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A computing tool is developed to automated identify somatic mutation-driven immune cells. The operation modes including: i) inferring the relative abundance matrix of tumor-infiltrating immune cells and integrating it with a particular gene mutation status, ii) detecting differential immune cells with respect to the gene mutation status and converting the abundance matrix of significant differential immune cell into two binary matrices (one for up-regulated and one for down-regulated), iii) identifying somatic mutation-driven immune cells by comparing the gene mutation status with each immune cell in the binary matrices across all samples, and iv) visualization of immune cell abundance of samples in different mutation status..
| Version: | 0.1.6 |
| Depends: | R (≥ 4.3.0), GSVA |
| Imports: | samr, e1071, parallel, preprocessCore, pheatmap, maftools, grDevices, survival, survminer, MASS, pracma, stats, RColorBrewer, backports |
| Suggests: | knitr, rmarkdown, R.utils |
| Published: | 2024-10-16 |
| DOI: | 10.32614/CRAN.package.SMDIC |
| Author: | Junwei Han [cre], Baotong Zheng [aut] |
| Maintainer: | Junwei Han <hanjunwei1981 at 163.com> |
| License: | GPL-2 | GPL-3 [expanded from: GPL (≥ 2)] |
| NeedsCompilation: | no |
| Citation: | SMDIC citation info |
| Materials: | README |
| In views: | Omics |
| CRAN checks: | SMDIC results |
| Reference manual: | SMDIC.pdf |
| Vignettes: |
SMDIC (source, R code) |
| Package source: | SMDIC_0.1.6.tar.gz |
| Windows binaries: | r-devel: SMDIC_0.1.6.zip, r-release: SMDIC_0.1.6.zip, r-oldrel: SMDIC_0.1.6.zip |
| macOS binaries: | r-release (arm64): SMDIC_0.1.6.tgz, r-oldrel (arm64): not available, r-release (x86_64): SMDIC_0.1.6.tgz, r-oldrel (x86_64): not available |
| Old sources: | SMDIC archive |
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