Uniquorn: Identification of cancer cell lines based on their weighted mutational/ variational fingerprint

Share:

This packages enables users to identify cancer cell lines. 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/ loci of somatic and germline mutations/ variations. The input format is vcf/ vcf.gz and the files have to contain a single cancer cell line sample (i.e. a single member/genotype/gt column in the vcf file). 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

Author
Raik Otto
Date of publication
None
Maintainer
'Raik Otto' <raik.otto@hu-berlin.de>
License
Artistic-2.0
Version
1.2.0

View on Bioconductor

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

Files in this package

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