Package: Uniquorn 2.25.0

Raik Otto

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

'Uniquorn' 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).

Authors:Raik Otto

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NEWS

# Install 'Uniquorn' in R:
install.packages('Uniquorn', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

On BioConductor:Uniquorn-2.25.0(bioc 3.20)Uniquorn-2.24.0(bioc 3.19)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

bioconductor-package

10 exports 1.51 score 81 dependencies 2 mentions

Last updated 2 months agofrom:bcacad3776

Exports:add_custom_vcf_to_databaseidentify_vcf_fileinitiate_canonical_databasesread_library_namesremove_ccls_from_databaseremove_library_from_databaseshow_contained_cclsshow_contained_variants_for_cclshow_contained_variants_in_libraryshow_which_ccls_contain_variant

Dependencies:abindAnnotationDbiaskpassBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobBSgenomecachemclicodetoolscpp11crayoncurldata.tableDBIDelayedArraydoParallelfastmapforeachformatRfutile.loggerfutile.optionsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesgluehttrIRangesiteratorsjsonliteKEGGRESTlambda.rlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpkgconfigplogrpngR.methodsS3R.ooR.utilsR6RCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorssnowSparseArraystringistringrSummarizedExperimentsysUCSC.utilsVariantAnnotationvctrsWriteXLSXMLXVectoryamlzlibbioc

Uniquorn vignette

Raik Otto

Rendered fromUniquorn.Rmdusingknitr::rmarkdownon Jul 05 2024.

Last update: 2022-10-14
Started: 2016-01-27

Readme and manuals

Help Manual

Help pageTopics
add_custom_vcf_to_database This function adds the variants of parsed custom CCLs to a monet DB instanceadd_custom_vcf_to_database
add_missing_clsadd_missing_cls
add_p_q_values_statisticsadd_p_q_values_statistics
add_penalty_statisticsadd_penalty_statistics
create_bed_filecreate_bed_file
identify_VCF_fileidentify_vcf_file
init_and_load_identificationinit_and_load_identification
initiate_canonical_databasesinitiate_canonical_databases
match_query_ccl_to_databasematch_query_ccl_to_database
Filter Parsed VCF Filesparse_vcf_file
parse_vcf_query_into_db This function adds the variants of parsed custom CCLs to a monet DB instanceparse_vcf_query_into_db
Library Name Readerread_library_names
read_mutation_grange_objectsread_mutation_grange_objects
Remove Cancer Cell Lineremove_ccls_from_database
Remove entire Library from Databaseremove_library_from_database
show_contained_cclsshow_contained_ccls
Variants In Cancer Cell Lineshow_contained_variants_for_ccl
All variants contained in reference libraryshow_contained_variants_in_library
Cancer cell lines with specific variantshow_which_ccls_contain_variant