Package: HD2013SGI 1.53.2
Hugo Gruson
HD2013SGI: Mapping genetic interactions in human cancer cells with RNAi and multiparametric phenotyping
This package contains the experimental data and a complete executable transcript (vignette) of the analysis of the HCT116 genetic interaction matrix presented in the paper "Mapping genetic interactions in human cancer cells with RNAi and multiparametric phenotyping" by C. Laufer, B. Fischer, M. Billmann, W. Huber, M. Boutros; Nature Methods (2013) 10:427-31. doi: 10.1038/nmeth.2436.
Authors:
HD2013SGI_1.53.2.tar.gz
HD2013SGI_1.53.2.zip(r-4.7-any)HD2013SGI_1.53.2.zip(r-4.6-any)HD2013SGI_1.53.2.zip(r-4.5-any)
HD2013SGI_1.53.2.tgz(r-4.6-any)HD2013SGI_1.53.2.tgz(r-4.5-any)
HD2013SGI_1.53.2.tar.gz(r-4.7-any)HD2013SGI_1.53.2.tar.gz(r-4.6-any)
HD2013SGI_1.53.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
HD2013SGI/json (API)
| # Install 'HD2013SGI' in R: |
| install.packages('HD2013SGI', repos = c('https://huber-group-embl.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/huber-group-embl/hd2013sgi/issues
experimentdatacancerdatacoloncancerdatamicrotitreplateassaydatacellculturehomo_sapiens_datahighthroughputimagingdata
Last updated from:8f64c179a4. Checks:7 WARNING, 1 ERROR, 1 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel | WARNING | 169 | ||
| source / vignettes | ERROR | 264 | ||
| linux-release | WARNING | 176 | ||
| macos-release | WARNING | 145 | ||
| macos-oldrel | WARNING | 105 | ||
| windows-devel | WARNING | 100 | ||
| windows-release | WARNING | 108 | ||
| windows-oldrel | WARNING | 97 | ||
| wasm-release | OK | 140 |
Exports:HD2013SGIdataHD2013SGIHeatmapHumanHD2013SGImaineffectsHD2013SGIorderDimHD2013SGIselectByStability
Dependencies:abindannotateAnnotationDbiaskpassbase64encBiobaseBiocBaseUtilsBiocGenericsBiostringsbitbit64bitopsblobbslibcachemcaToolsclicolorspacecpp11crayoncurlDBIdigestEBImageevaluatefastmapfftwtoolsfontawesomefsgeneplottergenericsgluegplotsgtoolshighrhtmltoolshtmlwidgetshttrhttr2IRangesjpegjquerylibjsonliteKEGGRESTKernSmoothknitrlatticelifecyclelimmalmtestlocfitLSDmagrittrMASSmemoisemimeopensslpkgconfigpngR6rappdirsRColorBrewerRCurlrlangrmarkdownRSQLiteS4VectorssassSeqinfosplotsstatmodsystifftinytexvcdvctrswithrxfunXMLxtableXVectoryamlzoo
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Experimental Data and Analysis of the HCT116 Genetic Interaction Matrix | HD2013SGI-package HD2013SGI |
| Phenotypic data after quality control and feature selection | datamatrix |
| Phenotypic data before quality control and feature selection | datamatrixfull |
| Original phenotypic measurements in screen order | featuresPerWell |
| Download a dataset from the HD2013SGI package | HD2013SGIdata |
| Plotting heatmaps of genetic interaction scores | HD2013SGIHeatmapHuman |
| Estimation of main effects | HD2013SGImaineffects |
| hclust on one out of three dimensions of an interaction matrix | HD2013SGIorderDim |
| Feature selection method | HD2013SGIselectByStability |
| The genetic interaction data. | Interactions |
| Estimated main effects | mainEffects |
| Number of interactions per target gene | nrOfInteractionsPerTarget |
| Annotation of all query genes in the screen | QueryAnnotation |
| Results from the feature selection method | stabilitySelection |
| Annotation of all target genes in the screen | TargetAnnotation |