{ "_id": "6aca2dadfe5cc25786e850fc", "Package": "Single.mTEC.Transcriptomes", "Type": "Package", "Title": "Single Cell Transcriptome Data and Analysis of Mouse mTEC cells", "Version": "1.40.0", "Date": "2025-07-28", "Author": "Alejandro Reyes", "Maintainer": "Alejandro Reyes ", "Description": "This data package contains the code used to analyse the\nsingle-cell RNA-seq and the bulk ATAC-seq data from the\nmanuscript titled: Single-cell transcriptome analysis reveals\ncoordinated ectopic-gene expression patterns in medullary\nthymic epithelial cells. This paper was published in Nature\nImmunology 16,933-941(2015). The data objects provided in this\npackage has been pre-processed: the raw data files can be\ndownloaded from ArrayExpress under the accession identifiers\nE-MTAB-3346 and E-MTAB-3624. The vignette of this data package\nprovides a documented and reproducible workflow that includes\nthe code that was used to generate each statistic and figure\nfrom the manuscript.", "License": "LGPL", "biocViews": "ExperimentData", "VignetteBuilder": "knitr", "RoxygenNote": "5.0.1", "NeedsCompilation": "no", "Repository": "Bioconductor 3.23", "Date/Publication": "2026-04-28 12:28:58 UTC", "RemoteUrl": "https://git.bioconductor.org/packages/Single.mTEC.Transcriptomes", "RemoteRef": "RELEASE_3_23", "RemoteSha": "5e82a36f27cfd60dd2de7754ff2341cfffad32e6", "Packaged": { "Date": "2026-10-10 11:15:23 UTC", "User": "root" }, "_user": "bioc-release", "_type": "src", "_file": "Single.mTEC.Transcriptomes_1.40.0.tar.gz", "_fileid": "https://r2.ropensci.org/e930449175c1bcf0e3855cea418a0409f6e94245edc9271929095ab22c732e6b", "_filesize": 956602646, "_sha256": "e930449175c1bcf0e3855cea418a0409f6e94245edc9271929095ab22c732e6b", "_expires": "2027-01-18T12:20:29.000Z", "_created": "2026-10-10T11:15:23.000Z", "_published": "2026-10-10T12:21:01.569Z", "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38047168050", "_status": "success", "_host": "GitHub-Actions", "_bioccheck": { "error": 2, "warning": 4, "note": 7 }, "_upstream": "https://git.bioconductor.org/packages/Single.mTEC.Transcriptomes", "_commit": { "id": "5e82a36f27cfd60dd2de7754ff2341cfffad32e6", "author": "lshep ", "committer": "lshep ", "message": "bump x.y.z version to even y prior to creation of RELEASE_3_23 branch\n", "time": 1777379338 }, "_maintainer": { "name": "Alejandro Reyes", "email": "alejandro.reyes.ds@gmail.com", "login": "areyesq89", "twitter": "@areyesq89", "description": "", "uuid": 12632413 }, "_distro": "resolute", "_jobs": [ { "job": 114209721669, "time": 240, "config": "bioc-checks", "r": "4.6.1", "check": "ERROR", "artifact": "11669467880" }, { "job": 114209721728, "time": 563, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "11669668269" }, { "job": 114209721729, "time": 517, "config": "linux-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "11670040178" }, { "job": 114198962787, "time": 3821, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "11668954232" } ], "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5.0", "role": "Depends" }, { "package": "DESeq2", "role": "Suggests" }, { "package": "GenomicRanges", "role": "Suggests" }, { "package": "GenomicFeatures", "role": "Suggests" }, { "package": "genefilter", "role": "Suggests" }, { "package": "statmod", "role": "Suggests" }, { "package": "gdata", "role": "Suggests" }, { "package": "RColorBrewer", "role": "Suggests" }, { "package": "ggplot2", "role": "Suggests" }, { "package": "gplots", "role": "Suggests" }, { "package": "cluster", "role": "Suggests" }, { "package": "clue", "role": "Suggests" }, { "package": "grid", "role": "Suggests" }, { "package": "gridExtra", "role": "Suggests" }, { "package": "ggbio", "role": "Suggests" }, { "package": "Gviz", "role": "Suggests" }, { "package": "geneplotter", "role": "Suggests" }, { "package": "matrixStats", "role": "Suggests" }, { "package": "pheatmap", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "BiocParallel", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 1 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.41.1", "bioc": "3.24", "repository": "data/experiment" }, { "branch": "release", "version": "1.40.0", "bioc": "3.23", "repository": "data/experiment" } ], "_topics": [ "experimentdata", "datapkg" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 476, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_searchresults": 1, "_datapkg": true, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/manual.pdf", "extra/Single.mTEC.Transcriptomes.html" ], "_cranurl": false, "_exports": [], "_datasets": [ { "name": "aireDependentSansom", "title": "List of Aire-dependent genes", "object": "aireDependentSansom", "file": "aireDependentSansom.RData", "class": [ "character" ], "fields": [], "table": false, "tojson": true }, { "name": "biotype", "title": "Mouse biotypes", "object": "biotypes", "file": "biotypes.RData", "class": [ "character" ], "fields": [], "table": false, "tojson": true }, { "name": "biotype", "title": "Mouse biotypes", "object": "biotypesHuman", "file": "biotypesHuman.RData", "class": [ "character" ], "fields": [], "table": false, "tojson": true }, { "name": "cea1Coexpression", "title": "Cea1 co-expression group data", "object": "cea1Coexpression", "file": "cea1Coexpression.RData", "class": [ "data.frame" ], "fields": [ "ID", "logFC", "AveExpr", "t", "P.Value", "adj.P.Val", "B", "SYMBOL", "ENTREZ_GENE_ID", "REFSEQ_ID", "CHROMOSOME", "DEFINITION" ], "rows": 48701, "table": true, "tojson": true }, { "name": "corMatSp", "title": "Gene-gene correlation network", "object": "corMatsSansom", "file": "corMatsSansom.RData", "class": [ "matrix", "array" ], "fields": [], "rows": 2129, "table": true, "tojson": true }, { "name": "corMatSpNoMarker", "title": "Gene-gene correlation network", "object": "corMatsNoMarker", "file": "corMatsNoMarker.RData", "class": [ "matrix", "array" ], "fields": [], "rows": 17511, "table": true, "tojson": false }, { "name": "deGenesNone", "title": "Highly variable genes.", "object": "deGenesNone", "file": "deGenesNone.RData", "class": [ "character" ], "fields": [], "table": false, "tojson": true }, { "name": "deGenesSansom", "title": "Highly variable genes from Sansom et al.", "object": "deGenesSansom", "file": "deGenesSansom.RData", "class": [ "character" ], "fields": [], "table": false, "tojson": true }, { "name": "dxd", "title": "Count data from the single-mTEC data.", "object": "mTECdxd", "file": "mTECdxd.RData", "class": [ "DESeqDataSet" ], "fields": [], "table": false, "tojson": false }, { "name": "dxdATAC", "title": "ATAC-seq summarized counts.", "object": "dxdATAC", "file": "dxdATAC.RData", "class": [ "DESeqDataSet" ], "fields": [], "table": false, "tojson": false }, { "name": "dxdFANTOM", "title": "FANTOM dataset", "object": "fantom", "file": "fantom.RData", "class": [ "DESeqDataSet" ], "fields": [], "table": false, "tojson": false }, { "name": "geneNames", "title": "Mouse gene names", "object": "geneNames", "file": "geneNames.RData", "class": [ "character" ], "fields": [], "table": false, "tojson": true }, { "name": "geneNames", "title": "Mouse gene names", "object": "geneNamesHuman", "file": "geneNamesHuman.RData", "class": [ "character" ], "fields": [], "table": false, "tojson": true }, { "name": "geneRanges", "title": "Genomic range coordinates.", "object": "geneRanges", "file": "geneRanges.RData", "class": [ "GRanges" ], "fields": [], "table": false, "tojson": false }, { "name": "muc1Coexpression", "title": "Muc1 co-expression group data", "object": "muc1Coexpression", "file": "muc1Coexpression.RData", "class": [ "data.frame" ], "fields": [ "ID", "logFC", "AveExpr", "t", "P.Value", "adj.P.Val", "B", "SYMBOL", "ENTREZ_GENE_ID", "REFSEQ_ID", "CHROMOSOME", "DEFINITION" ], "rows": 48701, "table": true, "tojson": true }, { "name": "nomarkerCellsClustering", "title": "Clustering results", "object": "nomarkerCellsClustering", "file": "nomarkerCellsClustering.RData", "class": [ "list" ], "fields": [], "table": false, "tojson": false }, { "name": "percentsGG", "title": "Mapping statistics", "object": "percentsGG", "file": "percentsGG.RData", "class": [ "data.frame" ], "fields": [ "percent", "type", "cell", "batch", "index" ], "rows": 1380, "table": true, "tojson": true }, { "name": "permsAllClusters", "title": "Permutation results", "object": "permutationResults", "file": "permutationResults.RData", "class": [ "list" ], "fields": [], "table": true, "tojson": true }, { "name": "realAllClusters", "title": "Permutation results", "object": "permutationResults", "file": "permutationResults.RData", "class": [ "numeric" ], "fields": [], "table": false, "tojson": true }, { "name": "tras", "title": "Tissue restricted antigens lists.", "object": "tras", "file": "tras.RData", "class": [ "data.frame" ], "fields": [ "gene.ids", "chrom", "start", "strand", "band", "symbol", "entrezID", "tiss.no.over.cutoff", "max.tissue", "tissues.over.cutoff" ], "rows": 4117, "table": true, "tojson": true }, { "name": "Ycorr", "title": "Output from scLVM", "object": "scLVM_output", "file": "scLVM_output.RData", "class": [ "data.frame" ], "fields": [], "rows": 17511, "table": true, "tojson": true } ], "_help": [ { "page": "Single.mTec.Transcriptomes-package", "title": "Single-cell transcriptome data of medullary thymic epithelial cells", "topics": [ "Single.mTec.Transcriptomes-package" ] }, { "page": "aireDependentSansom", "title": "List of Aire-dependent genes", "topics": [ "aireDependentSansom" ] }, { "page": "biotype", "title": "Mouse biotypes", "topics": [ "biotype" ] }, { "page": "biotypesHuman", "title": "Human biotypes", "topics": [ "biotypesHuman" ] }, { "page": "cea1Coexpression", "title": "Cea1 co-expression group data", "topics": [ "cea1Coexpression" ] }, { "page": "corMatsNoMarker", "title": "Gene-gene correlation network", "topics": [ "corMatsNoMarker", "corMatSp", "corMatSpNoMarker" ] }, { "page": "deGenesNone", "title": "Highly variable genes.", "topics": [ "deGenesNone" ] }, { "page": "deGenesSansom", "title": "Highly variable genes from Sansom et al.", "topics": [ "deGenesSansom" ] }, { "page": "dxdATAC", "title": "ATAC-seq summarized counts.", "topics": [ "dxdATAC" ] }, { "page": "fantom", "title": "FANTOM dataset", "topics": [ "dxdFANTOM", "fantom" ] }, { "page": "geneNames", "title": "Mouse gene names", "topics": [ "geneNames" ] }, { "page": "geneNamesHuman", "title": "Human gene names", "topics": [ "geneNamesHuman" ] }, { "page": "geneRanges", "title": "Genomic range coordinates.", "topics": [ "geneRanges" ] }, { "page": "mTECdxd", "title": "Count data from the single-mTEC data.", "topics": [ "dxd", "mTECdxd" ] }, { "page": "muc1Coexpression", "title": "Muc1 co-expression group data", "topics": [ "muc1Coexpression" ] }, { "page": "nomarkerCellsClustering", "title": "Clustering results", "topics": [ "nomarkerCellsClustering" ] }, { "page": "percentsGG", "title": "Mapping statistics", "topics": [ "percentsGG" ] }, { "page": "permutationResults", "title": "Permutation results", "topics": [ "permsAllClusters", "permutationResults", "realAllClusters" ] }, { "page": "scLVM_output", "title": "Output from scLVM", "topics": [ "beta", "beta0", "h5GeneNames", "heter", "scLVM_output", "vars", "Ycorr" ] }, { "page": "tras", "title": "Tissue restricted antigens lists.", "topics": [ "tras" ] } ], "_rundeps": [], "_vignettes": [ { "source": "mTECs.Rnw", "filename": "mTECs.pdf", "title": "Analysis of single cell mTEC data.", "engine": "knitr::knitr", "headings": [ "1 Mapping statistics", "2 Identifying variable genes", "3 Number of TRA genes detected per cell compared to the number of genes.", "4 Variable genes are enriched for TRA genes ", "5 Both Aire-dependent and Aire-independent TRAs are expressed at low frequencies in single mTECs", "6 Gene-gene correlation analyses ", "7 Data analysis for TRA-selected cells", "8 Co-expressed genes tend to be clustered in the genome", "9 ATAC-seq data", "10 Session Information" ], "created": "2016-01-25 18:47:40", "modified": "2025-07-29 01:33:47", "commits": 8 } ], "_score": 3.3010299956639813, "_indexed": false, "_nocasepkg": "single.mtec.transcriptomes", "_universes": [ "bioc-release" ], "_indexurl": "https://bioc.r-universe.dev/Single.mTEC.Transcriptomes", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.40.0", "date": "2026-10-10T12:13:23.000Z", "distro": "resolute", "commit": "5e82a36f27cfd60dd2de7754ff2341cfffad32e6", "fileid": "https://r2.ropensci.org/455c934dff64ba44214c7efff1797f83a9e0ad276ae09c307fc7d9aa0389c34f", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38047168050" }, { "r": "4.6.1", "os": "linux", "version": "1.40.0", "date": "2026-10-10T12:14:28.000Z", "distro": "resolute", "commit": "5e82a36f27cfd60dd2de7754ff2341cfffad32e6", "fileid": "https://r2.ropensci.org/566bc679e8b9cd66c050d3fed9d804c0cb2a4320ada9e240e975a879a265dc8b", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38047168050" } ] }