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CLONETv2
View on CRAN: Click
here
Download and install CLONETv2 package within the R console
Install from CRAN:
install.packages("CLONETv2")
Install from Github:
library("remotes")
install_github("cran/CLONETv2")
Install by package version:
library("remotes")
install_version("CLONETv2", "2.2.1")
Attach the package and use:
library("CLONETv2")
Maintained by
Yari Ciani
[Scholar Profile | Author Map]
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2019-04-05
Latest Update: 2021-10-13
Description:
Analyze data from next-generation sequencing experiments on genomic samples. 'CLONETv2' offers a set of functions to compute allele specific copy number and clonality from segmented data and SNPs position pileup. The package has also calculated the clonality of single nucleotide variants given read counts at mutated positions. The package has been developed at the laboratory of Computational and Functional Oncology, Department of CIBIO, University of Trento (Italy), under the supervision of prof Francesca Demichelis. References: Prandi et al. (2014) ; Carreira et al. (2014) ; Romanel et al. (2015) .
How to cite:
Yari Ciani (2019). CLONETv2: Clonality Estimates in Tumor. R package version 2.2.1, https://cran.r-project.org/web/packages/CLONETv2
Other packages that cited CLONETv2 R package
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Other R packages that CLONETv2 depends,
imports, suggests or enhances
Functions, R codes and Examples using
the CLONETv2 R package
Some associated functions: CLONETv2-package . adm_table_toy . allele_specific_cna_table_toy . bt_toy . check_ploidy_and_admixture . compute_allele_specific_scna_table . compute_beta_table . compute_dna_admixture . compute_ploidy . compute_scna_clonality_table . compute_snv_clonality . error_table . pileup_normal_toy . pileup_tumor_toy . pl_table_toy . scna_clonality_table_toy . seg_tb_toy . snv_clonality_table_toy . snv_reads_toy .
Some associated R codes: CLONETv2_basic_functions.R . CLONETv2_check_ploidy_and_admixture.R . CLONETv2_compute_admixture.R . CLONETv2_compute_allele_specific_scna_table.R . CLONETv2_compute_beta_table.R . CLONETv2_compute_ploidy.R . CLONETv2_compute_scna_clonality_table.R . CLONETv2_compute_snv_clonality.R . CLONETv2_data.R . Full CLONETv2 package functions and examples
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