Package: Seqtometry 1.0.0

Robert Kousnetsov

Seqtometry: Signature scoring for single cell analysis

This package provides functions used in Seqtometry (Kousnetsov et al. 2024), a method for analyzing single cell (scRNA-seq or scATAC-seq) data via signature (gene set) enrichment scores. The Seqtometry scores may be useful for annotating or characterizing cells, either in a flow cytometry like workflow (where scores are standalone features used for progressive partitoning as described in the Seqtometry publication) or in a cluster-based workflow (as features of clusters). The exported impute function (a port of Python's MAGIC-impute, van Dijk et al. 2018), may also be useful for single cell analysis on its own.

Authors:Robert Kousnetsov [aut, cre], Daniel Hawiger [cph, fnd]

Seqtometry_1.0.0.tar.gz
Seqtometry_1.0.0.zip(r-4.7)Seqtometry_1.0.0.zip(r-4.6)Seqtometry_1.0.0.zip(r-4.5)
Seqtometry_1.0.0.tgz(r-4.6-x86_64)Seqtometry_1.0.0.tgz(r-4.6-arm64)Seqtometry_1.0.0.tgz(r-4.5-x86_64)Seqtometry_1.0.0.tgz(r-4.5-arm64)
Seqtometry_1.0.0.tar.gz(r-4.7-arm64)Seqtometry_1.0.0.tar.gz(r-4.7-x86_64)Seqtometry_1.0.0.tar.gz(r-4.6-arm64)Seqtometry_1.0.0.tar.gz(r-4.6-x86_64)
Seqtometry_1.0.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
Seqtometry/json (API)
NEWS

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

Bug tracker:https://github.com/hawigerlab/seqtometry/issues

Uses libs:
  • c++– GNU Standard C++ Library v3

On BioConductor:Seqtometry-1.1.0(bioc 3.24)Seqtometry-1.0.0(bioc 3.23)

singlecellgenesetenrichmentgeneexpressioncpp

4.54 score 1 stars 204 downloads 2 exports 50 dependencies

Last updated from:d1ef7d640c (on RELEASE_3_23). Checks:1 NOTE, 11 WARNING, 2 OK. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksNOTE226
linux-devel-arm64WARNING390
linux-devel-x86_64WARNING492
source / vignettesOK406
linux-release-arm64WARNING377
linux-release-x86_64WARNING503
macos-release-arm64WARNING280
macos-release-x86_64WARNING816
macos-oldrel-arm64WARNING370
macos-oldrel-x86_64WARNING655
windows-develWARNING1367
windows-releaseWARNING1289
windows-oldrelWARNING1333
wasm-releaseOK168

Exports:imputescore

Dependencies:abindassortheadbackportsbeachmatBHBiocGenericsBiocParallelBiocSingularcheckmateclicodetoolscpp11data.tableDelayedArraydigestformatRfutile.loggerfutile.optionsfuturefuture.applygenericsglobalsglueIRangesirlbalambda.rlatticelifecyclelistenvmagrittrMatrixMatrixGenericsmatrixStatsparallellypurrrRcppRcppArmadilloRcppEigenRcppHNSWrlangRSpectrarsvdS4ArraysS4VectorsScaledMatrixsnowSparseArrayvctrsXVectorzeallot

Seqtometry vignette

Rendered fromSeqtometry.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2026-03-15
Started: 2026-01-11