Uniquorn: Identification of cancer cell lines based on their weighted mutational or variational fingerprint
Version 1.4.2

Identifies cancer cell lines with their small variant fingerprint. Cancer cell line misidentification and cross-contamination reprents a significant challenge for cancer researchers. The identification is vital and in the frame of this package based on the locations or loci of somatic and germline mutations or variations. The input format is vcf and the files have to contain a single cancer cell line sample. The implemented method is optimized for the Next-generation whole exome and whole genome DNA-sequencing technology. RNA-seq data is very likely to work as well but hasn't been rigiously tested yet. Panel-seq will require manual adjustment of thresholds.

AuthorRaik Otto
Bioconductor views ExomeSeq Software StatisticalMethod WholeGenome
Date of publicationNone
Maintainer'Raik Otto' <raik.otto@hu-berlin.de>
LicenseArtistic-2.0
Version1.4.2
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("Uniquorn")

Getting started

README.md
Uniquorn vignette

Popular man pages

create_bed_file: create_bed_file
identify_vcf_file: identify_VCF_file
parse_ccle_genotype_data: parse_ccle_genotype_data
parse_vcf_file: parse_vcf_file
remove_custom_vcf_from_database: Removes a cancer cell line training fingerprint (vcf file)...
show_contained_mutations_for_cl: show_contained_mutations_for_cl
show_which_cls_contain_mutation: show_which_cls_contain_mutation
See all...

All man pages Function index File listing

Man pages

add_custom_vcf_to_database: Adds a custom vcf file to the three existing cancer cell line...
create_bed_file: create_bed_file
identify_vcf_file: identify_VCF_file
initiate_canonical_databases: initiate_canonical_databases
initiate_db_and_load_data: initiate_db_and_load_data
parse_ccle_genotype_data: parse_ccle_genotype_data
parse_cosmic_genotype_data: parse_cosmic_genotype_data
parse_vcf_file: parse_vcf_file
re_calculate_cl_weights: Re-calculate sim_list_weights
remove_custom_vcf_from_database: Removes a cancer cell line training fingerprint (vcf file)...
show_contained_cls: show_contained_cls
show_contained_mutations: show_contained_mutations
show_contained_mutations_for_cl: show_contained_mutations_for_cl
show_which_cls_contain_mutation: show_which_cls_contain_mutation
split_add: split_add
write_data_to_db: write_data_to_db

Functions

Files

DESCRIPTION
NAMESPACE
R
R/Add_custom_vcf_to_database.R
R/Create_BED_files.R
R/Identify_VCF_file.R
R/Init_and_load_identification.R
R/Parse_raw_data.R
R/Parser_scripts.R
R/Show_database_information.R
R/Utility.R
R/add_missing_cls.R
R/add_single_file.R
R/calculate_p_q_values.R
R/calculate_similarity_results.R
R/filter_for_weights.R
R/remove_custom_vcf_from_uniquorn.R
README.md
build
build/vignette.rds
inst
inst/NEWS.Rd
inst/doc
inst/doc/Uniquorn.R
inst/doc/Uniquorn.Rmd
inst/doc/Uniquorn.html
inst/extdata
inst/extdata/HT29.vcf.gz
inst/extdata/HT29.vcf.gz_uniquorn_ident.tab
inst/uniquorn_db_default.sqlite
inst/unitTests
inst/unitTests/test_identification.R
man
man/add_custom_vcf_to_database.Rd
man/create_bed_file.Rd
man/identify_vcf_file.Rd
man/initiate_canonical_databases.Rd
man/initiate_db_and_load_data.Rd
man/parse_ccle_genotype_data.Rd
man/parse_cosmic_genotype_data.Rd
man/parse_vcf_file.Rd
man/re_calculate_cl_weights.Rd
man/remove_custom_vcf_from_database.Rd
man/show_contained_cls.Rd
man/show_contained_mutations.Rd
man/show_contained_mutations_for_cl.Rd
man/show_which_cls_contain_mutation.Rd
man/split_add.Rd
man/write_data_to_db.Rd
tests
tests/runTests.R
tests/testthat
tests/testthat.R
tests/testthat/test_identification.R
tests/testthat/test_show_cls.R
tests/uniquorn-Tests.R
unitTests
unitTests/test_identification.R
unitTests/test_show_cls.R
vignettes
vignettes/Uniquorn.Rmd
Uniquorn documentation built on May 20, 2017, 10:25 p.m.

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