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An open, multi-algorithmic pipeline for easy, fast and efficient analysis of cellular sub-populations and the molecular signatures that characterize them. The pipeline consists of four successive steps: data pre-processing, cellular clustering with pseudo-temporal ordering, defining differential expressed genes and biomarker identification. More details on Ghannoum et. al. (2021) <doi:10.3390/ijms22031399>. This package implements extensions of the work published by Ghannoum et. al. (2019) <doi:10.1101/700989>.
| Version: | 1.2.2 |
| Depends: | R (≥ 4.0), SingleCellExperiment |
| Imports: | methods, TSCAN, httr, mclust, statmod, igraph, RWeka, vegan, NetIndices, png, grDevices, RColorBrewer, ggplot2, rpart, fpc, cluster, rpart.plot, tsne, AnnotationDbi, org.Hs.eg.db, graphics, stats, utils, impute, withr |
| Suggests: | testthat, Seurat |
| Published: | 2023-11-06 |
| DOI: | 10.32614/CRAN.package.DIscBIO |
| Author: | Salim Ghannoum [aut, cph], Alvaro Köhn-Luque [aut, ths], Waldir Leoncio [cre, aut], Damiano Fantini [ctb] |
| Maintainer: | Waldir Leoncio <w.l.netto at medisin.uio.no> |
| BugReports: | https://github.com/ocbe-uio/DIscBIO/issues |
| License: | MIT + file LICENSE |
| URL: | https://github.com/ocbe-uio/DIscBIO |
| NeedsCompilation: | no |
| Materials: | NEWS |
| In views: | Omics |
| CRAN checks: | DIscBIO results |
| Reference manual: | DIscBIO.pdf |
| Package source: | DIscBIO_1.2.2.tar.gz |
| Windows binaries: | r-devel: DIscBIO_1.2.2.zip, r-release: DIscBIO_1.2.2.zip, r-oldrel: DIscBIO_1.2.2.zip |
| macOS binaries: | r-release (arm64): DIscBIO_1.2.2.tgz, r-oldrel (arm64): DIscBIO_1.2.2.tgz, r-release (x86_64): DIscBIO_1.2.2.tgz, r-oldrel (x86_64): DIscBIO_1.2.2.tgz |
| Old sources: | DIscBIO archive |
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These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.