Package: smer 0.0.2

Julian Stamp

smer: Sparse Marginal Epistasis Test

The Sparse Marginal Epistasis Test is a computationally efficient genetics method which detects statistical epistasis in complex traits; see Stamp et al. (2025, <doi:10.1101/2025.01.11.632557>) for details.

Authors:Julian Stamp [cre, aut], Lorin Crawford [aut], sriramlab [cph]

smer_0.0.2.tar.gz
smer_0.0.2.zip(r-4.7)smer_0.0.2.zip(r-4.6)smer_0.0.2.zip(r-4.5)
smer_0.0.2.tgz(r-4.6-x86_64)smer_0.0.2.tgz(r-4.6-arm64)smer_0.0.2.tgz(r-4.5-x86_64)smer_0.0.2.tgz(r-4.5-arm64)
smer_0.0.2.tar.gz(r-4.7-arm64)smer_0.0.2.tar.gz(r-4.7-x86_64)smer_0.0.2.tar.gz(r-4.6-arm64)smer_0.0.2.tar.gz(r-4.6-x86_64)
manual.pdf |manual.html✨
card.svg |card.png
smer/json (API)
NEWS

# Install 'smer' in R:
install.packages('smer', repos = c('https://lcrawlab.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/lcrawlab/sme/issues

Pkgdown/docs site:https://lcrawlab.github.io

Uses libs:
  • curl– Easy-to-use client-side URL transfer library
  • openssl– Secure Sockets Layer toolkit
  • c++– GNU Standard C++ Library v3
  • openmp– GCC OpenMP (GOMP) support library
Datasets:

On CRAN:

Conda:

genomewideassociationepistasisgeneticssnplinearmixedmodelcppepistasis-analysisepistatisgwasgwas-toolsmapitcurlopensslcppopenmp

5.38 score 4 stars 8 scripts 352 downloads 6 exports 70 dependencies

Last updated from:647209cd62. Checks:10 OK, 2 WARNING, 1 FAIL. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64OK222
linux-devel-x86_64OK229
source / vignettesOK394
linux-release-arm64OK221
linux-release-x86_64OK238
macos-release-arm64WARNING259
macos-release-x86_64WARNING350
macos-oldrel-arm64OK352
macos-oldrel-x86_64OK426
windows-develOK287
windows-releaseOK321
windows-oldrelOK281
wasm-releaseFAIL196

Exports:approximate_memory_requirementscreate_hdf5_fileread_hdf5_datasetsimulate_traitssmewrite_hdf5_dataset

Dependencies:backportsBHbiocmakebitbit64briocallrcheckmateclicliprcodetoolsCompQuadFormcpp11crayondescdiffobjdir.expirydplyrevaluatefilelockFMStableforeachfsgenericsgenioglueharmonicmeanpHighFivehmsiteratorsjsonlitelifecycleloggingmagrittrmvMAPITmvtnormpillarpkgbuildpkgconfigpkgloadpraiseprettyunitsprocessxprogresspspurrrR6RcppRcppArmadilloRcppEigenRcppParallelRcppProgressRcppSpdlogreadrRhdf5librlangrprojrootstringistringrtestthattibbletidyrtidyselecttruncnormtzdbutf8vctrsvroomwaldowithr

Conditioning Epistasis Search on Open Chromatin

Rendered fromstudy-erythroid-differentiation-data.Rmdusingknitr::rmarkdownon May 21 2026.

Last update: 2025-01-17
Started: 2024-12-15

How To Cite Our Work

Rendered fromtutorial-cite-us.Rmdusingknitr::rmarkdownon May 21 2026.

Last update: 2025-01-14
Started: 2024-12-15

How To Create a Mask File

Rendered fromtutorial-create-mask-file.Rmdusingknitr::rmarkdownon May 21 2026.

Last update: 2025-01-14
Started: 2024-12-15

How To Optimize the Memory Requirements of SME

Rendered fromtutorial-memory-optimization.Rmdusingknitr::rmarkdownon May 21 2026.

Last update: 2025-01-17
Started: 2024-12-15

How To Simulate Traits

Rendered fromtutorial-simulate-traits.Rmdusingknitr::rmarkdownon May 21 2026.

Last update: 2025-01-14
Started: 2024-12-15

How To Use the Sparse Marginal Epistasis Test

Rendered fromsmer.Rmdusingknitr::rmarkdownon May 21 2026.

Last update: 2025-07-14
Started: 2025-01-14