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driveR
View on CRAN: Click
here
Download and install driveR package within the R console
Install from CRAN:
install.packages("driveR")
Install from Github:
library("remotes")
install_github("cran/driveR")
Install by package version:
library("remotes")
install_version("driveR", "0.4.1")
Attach the package and use:
library("driveR")
Maintained by
Ege Ulgen
[Scholar Profile | Author Map]
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2020-11-18
Latest Update: 2023-08-19
Description:
Cancer genomes contain large numbers of somatic alterations but few
genes drive tumor development. Identifying cancer driver genes is critical
for precision oncology. Most of current approaches either identify driver
genes based on mutational recurrence or using estimated scores predicting
the functional consequences of mutations. 'driveR' is a tool for
personalized or batch analysis of genomic data for driver gene prioritization
by combining genomic information and prior biological knowledge. As features,
'driveR' uses coding impact metaprediction scores, non-coding impact scores,
somatic copy number alteration scores, hotspot gene/double-hit gene
condition, 'phenolyzer' gene scores and memberships to cancer-related KEGG
pathways. It uses these features to estimate cancer-type-specific
probability for each gene of being a cancer driver using the related task of
a multi-task learning classification model. The method is described in detail
in Ulgen E, Sezerman OU. 2021. driveR: driveR: a novel method for
prioritizing cancer driver genes using somatic genomics data. BMC
Bioinformatics .
How to cite:
Ege Ulgen (2020). driveR: Prioritizing Cancer Driver Genes Using Genomics Data. R package version 0.4.1, https://cran.r-project.org/web/packages/driveR. Accessed 21 Nov. 2024.
Previous versions and publish date:
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imports, suggests or enhances
Complete documentation for driveR
Functions, R codes and Examples using
the driveR R package
Some associated functions: KEGG_cancer_pathways_descriptions . MTL_submodel_descriptions . create_SCNA_score_df . create_features_df . create_gene_level_scna_df . create_noncoding_impact_score_df . determine_double_hit_genes . determine_hotspot_genes . driveR . example_cohort_features_table . example_cohort_scna_table . example_features_table . example_scna_table . predict_coding_impact . prioritize_driver_genes . specific_thresholds .
Some associated R codes: core_functions.R . data.R . driveR.R . utility.R . Full driveR package functions and examples
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