DOI: 10.18129/B9.bioc.SingscoreAMLMutations    

This is the development version of SingscoreAMLMutations; for the stable release version, see SingscoreAMLMutations.

Using singscore to predict mutations in AML from transcriptomic signatures

Bioconductor version: Development (3.16)

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>

Citation (from within R, enter citation("SingscoreAMLMutations")):


To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.



biocViews GeneExpressionWorkflow, GenomicVariantsWorkflow, ImmunoOncologyWorkflow, Workflow
Version 1.13.0
License Artistic-2.0
Depends R (>= 4.1.0)
Imports dcanr, edgeR, ggplot2, gridExtra, GSEABase, mclust,, plyr, reshape2, rtracklayer, singscore, SummarizedExperiment, TCGAbiolinks, BiocFileCache
Suggests knitr, rmarkdown, BiocStyle, BiocWorkflowTools, spelling
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
Windows Binary
macOS 10.13 (High Sierra)
Source Repository git clone
Source Repository (Developer Access) git clone
Package Short Url
Package Downloads Report Download Stats

Documentation »


R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: