Package: CSeQTL 1.0.0

Paul Little

CSeQTL: Cell Type-Specific Expression Quantitative Trail Loci Mapping

Perform bulk and cell type-specific expression quantitative trail loci mapping with our novel method (Little et al. (2023) <doi:10.1038/s41467-023-38795-w>).

Authors:Paul Little [aut, cre]

CSeQTL_1.0.0.tar.gz
CSeQTL_1.0.0.tar.gz(r-4.5-noble)CSeQTL_1.0.0.tar.gz(r-4.4-noble)
CSeQTL_1.0.0.tgz(r-4.4-emscripten)CSeQTL_1.0.0.tgz(r-4.3-emscripten)
CSeQTL.pdf |CSeQTL.html✨
CSeQTL/json (API)

# Install 'CSeQTL' in R:

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

Uses libs:

openblas– Optimized BLAS
c++– GNU Standard C++ Library v3
openmp– GCC OpenMP (GOMP) support library

On CRAN:

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

openblas cpp openmp

2.00 score 11 exports 180 dependencies

Last updated 15 days agofrom:4890a1e41f. Checks:3 OK. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Mar 06 2025
R-4.5-linux-x86_64	OK	Mar 06 2025
R-4.4-linux-x86_64	OK	Mar 06 2025

Exports:CSeQTL_dataGen CSeQTL_full_analysis CSeQTL_GS CSeQTL_linearTest CSeQTL_oneExtremeSim CSeQTL_run_MatrixEQTL CSeQTL_smart gen_true_RHO OLS_sim plot_RHO prep_gene_info

Dependencies:abind AnnotationDbi askpass base64enc bbmle bdsmatrix BH Biobase BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob brew brio bslib cachem callr caTools cli clipr coda codetools colorspace commonmark cpp11 crayon credentials curl data.table DBI DelayedArray desc devtools diffobj digest downlit ellipsis emdbook evaluate fansi farver fastmap fontawesome formatR fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges gert ggplot2 gh gitcreds glue gplots gtable gtools HelpersMG highr htmltools htmlwidgets httpuv httr httr2 ini IRanges isoband jquerylib jsonlite KEGGREST KernSmooth knitr labeling lambda.r later lattice lifecycle magrittr MASS Matrix MatrixEQTL MatrixGenerics matrixStats memoise mgcv mime miniUI multcomp munsell mvtnorm nlme numDeriv openssl pillar pkgbuild pkgconfig pkgdown pkgload plogr plyr png praise prettyunits processx profvis promises ps purrr R.methodsS3 R.oo R.utils R6 ragg rappdirs rcmdcheck RColorBrewer Rcpp RcppArmadillo RCurl remotes restfulr Rhtslib rjson rlang rmarkdown roxygen2 rprojroot Rsamtools RSQLite rstudioapi rtracklayer rversions S4Arrays S4Vectors sandwich sass scales sessioninfo shiny smarter snow sourcetools SparseArray stringi stringr SummarizedExperiment survival sys systemfonts testthat textshaping TH.data tibble tinytex UCSC.utils urlchecker usethis utf8 vctrs viridisLite waldo whisker withr xfun XML xml2 xopen xtable XVector yaml zip zoo

Introduction to CSeQTL

Paul Little

Rendered fromintro.Rmdusingknitr::rmarkdownon Mar 06 2025.

Last update: 2025-03-06
Started: 2025-03-06

Citation

Readme and manuals

Help Manual

Help page	Topics
CSeQTL_dataGen	CSeQTL_dataGen
CSeQTL_full_analysis	CSeQTL_full_analysis
CSeQTL_GS	CSeQTL_GS
CSeQTL_linearTest	CSeQTL_linearTest
CSeQTL_oneExtremeSim	CSeQTL_oneExtremeSim
CSeQTL_run_MatrixEQTL	CSeQTL_run_MatrixEQTL
CSeQTL_smart	CSeQTL_smart
gen_true_RHO	gen_true_RHO
OLS_sim	OLS_sim
plot_RHO	plot_RHO
prep_gene_info	prep_gene_info