Package: survtype 1.23.0

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

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survtype.pdf |survtype.html✨
survtype/json (API)
NEWS

# Install 'survtype' in R:

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

On BioConductor:survtype-1.23.0(bioc 3.21)survtype-1.22.0(bioc 3.20)

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 3 scripts 218 downloads 9 exports 129 dependencies

Last updated 5 months agofrom:150b74acd7. Checks:8 OK. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Feb 28 2025
R-4.5-win	OK	Feb 28 2025
R-4.5-mac	OK	Feb 28 2025
R-4.5-linux	OK	Feb 28 2025
R-4.4-win	OK	Feb 28 2025
R-4.4-mac	OK	Feb 28 2025
R-4.3-win	OK	Feb 28 2025
R-4.3-mac	OK	Feb 28 2025

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

Dependencies:abind askpass backports Biobase BiocGenerics BMA boot broom car carData cli clustvarsel codetools colorspace commonmark corrplot cowplot cpp11 crayon curl data.table DelayedArray DEoptimR Deriv doBy dplyr evaluate exactRankTests fansi farver foreach Formula generics GenomeInfoDb GenomeInfoDbData GenomicRanges ggplot2 ggpubr ggrepel ggsci ggsignif ggtext glue gridExtra gridtext gtable highr httr inline IRanges isoband iterators jpeg jsonlite km.ci KMsurv knitr labeling lattice leaps lifecycle lme4 magrittr markdown MASS Matrix MatrixGenerics MatrixModels matrixStats maxstat mclust mgcv microbenchmark mime minqa modelr munsell mvtnorm nlme nloptr nnet numDeriv openssl pbkrtest pcaPP pheatmap pillar pkgconfig png polynom purrr quantreg R6 rbibutils RColorBrewer Rcpp RcppEigen Rdpack reformulas rlang robustbase rrcov rstatix S4Arrays S4Vectors scales SparseArray SparseM stringi stringr SummarizedExperiment survival survminer survMisc sys tibble tidyr tidyselect UCSC.utils utf8 vctrs viridisLite withr xfun xml2 xtable XVector yaml zoo

Subtype Identification with Survival Data

Dongmin Jung

Rendered fromsurvtype.Rmdusingknitr::rmarkdownon Feb 28 2025.

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