SingscoreAMLMutations
Using singscore to predict mutations in AML from transcriptomic signatures
Bioconductor version: Release (3.20)
This workflow package shows how transcriptomic signatures can be used to infer phenotypes. The workflow begins by showing how the TCGA AML transcriptomic data can be downloaded and processed using the TCGAbiolinks packages. It then shows how samples can be scored using the singscore package and signatures from the MSigDB. Finally, the predictive capacity of scores in the context of predicting a specific mutation in AML is shown.The workflow exhibits the interplay of Bioconductor packages to achieve a gene-set level analysis.
Author: Dharmesh D. Bhuva [aut, cre] 
, Momeneh Foroutan [aut] , Yi Xie [aut] , Ruqian Lyu [aut], Malvika Kharbanda [aut] , Joseph Cursons [aut] , Melissa J. Davis [aut]
Maintainer: Dharmesh D. Bhuva <bhuva.d at wehi.edu.au>
citation("SingscoreAMLMutations")):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("SingscoreAMLMutations")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("SingscoreAMLMutations")| Using singscore to predict mutations in AML from transcriptomic signatures | HTML | R Script |
| Using singscore to predict mutations in AML from transcriptomic signatures (Chinese version) | HTML | R Script |
| NEWS | Text |
Details
| biocViews | GeneExpressionWorkflow, GenomicVariantsWorkflow, ImmunoOncologyWorkflow, Workflow |
| Version | 1.22.0 |
| License | Artistic-2.0 |
| Depends | R (>= 4.1.0) |
| Imports | dcanr, edgeR, ggplot2, gridExtra, GSEABase, mclust, org.Hs.eg.db, plyr, reshape2, rtracklayer, singscore, SummarizedExperiment, TCGAbiolinks, BiocFileCache |
| System Requirements | |
| URL | https://github.com/DavisLaboratory/SingscoreAMLMutations |
| Bug Reports | https://github.com/DavisLaboratory/SingscoreAMLMutations/issues |
See More
| Suggests | knitr, rmarkdown, BiocStyle, BiocWorkflowTools, spelling |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | SingscoreAMLMutations_1.22.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/SingscoreAMLMutations |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/SingscoreAMLMutations |
| Package Short Url | https://bioconductor.org/packages/SingscoreAMLMutations/ |
| Package Downloads Report | Download Stats |