Package: omicsPrint 1.27.0

Davy Cats

omicsPrint: Cross omic genetic fingerprinting

omicsPrint provides functionality for cross omic genetic fingerprinting, for example, to verify sample relationships between multiple omics data types, i.e. genomic, transcriptomic and epigenetic (DNA methylation).

Authors:Maarten van Iterson [aut], Davy Cats [cre]

omicsPrint_1.27.0.tar.gz
omicsPrint_1.27.0.zip(r-4.5)omicsPrint_1.27.0.zip(r-4.4)omicsPrint_1.27.0.zip(r-4.3)
omicsPrint_1.27.0.tgz(r-4.4-any)omicsPrint_1.27.0.tgz(r-4.3-any)
omicsPrint_1.27.0.tar.gz(r-4.5-noble)omicsPrint_1.27.0.tar.gz(r-4.4-noble)
omicsPrint_1.27.0.tgz(r-4.4-emscripten)omicsPrint_1.27.0.tgz(r-4.3-emscripten)
omicsPrint.pdf |omicsPrint.html✨
omicsPrint/json (API)
NEWS

# Install 'omicsPrint' in R:

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

Datasets:

hg19.GoNLsnps - Dataframe with overlaps GoNL variants and 450K probes
hm450.manifest.pop.GoNL - HM450 population-specific probe-masking recommendations

On BioConductor:omicsPrint-1.27.0(bioc 3.21)omicsPrint-1.26.0(bioc 3.20)

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

qualitycontrol genetics epigenetics transcriptomics dnamethylation transcription geneticvariability immunooncology

5.20 score 32 scripts 213 downloads 5 mentions 3 exports 52 dependencies

Last updated 2 months agofrom:8c45530ded. Checks:OK: 1 WARNING: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 29 2024
R-4.5-win	WARNING	Nov 29 2024
R-4.5-linux	WARNING	Nov 29 2024
R-4.4-win	WARNING	Nov 29 2024
R-4.4-mac	WARNING	Nov 29 2024
R-4.3-win	WARNING	Nov 29 2024
R-4.3-mac	WARNING	Nov 29 2024

Exports:alleleSharing beta2genotype inferRelations

Dependencies:abind askpass Biobase BiocBaseUtils BiocGenerics cli cpp11 crayon curl DelayedArray dplyr fansi generics GenomeInfoDb GenomeInfoDbData GenomicRanges glue httr IRanges jsonlite lattice lifecycle magrittr MASS Matrix MatrixGenerics matrixStats mime MultiAssayExperiment openssl pillar pkgconfig purrr R6 RaggedExperiment rlang S4Arrays S4Vectors SparseArray stringi stringr SummarizedExperiment sys tibble tidyr tidyselect UCSC.utils utf8 vctrs withr XVector zlibbioc

omicsPrint: detection of data linkage errors in multiple omics studies

Maarten van Iterson, Davy Cats, Paul Hop, Bas T. Heijmans

Rendered fromomicsPrint.Rmdusingknitr::rmarkdownon Nov 29 2024.

Last update: 2017-12-14
Started: 2017-05-12

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
allele sharing based on ibs	alleleSharing
converts beta-values to genotypes (1, 2 and 3)	beta2genotype
Dataframe with overlaps GoNL variants and 450K probes	hg19.GoNLsnps
HM450 population-specific probe-masking recommendations	hm450.manifest.pop.GoNL
predict mismatches	inferRelations