Package: seqCAT 1.29.0

Erik Fasterius

seqCAT: High Throughput Sequencing Cell Authentication Toolkit

The seqCAT package uses variant calling data (in the form of VCF files) from high throughput sequencing technologies to authenticate and validate the source, function and characteristics of biological samples used in scientific endeavours.

Authors:Erik Fasterius [aut, cre]

seqCAT_1.29.0.tar.gz
seqCAT_1.29.0.zip(r-4.5)seqCAT_1.29.0.zip(r-4.4)seqCAT_1.29.0.zip(r-4.3)
seqCAT_1.29.0.tgz(r-4.5-any)seqCAT_1.29.0.tgz(r-4.4-any)seqCAT_1.29.0.tgz(r-4.3-any)
seqCAT_1.29.0.tar.gz(r-4.5-noble)seqCAT_1.29.0.tar.gz(r-4.4-noble)
seqCAT_1.29.0.tgz(r-4.4-emscripten)seqCAT_1.29.0.tgz(r-4.3-emscripten)
seqCAT.pdf |seqCAT.html✨
seqCAT/json (API)
NEWS

# Install 'seqCAT' in R:

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

Datasets:

test_comparison - Overlapping and compared SNVs
test_profile_1 - SNV profile 1
test_profile_2 - SNV profile 2
test_profile_3 - SNV profile 3
test_similarities - Collated similarities object
test_variant_list - Modified variant list object

On BioConductor:seqCAT-1.29.0(bioc 3.21)seqCAT-1.28.0(bioc 3.20)

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

coverage genomicvariation sequencing variantannotation

4.00 score 250 downloads 17 exports 95 dependencies

Last updated 4 months agofrom:ecf25e0261. Checks:3 OK, 5 NOTE. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Jan 29 2025
R-4.5-win	NOTE	Jan 29 2025
R-4.5-mac	NOTE	Jan 29 2025
R-4.5-linux	NOTE	Jan 29 2025
R-4.4-win	NOTE	Jan 29 2025
R-4.4-mac	NOTE	Jan 29 2025
R-4.3-win	OK	Jan 29 2025
R-4.3-mac	OK	Jan 29 2025

Exports:calculate_similarity compare_many compare_profiles create_profile create_profiles filter_duplicates filter_variants list_cosmic list_variants plot_heatmap plot_impacts plot_variant_list read_cosmic read_profile read_profiles write_profile write_profiles

Dependencies:abind AnnotationDbi askpass BH Biobase BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob BSgenome cachem cli codetools colorspace cpp11 crayon curl DBI DelayedArray dplyr fansi farver fastmap formatR futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges ggplot2 glue gtable httr IRanges isoband jsonlite KEGGREST labeling lambda.r lattice lifecycle magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime munsell nlme openssl pillar pkgconfig plogr png purrr R6 RColorBrewer RCurl restfulr Rhtslib rjson rlang Rsamtools RSQLite rtracklayer S4Arrays S4Vectors scales snow SparseArray stringi stringr SummarizedExperiment sys tibble tidyr tidyselect UCSC.utils utf8 VariantAnnotation vctrs viridisLite withr XML XVector yaml

seqCAT: The High Throughput Sequencing Cell Authentication Toolkit

Erik Fasterius

Rendered fromseqCAT.Rmdusingknitr::rmarkdownon Jan 29 2025.

Last update: 2019-06-20
Started: 2017-08-31

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
SNV profile similarity calculations	calculate_similarity
Comparisons of many SNV profiles	compare_many
Binary SNV profile comparisons	compare_profiles
SNV profile creation	create_profile
SNV profile creation	create_profiles
Variant de-duplication	filter_duplicates
Variant filtering	filter_variants
List COSMIC sample names	list_cosmic
List known variants	list_variants
Plot similarity heatmap	plot_heatmap
Plot SNV impact distribution	plot_impacts
Plot known variants list	plot_variant_list
Read COSMIC data	read_cosmic
Read SNV profile	read_profile
Read SNV profiles	read_profiles
seqCAT: High Throughput Sequencing Cell Authentication Toolkit	seqCAT-package seqCAT
Overlapping and compared SNVs	test_comparison
SNV profile 1	test_profile_1
SNV profile 2	test_profile_2
SNV profile 3	test_profile_3
Collated similarities object	test_similarities
Modified variant list object	test_variant_list
Write SNV profile	write_profile
Write SNV profiles	write_profiles