CRAN/E | sigminer

sigminer

Extract, Analyze and Visualize Mutational Signatures for Genomic Variations

Installation

About

Genomic alterations including single nucleotide substitution, copy number alteration, etc. are the major force for cancer initialization and development. Due to the specificity of molecular lesions caused by genomic alterations, we can generate characteristic alteration spectra, called 'signature' (Wang, Shixiang, et al. (2021) doi:10.1371/journal.pgen.1009557 & Alexandrov, Ludmil B., et al. (2020) doi:10.1038/s41586-020-1943-3 & Steele Christopher D., et al. (2022) doi:10.1038/s41586-022-04738-6). This package helps users to extract, analyze and visualize signatures from genomic alteration records, thus providing new insight into cancer study.

Citation sigminer citation info
github.com/ShixiangWang/sigminer
shixiangwang.github.io/sigminer/
shixiangwang.github.io/sigminer-book/
Bug report File report

Key Metrics

Version 2.3.1
R ≥ 3.5
Published 2024-05-11 149 days ago
Needs compilation? yes
License MIT
License File
CRAN checks sigminer results

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Maintainer

Maintainer

Shixiang Wang

Authors

Shixiang Wang

aut / cre

Ziyu Tao

aut

Huimin Li

aut

Tao Wu

aut

Xue-Song Liu

aut / ctb

An
Mayakonda

ctb

Material

README
NEWS
Reference manual
Package source

In Views

Omics

Vignettes

Analyze Copy Number Signatures with sigminer
A Quick Start of sigminer Package

macOS

r-release

arm64

r-oldrel

arm64

r-release

x86_64

r-oldrel

x86_64

Windows

r-devel

x86_64

r-release

x86_64

r-oldrel

x86_64

Old Sources

sigminer archive

Depends

R ≥ 3.5

Imports

cli ≥ 2.0.0
cowplot
data.table
dplyr
furrr ≥ 0.2.0
future
ggplot2 ≥ 3.3.0
ggpubr
maftools
magrittr
methods
NMF
purrr
Rcpp
rlang ≥ 0.1.2
stats
tidyr

Suggests

Biobase
Biostrings
BSgenome
BSgenome.Hsapiens.UCSC.hg19
circlize
cluster
covr
digest
GenomicRanges
GenSA
ggalluvial
ggcorrplot
ggfittext
ggplotify
ggrepel
IRanges
knitr
lpSolve
markdown
matrixStats
nnls
parallel
patchwork
pheatmap
quadprog
R.utils
RColorBrewer
reticulate
rmarkdown
roxygen2
scales
synchronicity
testthat ≥ 3.0.0
tibble
UCSCXenaTools

LinkingTo

Rcpp