { "version": "0.2.3", "date": "2020-02-23" }, { "version": "0.2.4", "date": "2020-06-09" }, { "version": "0.2.5", "date": "2021-06-06" }, { "version": "1.0.0", "date": "2021-07-16" }, { "version": "1.0.0.1", "date": "2021-07-26" }, { "version": "1.0.1", "date": "2021-08-02" }, { "version": "1.0.2", "date": "2021-10-24" }, { "version": "1.1.0", "date": "2022-08-06" }, { "version": "1.1.1", "date": "2022-08-12" }, { "version": "1.1.1.992", "date": "2022-09-23" } ], "_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" ], "_datasets": [ { "name": "gene_cov", "title": "a data.frame of gene length and GC content", "object": "gene_cov", "file": "gene_cov.rda", "class": [ "data.frame" ], "fields": [ "length", "GC" ], "rows": 27341, "table": true, "tojson": true }, { "name": "geneExpress", "title": "a data.frame of gene expression data", "object": "geneExpress", "file": "geneExpress.rda", "class": [ "data.frame" ], "fields": [ "V2", "V3" ], "rows": 10779, "table": true, "tojson": true }, { "name": "GSE66705_sample2", "title": "a matrix of gene expression data in GEO", "object": "GSE66705_sample2", "file": "GSE66705_sample2.rda", "class": [ "matrix", "array" ], "fields": [ "Gene Symbol", "GSM1629982", "GSM1629983" ], "rows": 999, "table": true, "tojson": true }, { "name": "kegg_liver", "title": "a matrix of gene expression data in TCGA", "object": "kegg_liver", "file": "kegg_liver.rda", "class": [ "matrix", "array" ], "fields": [ "V1", "V2", "V3", "V4", "V5", "V6", "V7", "V8", "V9", "V10", "V11", "V12", "V13", "V14", "V15", "V16", "V17", "V18", "V19", "V20", "V21", "V22", "V23", "V24", "V25", "V26", "V27", "V28", "V29", "V30", "V31", "V32", "V33", "V34", "V35", "V36", "V37", "V38", "V39", "V40", "V41", "V42", "V43", "V44", "V45", "V46", "V47", "V48", "V49", "V50", "V51", "V52", "V53", "V54", "V55", "V56", "V57", "V58", "V59", "V60", "V61", "V62", "V63", "V64", "V65", "V66", "V67", "V68", "V69", "V70", "V71", "V72", "V73", "V74", "V75", "V76", "V77", "V78", "V79", "V80", "V81", "V82", "V83", "V84", "V85", "V86", "V87", "V88", "V89", "V90", "V91", "V92", "V93", "V94", "V95", "V96", "V97", "V98", "V99", "V100", "V101", "V102", "V103", "V104", "V105", "V106", "V107", "V108", "V109", "V110", "V111", "V112", "V113", "V114", "V115", "V116", "V117", "V118", "V119", "V120", "V121", "V122", "V123", "V124", "V125", "V126", "V127", "V128", "V129", "V130", "V131", "V132", "V133", "V134", "V135", "V136", "V137", "V138", "V139", "V140", "V141", "V142", "V143", "V144", "V145", "V146", "V147", "V148", "V149", "V150" ], "rows": 100, "table": true, "tojson": true }, { "name": "module", "title": "a matrix of module name, gene symbols, and the number of gene symbols", "object": "module", "file": "module.rda", "class": [ "matrix", "array" ], "fields": [ "V1", "V2", "V3" ], "rows": 176, "table": true, "tojson": true }, { "name": "profile", "title": "a matrix of gene expression data in TCGA", "object": "profile", "file": "profile.rda", "class": [ "matrix", "array" ], "fields": [ "TCGA-DD-A11D-01", "TCGA-DD-AACT-01", "TCGA-G3-AAUZ-01", "TCGA-EP-A26S-11", "TCGA-RC-A6M4-01", "TCGA-DD-A4ND-01", "TCGA-UB-AA0U-01", "TCGA-G3-A7M6-01", "TCGA-ED-A66X-01" ], "rows": 9, "table": true, "tojson": true }, { "name": "ventricle", "title": "a matrix of gene expression data in GEO", "object": "ventricle", "file": "ventricle.rda", "class": [ "matrix", "array" ], "fields": [ "V1", "V2", "V3", "V4", "V5", "V6", "V7", "V8", "V9", "V10", "V11", "V12", "V13", "V14", "V15", "V16", "V17", "V18", "V19", "V20" ], "rows": 32, "table": true, "tojson": true } ], "_help": [ { "page": "array_preprocess", "title": "Preprocess of Microarray data", "topics": [ "array_preprocess" ] }, { "page": "cal_mean_module", "title": "Find the mean value of the gene in each module", "topics": [ "cal_mean_module" ] }, { "page": "cluster_array", "title": "cluster probes of Microarray data", "topics": [ "cluster_array" ] }, { "page": "combine_pvalue", "title": "combine pvalues of SNP difference analysis result", "topics": [ "combine_pvalue" ] }, { "page": "countToFpkm", "title": "Convert count to FPKM", "topics": [ "countToFpkm" ] }, { "page": "countToTpm", "title": "Convert count to Tpm", "topics": [ "countToTpm" ] }, { "page": "differential_array", "title": "Differential analysis of Microarray data", "topics": [ "differential_array" ] }, { "page": "differential_cnv", "title": "Do difference analysis of gene level copy number variation data", "topics": [ "differential_CNV" ] }, { "page": "differential_limma", "title": "differential_limma", "topics": [ "differential_limma" ] }, { "page": "differential_methy", "title": "differential_methy", "topics": [ "differential_methy" ] }, { "page": "differential_RNA", "title": "differential_RNA", "topics": [ "differential_RNA" ] }, { "page": "differential_SNP", "title": "Do difference analysis of SNP data", "topics": [ "differential_SNP" ] }, { "page": "differential_SNP_GEO", "title": "Do difference analysis of SNP data downloaded from GEO", "topics": [ "differential_SNP_GEO" ] }, { "page": "differential_SNP_tcga", "title": "Do difference analysis of SNP data downloaded from TCGAbiolinks", "topics": [ "differential_SNP_tcga" ] }, { "page": "fpkmToTpm", "title": "Convert fpkm to Tpm", "topics": [ "fpkmToTpm" ] }, { "page": "gene_ave", "title": "Average the values of same genes in gene expression profile", "topics": [ "gene_ave" ] }, { "page": "gene_cov", "title": "a data.frame of gene length and GC content", "topics": [ "gene_cov" ] }, { "page": "geneExpress", "title": "a data.frame of gene expression data", "topics": [ "geneExpress" ] }, { "page": "get_geo_array", "title": "Get Microarray matrix data from GEO", "topics": [ "get_geo_array" ] }, { "page": "GSE66705_sample2", "title": "a matrix of gene expression data in GEO", "topics": [ "GSE66705_sample2" ] }, { "page": "id_conversion_TCGA", "title": "Convert ENSEMBL gene id to gene Symbol in TCGA", "topics": [ "id_conversion_TCGA" ] }, { "page": "kegg_liver", "title": "a matrix of gene expression data in TCGA", "topics": [ "kegg_liver" ] }, { "page": "Merge_methy_tcga", "title": "Merge methylation data downloaded from TCGA", "topics": [ "Merge_methy_tcga" ] }, { "page": "module", "title": "a matrix of module name, gene symbols, and the number of gene symbols", "topics": [ "module" ] }, { "page": "prepare_chi", "title": "Preparer file for chi-square test", "topics": [ "prepare_chi" ] }, { "page": "profile", "title": "a matrix of gene expression data in TCGA", "topics": [ "profile" ] }, { "page": "repAssign", "title": "Handle the case where one id corresponds to multiple genes", "topics": [ "repAssign" ] }, { "page": "repRemove", "title": "Handle the case where one id corresponds to multiple genes", "topics": [ "repRemove" ] }, { "page": "SNP_QC", "title": "Do quality control of SNP data downloaded from TCGAbiolinks", "topics": [ "SNP_QC" ] }, { "page": "ventricle", "title": "a matrix of gene expression data in GEO", "topics": [ "ventricle" ] } ], "_readme": "https://github.com/bioc/GeoTcgaData/raw/HEAD/README.md", "_rundeps": [ "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" ], "_vignettes": [ { "source": "GeoTcgaData.Rmd", "filename": "GeoTcgaData.html", "title": "GeoTcgaData", "engine": "knitr::rmarkdown", "headings": [ "Authors", "Introduction", "Example", "RNA-seq data differential expression analysis", "DNA Methylation data integration", "Copy number variation data integration and differential gene extraction", "Difference analysis of single nucleotide Variation data", "GEO chip data processing", "Other downstream analyses", "References" ], "created": "2019-09-04 11:51:03", "modified": "2023-02-20 08:22:09", "commits": 31 } ], "_score": 5.878521795501206, "_indexed": true, "_nocasepkg": "geotcgadata", "_universes": [ "bioc", "huerqiang", "yulab-smu" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "2.13.0", "date": "2026-07-03T22:09:07.000Z", "distro": "resolute", "commit": "9ffceb9e2fdfcd89ec52afabb14f510a85a1c583", "fileid": "https://r2.ropensci.org/f4d1660b3a1df868cfecdd66e913925867b2f8a38d3416b0113bff807ab087f3", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28683963949" }, { "r": "4.6.1", "os": "linux", "version": "2.13.0", "date": "2026-07-03T22:09:20.000Z", "distro": "resolute", "commit": "9ffceb9e2fdfcd89ec52afabb14f510a85a1c583", "fileid": "https://r2.ropensci.org/9ca9dc03aa092e510a3a22115f2fd2e7c6f4b45d18edb13e91abac99f85b78c5", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28683963949" }, { "r": "4.5.3", "os": "mac", "version": "2.13.0", "date": "2026-07-03T22:03:35.000Z", "commit": "9ffceb9e2fdfcd89ec52afabb14f510a85a1c583", "fileid": "https://r2.ropensci.org/846884b7da3e360520c2c767fe1e38852fa81de705b81d06ca757515d8b0313d", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28683963949" }, { "r": "4.6.1", "os": "mac", "version": "2.13.0", "date": "2026-07-03T22:03:17.000Z", "commit": "9ffceb9e2fdfcd89ec52afabb14f510a85a1c583", "fileid": "https://r2.ropensci.org/8825812adee1bbccc9fb89d2292316366ec4ab205588b9a0dda58d1d9e2528c2", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28683963949" }, { "r": "4.6.0", "os": "wasm", "version": "2.13.0", "date": "2026-07-03T22:09:44.000Z", "commit": "9ffceb9e2fdfcd89ec52afabb14f510a85a1c583", "fileid": "https://r2.ropensci.org/450db20fa7faa9e8da0afefb8cfc59e01dae759167d7f656e549dcc33028e983", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28683963949" }, { "r": "4.7.0", "os": "win", "version": "2.13.0", "date": "2026-07-03T22:06:50.000Z", "commit": "9ffceb9e2fdfcd89ec52afabb14f510a85a1c583", "fileid": "https://r2.ropensci.org/ad7b74c98587baa762ec7f41a2e6da63b726621afd75d3c6aa496762524d8847", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28683963949" }, { "r": "4.5.3", "os": "win", "version": "2.13.0", "date": "2026-07-03T22:05:02.000Z", "commit": "9ffceb9e2fdfcd89ec52afabb14f510a85a1c583", "fileid": "https://r2.ropensci.org/29cabf39da13cfa8bf7894fc43c66f7965602fdba11825316cbfd51ffd60e857", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28683963949" }, { "r": "4.6.1", "os": "win", "version": "2.13.0", "date": "2026-07-03T22:05:06.000Z", "commit": "9ffceb9e2fdfcd89ec52afabb14f510a85a1c583", "fileid": "https://r2.ropensci.org/e6700e49bffff69a4d03a6937232d82c6710dea1e32d9948248abf405e5fc242", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28683963949" } ] }