Package: survtype 1.29.0

Dongmin Jung

survtype: Subtype Identification with Survival Data

Subtypes are defined as groups of samples that have distinct molecular and clinical features. Genomic data can be analyzed for discovering patient subtypes, associated with clinical data, especially for survival information. This package is aimed to identify subtypes that are both clinically relevant and biologically meaningful.

Authors:Dongmin Jung

survtype_1.29.0.tar.gz
survtype_1.29.0.zip(r-4.7)survtype_1.29.0.zip(r-4.6)survtype_1.29.0.zip(r-4.5)
survtype_1.29.0.tgz(r-4.6-any)survtype_1.29.0.tgz(r-4.5-any)
survtype_1.29.0.tar.gz(r-4.7-any)survtype_1.29.0.tar.gz(r-4.6-any)
survtype_1.29.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
survtype/json (API)

# Install 'survtype' in R:

install.packages('survtype', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

On BioConductor:survtype-1.29.0(bioc 3.24)survtype-1.28.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

software statisticalmethod geneexpression survival clustering sequencing coverage

4.00 score 6 scripts 346 downloads 9 exports 116 dependencies

Last updated from:27f8a70f56. Checks:1 ERROR, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	188
linux-devel-x86_64	OK	359
source / vignettes	OK	265
linux-release-x86_64	OK	344
macos-release-arm64	OK	174
macos-oldrel-arm64	OK	161
windows-devel	OK	191
windows-release	OK	207
windows-oldrel	OK	203
wasm-release	OK	145

Exports:Exprs.survtype gene.clust MAF.survgroup maf2matrix plot plot.survtype quantile_normalization Single.survgroup Surv.survtype

Dependencies:abind backports Biobase BiocGenerics BMA boot broom car carData cli clustvarsel codetools colorspace commonmark corrplot cowplot cpp11 curl DelayedArray DEoptimR Deriv doBy dplyr exactRankTests farver foreach forecast Formula fracdiff generics GenomicRanges ggplot2 ggpubr ggrepel ggsci ggsignif ggtext glue gridExtra gridtext gtable inline IRanges isoband iterators jpeg labeling lattice leaps lifecycle litedown lme4 lmtest magrittr markdown MASS Matrix MatrixGenerics MatrixModels matrixStats maxstat mclust mgcv minqa modelr mvtnorm nlme nloptr nnet numDeriv pbkrtest pcaPP pheatmap pillar pkgconfig png polynom purrr quantreg R6 rbibutils RColorBrewer Rcpp RcppArmadillo RcppEigen Rdpack reformulas rlang robustbase rrcov rstatix S4Arrays S4Vectors S7 scales Seqinfo SparseArray SparseM stringi stringr SummarizedExperiment survival survminer tibble tidyr tidyselect timeDate urca utf8 vctrs viridisLite withr xfun xml2 XVector zoo

Subtype Identification with Survival Data

Rendered fromsurvtype.Rmdusingknitr::rmarkdown

Last update: 2019-03-19
Started: 2019-02-05

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Sample subtype identification via survival information and gene expression data	Exprs.survtype
Plots of the heatmap for each cluster of expression data	gene.clust
Patient group identification via survival data and mutation annotation information	MAF.survgroup
Convert a MAF file to a mutation matrix	maf2matrix
Plot of survival curves of sample subtypes	plot plot.survtype
Normalize a gene expression profile	quantile_normalization
Patient group identification via survival information and expression of a single gene	Single.survgroup
Sample subtype identification via survival information	Surv.survtype