Package: CSeQTL 1.0.1

Paul Little

CSeQTL: Cell Type-Specific Expression Quantitative Trait Loci Mapping

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

Authors:Paul Little [aut, cre]

CSeQTL_1.0.1.tar.gz
CSeQTL_1.0.1.zip(r-4.7)CSeQTL_1.0.1.zip(r-4.6)CSeQTL_1.0.1.zip(r-4.5)
CSeQTL_1.0.1.tgz(r-4.6-x86_64)CSeQTL_1.0.1.tgz(r-4.6-arm64)CSeQTL_1.0.1.tgz(r-4.5-x86_64)CSeQTL_1.0.1.tgz(r-4.5-arm64)
CSeQTL_1.0.1.tar.gz(r-4.7-arm64)CSeQTL_1.0.1.tar.gz(r-4.7-x86_64)CSeQTL_1.0.1.tar.gz(r-4.6-arm64)CSeQTL_1.0.1.tar.gz(r-4.6-x86_64)
CSeQTL_1.0.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
CSeQTL/json (API)

# Install 'CSeQTL' in R:

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

Bug tracker:https://github.com/pllittle/cseqtl/issues

Uses libs:

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

On CRAN:

cell-types enrichment-analysis eqtl-mapping gene-expression genomics phased-genotypes rna-seq openblas cpp openmp

4.18 score 3 stars 2 scripts 468 downloads 10 exports 132 dependencies

Last updated from:5f05bc3bea. Checks:13 OK. Indexed: yes.

Target	Result	Time
linux-devel-arm64	OK	264
linux-devel-x86_64	OK	280
source / vignettes	OK	347
linux-release-arm64	OK	254
linux-release-x86_64	OK	248
macos-release-arm64	OK	250
macos-release-x86_64	OK	448
macos-oldrel-arm64	OK	212
macos-oldrel-x86_64	OK	670
windows-devel	OK	232
windows-release	OK	254
windows-oldrel	OK	237
wasm-release	OK	228

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

Dependencies:askpass base64enc bbmle bdsmatrix bitops brew brio bslib cachem callr caTools cli clipr coda codetools commonmark cpp11 crayon credentials curl data.table desc devtools diffobj digest downlit ellipsis emdbook evaluate fansi farver fastmap fontawesome fs gert ggplot2 gitcreds glue gplots gtable gtools HelpersMG highr htmltools htmlwidgets httpuv httr2 ini isoband jquerylib jsonlite KernSmooth knitr labeling later lattice lifecycle magrittr MASS Matrix MatrixEQTL memoise mime miniUI multcomp mvtnorm numDeriv openssl otel pak pillar pkgbuild pkgconfig pkgdown pkgload plyr praise prettyunits processx profvis promises ps purrr R.methodsS3 R.oo R.utils R6 ragg rappdirs rcmdcheck RColorBrewer Rcpp RcppArmadillo RCurl rlang rmarkdown roxygen2 rprojroot rstudioapi rversions S7 sandwich sass scales sessioninfo shiny smarter sourcetools stringi survival sys systemfonts testthat textshaping TH.data tibble tinytex urlchecker usethis utf8 vctrs viridisLite waldo whisker withr xfun xml2 xopen xtable yaml zip zoo

Introduction to CSeQTL

Rendered fromintro.Rmdusingknitr::rmarkdown

Last update: 2025-02-19
Started: 2022-04-03

Citation

Development and contributors

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