- Home
- Bioconductor 2.8
- 2.8 ExperimentData Packages
Bioconductor ExperimentData Packages
Bioconductor version: 2.8
| Package | Maintainer | Title |
|---|---|---|
| affycompData | Harris Jaffee | affycomp data |
| affydata | Harris Jaffee | Affymetrix Data for Demonstration Purpose |
| AffymetrixDataTestFiles | Henrik Bengtsson | Affymetrix data files (CEL, CDF, CHP, EXP, PSI) for testing |
| ALL | Robert Gentleman | A data package |
| ALLMLL | B. M. Bolstad | A subset of arrays from a large acute lymphoblastic leukemia (ALL) study |
| AmpAffyExample | Rafael A. Irizarry | Example of Amplified Data |
| beta7 | Jean Yang | Rodriguez et al. (2004) Differential Gene Expression by Memory/Effector T Helper Cells Bearing the Gut-Homing Receptor Integrin alpha4 beta7. |
| bladderbatch | Jeffrey T. Leek | Bladder gene expression data illustrating batch effects |
| breastCancerMAINZ | Markus Schroeder, Benjamin Haibe-Kains | Gene expression dataset published by Schmidt et al. [2008] (MAINZ). |
| breastCancerNKI | Markus Schroeder, Benjamin Haibe-Kains | Genexpression dataset published by van't Veer et al. [2002] and van de Vijver et al. [2002] (NKI). |
| breastCancerTRANSBIG | Markus Schroeder, Benjamin Haibe-Kains | Gene expression dataset published by Desmedt et al. [2007] (TRANSBIG). |
| breastCancerUNT | Markus Schroeder, Benjamin Haibe-Kains | Gene expression dataset published by Sotiriou et al. [2007] (UNT). |
| breastCancerUPP | Markus Schroeder, Benjamin Haibe-Kains | Gene expression dataset published by Miller et al. [2005] (UPP). |
| breastCancerVDX | Markus Schroeder, Benjamin Haibe-Kains | Gene expression datasets published by Wang et al. [2005] and Minn et al. [2007] (VDX). |
| bronchialIL13 | Vince Carey | time course experiment involving il13 |
| CCl4 | Audrey Kauffmann | Carbon Tetrachloride (CCl4) treated hepatocytes |
| ccTutorial | Joern Toedling | Data package for ChIP-chip tutorial |
| ceu1kg | VJ Carey | CEU (N=60) genotypes from 1000 genomes pilot phase I |
| ceuhm3 | VJ Carey | ceuhm3: genotype (HapMap phase III) and expression data for CEPH CEU cohort |
| charmData | Martin Aryee | An example dataset for use with the charm package |
| cheung2010 | Vince Carey | resources for genetics of gene expression based on Cheung et al 2010 |
| CLL | Robert Gentleman | A Package for CLL Gene Expression Data |
| colonCA | W Sylvia Merk | exprSet for Alon et al. (1999) colon cancer data |
| davidTiling | Wolfgang Huber | Data and analysis scripts for David, Huber et al. yeast tiling array paper |
| DLBCL | Marcus Dittrich | Diffuse large B-cell lymphoma expression data |
| dressCheck | Vincent Carey | data and software for checking Dressman JCO 25(5) 2007 |
| dyebiasexamples | Philip Lijnzaad | Example data for the dyebias package, which implements the GASSCO method. |
| EatonEtAlChIPseq | Patrick Aboyoun | ChIP-seq data of ORC-binding sites in Yeast excerpted from Eaton et al. 2010 |
| ecoliLeucine | Laurent Gautier | Experimental data with Affymetrix E. coli chips |
| encoDnaseI | VJ Carey | data provided by UCSC for Cd4 raw measures of DnaseI hypersensitivity |
| estrogen | R. Gentleman | 2x2 factorial design exercise for the Bioconductor short course |
| faahKO | Colin A. Smith | Saghatelian et al. (2004) FAAH knockout LC/MS data |
| facsDorit | Florian Hahne | DKFZ FACS example data |
| fibroEset | Sylvia Merk | exprSet for Karaman et al. (2003) fibroblasts data |
| flowWorkspaceData | Greg Finak | A data package containing a flowJo xml workspace and associated fcs files for testing the flowWorkspace package. |
| frmaExampleData | Matthew N. McCall | Frma Example Data |
| gageData | Weijun Luo | Auxillary data for gage package |
| gaschYHS | Vince Carey | ExpressionSet for response of yeast to heat shock and other environmental stresses |
| gatingMLData | Nishant Gopalakrishnan | Data and XML files for GatingML Test suite |
| gcspikelite | Mark Robinson | Spike-in data for GC/MS data and methods within flagme |
| geneLenDataBase | Matthew Young | Lengths of mRNA transcripts for a number of genomes |
| GenomicFeatures.Hsapiens.UCSC.hg18 | Biocore Data Team | A transient package to store various Genomic Features for Human |
| GenomicFeatures.Mmusculus.UCSC.mm9 | Biocore Data Team | A transient package to store various Genomic Features for Mouse |
| GGdata | VJ Carey | all 90 hapmap CEU samples, 47K expression, 4mm SNP |
| golubEsets | Vince Carey | exprSets for golub leukemia data |
| GSVAdata | Robert Castelo | Data employed in the vignette of the GSVA package |
| GWASdata | Stephanie Gogarten | Data used in the examples and vignettes of the GWASTools package |
| hapmap100khind | Benilton Carvalho | Sample data - Hapmap 100K HIND Affymetrix |
| hapmap100kxba | Benilton Carvalho | Sample data - Hapmap 100K XBA Affymetrix |
| hapmap500knsp | Benilton Carvalho | Sample data - Hapmap 500K NSP Affymetrix |
| hapmap500ksty | Benilton Carvalho | Sample data - Hapmap 500K STY Affymetrix |
| hapmapsnp5 | Benilton Carvalho | Sample data - Hapmap SNP 5.0 Affymetrix |
| hapmapsnp6 | Benilton Carvalho | Sample data - Hapmap SNP 5.0 Affymetrix |
| harbChIP | VJ Carey | Experimental Data Package: harbChIP |
| HEEBOdata | Agnes Paquet | HEEBO set and HEEBO controls. |
| hgu133abarcodevecs | Matthew N. McCall | hgu133a data for barcode |
| hgu133afrmavecs | Matthew N. McCall | Vectors used by frma for microarrays of type hgu133a |
| hgu133plus2barcodevecs | Matthew N. McCall | hgu133plus2 data for barcode |
| hgu133plus2frmavecs | Matthew N. McCall | Vectors used by frma for microarrays of type hgu133plus2 |
| hgu2beta7 | Biocore Team c/o BioC user list | A data package containing annotation data for hgu2beta7 |
| HIVcDNAvantWout03 | Chris Fraley | T cell line infections with HIV-1 LAI (BRU) |
| hmyriB36 | Vincent Carey | YRI hapmap + expression (GENEVAR), Build 36, r23a genotypes |
| humanStemCell | R. Gentleman | Human Stem Cells time course experiment |
| ind1KG | VJ Carey | Data from 1000 Genomes, NA19240 (female) chr6 excerpt |
| iontreeData | Mingshu Cao | Data provided to show the usage of functions in iontree package |
| ITALICSData | Guillem Rigaill | ITALICSData |
| Iyer517 | Vince Carey | exprSets for Iyer, Eisen et all 1999 Science paper |
| kidpack | Wolfgang Huber | DKFZ kidney package |
| leeBamViews | VJ Carey | leeBamViews -- multiple yeast RNAseq samples excerpted from Lee 2009 |
| lumiBarnes | Pan Du | Barnes Benchmark Illumina Tissues Titration Data |
| lungExpression | Robert Scharpf | ExpressionSets for Parmigiani et al., 2004 Clinical Cancer Research paper |
| maqcExpression4plex | Benilton Carvalho | Sample Expression Data - MAQC / HG18 - NimbleGen |
| MAQCsubset | VJ Carey | Experimental Data Package: MAQCsubset |
| MAQCsubsetAFX | Laurent Gatto | MAQC data subset for the Affymetrix platform |
| MAQCsubsetILM | Laurent Gatto | MAQC data subset for the Illumina platform |
| MEEBOdata | Agnes Paquet | MEEBO set and MEEBO controls. |
| mosaicsExample | Dongjun Chung | Example data for the mosaics package, which implements MOSAiCS, a statistical framework to analyze one-sample or two-sample ChIP-seq data |
| mouse4302barcodevecs | Matthew N. McCall | mouse4302 data for barcode |
| mouse4302frmavecs | Matthew N. McCall | Vectors used by frma for microarrays of type mouse4302 |
| msdata | Steffen Neumann | Various Mass Spectrometry raw data example files |
| mvoutData | VJ Carey | affy and illumina raw data for assessing outlier detector performance |
| NCIgraphData | Laurent Jacob | Data for the NCIgraph software package |
| Neve2006 | VJ Carey | expression and CGH data on breast cancer cell lines |
| ppiData | Tony Chiang | A package that contains the bait to prey directed graphs for protein-protein interactions. |
| ProData | Xiaochun Li | SELDI-TOF data of Breast cancer samples |
| pumadata | Richard Pearson | Various data sets for use with the puma package |
| rfcdmin | N. Le Meur | Minimal Data Library for RFlowCyt examples |
| RNAinteractMAPK | Bernd Fischer | Mapping of Signalling Networks through Synthetic Genetic Interaction Analysis by RNAi |
| simpIntLists | Kircicegi Korkmaz | The package contains BioGRID interactions for various organisms in a simple format |
| SNAData | Denise Scholtens | Social Networks Analysis Data Examples |
| SpikeIn | Rafael A. Irizarry | Affymetrix Spike-In Experiment Data |
| SpikeInSubset | Rafael A. Irizarry | Part of Affymetrix's Spike-In Experiment Data |
| stjudem | Joern Toedling | Microarray Data from Yeoh et al. in MACAT format |
| TargetSearchData | Alvaro Cuadros-Inostroza Henning Redestig, Matt Hannah | Example GC-MS data for TargetSearch Package |
| tinesath1cdf | Tine Casneuf | tinesath1cdf |
| tinesath1probe | Tine Casneuf | Probe sequence data for microarrays of type tinesath1 |
| XhybCasneuf | Tineke Casneuf | EBI/PSB cross-hybridisation study package |
| yeastCC | Sandrine Dudoit | Spellman et al. (1998) and Pramila/Breeden (2006) yeast cell cycle microarray data |
| yeastExpData | R. Gentleman | Yeast Experimental Data |
| yeastGSData | R. Gentleman | Yeast Gold Standard Data |
| yeastNagalakshmi | Biocore Team c/o BioC user list | Yeast genome RNA sequencing data based on Nagalakshmi et. al. |
| yeastRNASeq | J. Bullard | Yeast RNA-Seq Experimental Data from Lee et al. 2008 |
Packages »
Bioconductor's stable, semi-annual release:
- Analysis software packages.
- Annotation packages.
- Illustrative experiment data packages.
- Latest release announcement.
Bioconductor is also available via Docker and Amazon Machine Images.
Development Version »
Bioconductor packages under development:
- Analysis software packages.
- Illustrative experiment data packages
Developer Resources:
