Package: hammers 1.1.0

Andrei-Florian Stoica

hammers: Utilities for scRNA-seq data analysis

hammers is a utilities suite for scRNA-seq data analysis compatible with both Seurat and SingleCellExperiment. It provides simple tools to address tasks such as retrieving aggregate gene statistics, finding and removing rare genes, performing representation analysis, computing the center of mass for the expression of a gene of interest in low-dimensional space, and calculating silhouette and cluster-normalized silhouette.

Authors:Andrei-Florian Stoica [aut, cre]

hammers_1.1.0.tar.gz
hammers_1.1.0.zip(r-4.7)hammers_1.1.0.zip(r-4.6)hammers_1.1.0.zip(r-4.5)
hammers_1.1.0.tgz(r-4.6-any)hammers_1.1.0.tgz(r-4.5-any)
hammers_1.1.0.tar.gz(r-4.7-any)hammers_1.1.0.tar.gz(r-4.6-any)
hammers_1.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
hammers/json (API)
NEWS

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

Bug tracker:https://github.com/andrei-stoica26/hammers/issues

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

softwaresinglecellgeneexpressionmultiplecomparisonvisualization

5.41 score 1 stars 1 packages 4 scripts 269 downloads 25 exports 108 dependencies

Last updated from:6a2356ee43. Checks:1 NOTE, 9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksNOTE275
linux-devel-x86_64OK486
source / vignettesOK395
linux-release-x86_64OK506
macos-release-arm64OK320
macos-oldrel-arm64OK271
windows-develOK1673
windows-releaseOK1606
windows-oldrelOK1229
wasm-releaseOK202

Exports:addCategoryaddMetadataCategoryaddNormSilhouettecenterOfMasscheckGenescolCenterscolsDimPlotcomputeSilhouettedevPlotdistributionPlotfindRareGenesgeneCellSetsgeneCentersgenePresencegenesDimPlotjoinCharCombskeyvalMapnormalizeSilhouettepointsDimPlotprepAlluvialpvalRiverPlotremoveRareGenesrepAnalysissafeMessagesafeMinmax

Dependencies:abdivabindapebase64encBiobaseBiocGenericscachemclasscliclustercodetoolscpp11data.tableDelayedArraydigestdotCall64dplyrfarverfastmapfloatfuturefuture.applygenericsGenomicRangesggalluvialggeasyggforceggnewscaleggplot2ggraphggrepelglobalsgluegraphlayoutsgridExtragtablehennaigraphIRangesisobandjsonlitelabelinglatticelazyevallgrlifecyclelistenvLISTOlivermagrittrMASSMatrixMatrixExtraMatrixGenericsmatrixStatsmemoisemlapinlmeomnibuspaletteerparallellypillarpkgconfigplyrpolyclipprimesprismaticprogressrpurrrR6RColorBrewerRcppRcppArmadilloRcppEigenrematch2reshape2RhpcBLASctlrlangrsparserstudioapiS4ArraysS4VectorsS7scalesscLangSeqinfoSeuratObjectSingleCellExperimentspspamSparseArraystatisfactorystringistringrSummarizedExperimentsystemfontstext2vectibbletidygraphtidyrtidyselecttweenrutf8vctrsviridisviridisLitewithrXVector

Introduction to hammers

Andrei-Florian Stoica

Rendered fromhammers.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2026-03-06
Started: 2025-09-09

Readme and manuals

Help Manual

Help pageTopics
Add a categorical column to a data frame based on another columnaddCategory
Add a categorical column to a Seurat metadata or SingleCellExperiment coldataaddMetadataCategory
Adds normalized silhouette column to a single-cell expression objectaddNormSilhouette
Calculate the center of mass of columnscenterOfMass
Check if all genes exist in the single-cell expression objectcheckGenes
Calculate the centers of mass of metadata/coldata columnscolCenters
Create a single-cell dimensionality reduction plot with added labeled points for numeric columnscolsDimPlot
Compute cluster silhouette for single-cell expression objectcomputeSilhouette
Saves plot or list of plotsdevPlot devPlot.default devPlot.function devPlot.ggplot devPlot.list
Plot the distribution of cells across two columnsdistributionPlot
Find rare genes in a Seurat or SingleCellExpression objectfindRareGenes
Generates cell sets for each input genegeneCellSets
Calculate the centers of mass of the expression of input genesgeneCenters
Extract gene presence from a Seurat or SingleCellExperiment objectgenePresence
Create a single-cell dimensionality reduction plot with added labeled points for genesgenesDimPlot
Join all combinations of elements from character vectorsjoinCharCombs
Create a map from keys to valueskeyvalMap
Normalize silhouette by identity class for single-cell expression objectnormalizeSilhouette
Create a single-cell dimensionality reduction plot with added labeled pointspointsDimPlot
Prepare dataframe for alluvial plotprepAlluvial
Plot representation data framepvalRiverPlot
Remove rare genes from a Seurat or SingleCellExpression objectremoveRareGenes
Find the differential representation of two Seurat or SingleCellExperiment columnsrepAnalysis
Message an input if verbose is set to TRUEsafeMessage
Perform min-max normalization when possible; otherwise return a single-value vector.safeMinmax