Package: Uniquorn 2.33.0

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

Uniquorn_2.33.0.tar.gz
Uniquorn_2.33.0.zip(r-4.7)Uniquorn_2.33.0.zip(r-4.6)Uniquorn_2.33.0.zip(r-4.5)
Uniquorn_2.33.0.tgz(r-4.6-any)Uniquorn_2.33.0.tgz(r-4.5-any)
Uniquorn_2.33.0.tar.gz(r-4.7-any)Uniquorn_2.33.0.tar.gz(r-4.6-any)
Uniquorn_2.33.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
Uniquorn/json (API)

# Install 'Uniquorn' in R:

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

On BioConductor:Uniquorn-2.33.0(bioc 3.24)Uniquorn-2.32.0(bioc 3.23)

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

immunooncology statisticalmethod wholegenome exomeseq

4.60 score 1 scripts 2 mentions 10 exports 80 dependencies

Last updated from:f9ade8c555. Checks:8 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	215
linux-devel-x86_64	NOTE	340
source / vignettes	OK	302
linux-release-x86_64	NOTE	453
macos-release-arm64	NOTE	259
macos-oldrel-arm64	NOTE	194
windows-devel	NOTE	317
windows-release	NOTE	309
windows-oldrel	NOTE	310
wasm-release	OK	163

Exports:add_custom_vcf_to_database identify_vcf_file initiate_canonical_databases read_library_names remove_ccls_from_database remove_library_from_database show_contained_ccls show_contained_variants_for_ccl show_contained_variants_in_library show_which_ccls_contain_variant

Dependencies:abind AnnotationDbi askpass BH Biobase BiocBaseUtils BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob BSgenome cachem cigarillo cli codetools cpp11 crayon curl data.table DBI DelayedArray doParallel fastmap foreach formatR futile.logger futile.options generics GenomicAlignments GenomicFeatures GenomicRanges glue httr IRanges iterators jsonlite KEGGREST lambda.r lattice lifecycle magrittr Matrix MatrixGenerics matrixStats memoise mime openssl pkgconfig png R.methodsS3 R.oo R.utils R6 RCurl restfulr Rhtslib rjson rlang Rsamtools RSQLite rtracklayer S4Arrays S4Vectors Seqinfo snow SparseArray stringi stringr SummarizedExperiment sys VariantAnnotation vctrs WriteXLS XML XVector yaml

Uniquorn vignette

Rendered fromUniquorn.Rmdusingknitr::rmarkdown

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

Help page	Topics
add_custom_vcf_to_database This function adds the variants of parsed custom CCLs to a monet DB instance	add_custom_vcf_to_database
add_missing_cls	add_missing_cls
add_p_q_values_statistics	add_p_q_values_statistics
add_penalty_statistics	add_penalty_statistics
create_bed_file	create_bed_file
identify_VCF_file	identify_vcf_file
init_and_load_identification	init_and_load_identification
initiate_canonical_databases	initiate_canonical_databases
match_query_ccl_to_database	match_query_ccl_to_database
Filter Parsed VCF Files	parse_vcf_file
parse_vcf_query_into_db This function adds the variants of parsed custom CCLs to a monet DB instance	parse_vcf_query_into_db
Library Name Reader	read_library_names
read_mutation_grange_objects	read_mutation_grange_objects
Remove Cancer Cell Line	remove_ccls_from_database
Remove entire Library from Database	remove_library_from_database
show_contained_ccls	show_contained_ccls
Variants In Cancer Cell Line	show_contained_variants_for_ccl
All variants contained in reference library	show_contained_variants_in_library
Cancer cell lines with specific variant	show_which_ccls_contain_variant

Package: Uniquorn 2.33.0

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

Citation

Development and contributors

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)