1 Data import and preparations | 2 How many genes are expressed? | 3 Cluster stability analysis | 4 Lineage Markers | 5 Differentially expressed genes from E3.25 to E3.5 | 6 Principal Component Analysis | 7 Further analyses of FGF4-KO | 8 Jensen-Shannon Divergence analysis | 9 Classification of temporal profiles | 10 qPCR data analysis | A Influence of cell position on gene expression | B Correlation between Fgf ligands and Fgf receptors | C Session info | D The data import script readdata.R
Package: Hiiragi2013 1.49.5
Wolfgang Huber
Hiiragi2013: Cell-to-cell expression variability followed by signal reinforcement progressively segregates early mouse lineages
This package contains the experimental data and a complete executable transcript (vignette) of the statistical analysis presented in the paper "Cell-to-cell expression variability followed by signal reinforcement progressively segregates early mouse lineages" by Y. Ohnishi, W. Huber, A. Tsumura, M. Kang, P. Xenopoulos, K. Kurimoto, A. K. Oles, M. J. Arauzo-Bravo, M. Saitou, A.-K. Hadjantonakis and T. Hiiragi; Nature Cell Biology (2014) 16(1): 27-37. doi: 10.1038/ncb2881."
Authors:
Hiiragi2013_1.49.5.tar.gz
Hiiragi2013_1.49.5.zip(r-4.7-any)Hiiragi2013_1.49.5.zip(r-4.6-any)Hiiragi2013_1.49.5.zip(r-4.5-any)
Hiiragi2013_1.49.5.tgz(r-4.6-any)Hiiragi2013_1.49.5.tgz(r-4.5-any)
Hiiragi2013_1.49.5.tar.gz(r-4.7-any)Hiiragi2013_1.49.5.tar.gz(r-4.6-any)
Hiiragi2013_1.49.5.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
Hiiragi2013/json (API)
| # Install 'Hiiragi2013' in R: |
| install.packages('Hiiragi2013', repos = c('https://huber-group-embl.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/huber-group-embl/hiiragi2013/issues
Datasets:
experimentdatamicroarraydataqpcrdatareproducibleresearch
Last updated from:c989baa870. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel | OK | 230 | ||
| source / vignettes | OK | 513 | ||
| linux-release | OK | 248 | ||
| macos-release | OK | 201 | ||
| macos-oldrel | OK | 184 | ||
| windows-devel | OK | 205 | ||
| windows-release | OK | 205 | ||
| windows-oldrel | OK | 185 | ||
| wasm-release | OK | 185 |
Exports:getDifferentialExpressedGenesMDSplotmyHeatmapmyHeatmap2pamClusterplotProjection
Dependencies:annotateAnnotationDbiaskpassBiobaseBiocBaseUtilsBiocGenericsBiostringsbitbit64bitopsblobcachemcaToolscliclustercpp11crayoncurlDBIdeldirfastmapgenefiltergenericsgluegplotsgtoolshttrinterpIRangesjpegjsonliteKEGGRESTKernSmoothlatticelatticeExtralifecycleMASSMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpkgconfigpngR6RColorBrewerRcppRcppEigenrlangRSQLiteS4VectorsSeqinfosurvivalsysvctrsXMLxtableXVector
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| RAW Microarray Data | a |
| Find Differentially Expressed Genes | getDifferentialExpressedGenes |
| Multidimensional Scaling Plots | MDSplot |
| Plot Heatmaps | myHeatmap |
| Plot Heatmaps | myHeatmap2 |
| Clustering of Most Variable Genes | pamCluster |
| Overview of the Sample Expression | plotProjection |
| Normalized Microarray Data | x |
| qPCR Gene Expression | xq |
| Position-dependent Gene Expression | xql |