Package: VariantToolsData 1.37.0

Michael Lawrence

VariantToolsData: Data for the VariantTools tutorial

Data from the sequencing of a 50/50 mixture of HapMap trio samples NA12878 (CEU) and NA19240 (YRI), subset to the TP53 region.

Authors:Michael Lawrence

VariantToolsData_1.37.0.tar.gz
VariantToolsData_1.37.0.tar.gz(r-4.7-any)VariantToolsData_1.37.0.tar.gz(r-4.6-any)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
VariantToolsData/json (API)

# Install 'VariantToolsData' in R:

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

Datasets:

geno - Reference genotypes
repeats - Simple repeats
tallies - Tally VRanges

On BioConductor:VariantToolsData-1.37.0(data/experiment 3.24)VariantToolsData-1.36.0(data/experiment 3.23)

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

experimentdata sequencingdata hapmap snpdata datapkg

3.60 score 1 scripts 2 exports 69 dependencies

Last updated from:82a2f41eb3. Checks:3 ERROR, 1 OK. Indexed: yes.

This is a data package. Data packages may be large and do not get checked across all platforms.

Target	Result	Time	Files	Syslog
bioc-checks	ERROR	163
linux-devel	ERROR	430
source / vignettes	OK	371
linux-release	ERROR	375

Exports:sumDepths TP53Region

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

VariantTools Example Data

Rendered fromintro.Rnwusingutils::Sweave

Last update: 2018-01-19
Started: 2016-12-17

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Reference genotypes	geno
Simple repeats	repeats
Sum Replicate Depths	sumDepths
Tally VRanges	tallies
Range around TP53	TP53Region

Usage by other packages (reverse dependencies)