Package: SignacX 2.2.0

SignacX: Cell Type Identification and Discovery from Single Cell Gene Expression Data

An implementation of neural networks trained with flow-sorted gene expression data to classify cellular phenotypes in single cell RNA-sequencing data. See Chamberlain M et al. (2021) <doi:10.1101/2021.02.01.429207> for more details.

Authors:Mathew Chamberlain [aut, cre], Virginia Savova [aut], Richa Hanamsagar [aut], Frank Nestle [aut], Emanuele de Rinaldis [aut], Sanofi US [fnd]

SignacX_2.2.0.tar.gz
SignacX_2.2.0.zip(r-4.7)SignacX_2.2.0.zip(r-4.6)SignacX_2.2.0.zip(r-4.5)
SignacX_2.2.0.tgz(r-4.6-any)SignacX_2.2.0.tgz(r-4.5-any)
SignacX_2.2.0.tar.gz(r-4.7-any)SignacX_2.2.0.tar.gz(r-4.6-any)
SignacX_2.2.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
SignacX/json (API)
NEWS

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

Bug tracker:https://github.com/mathewchamberlain/signacx/issues

Datasets:

On CRAN:

Conda:

cellular-phenotypesseuratsingle-cell-rna-seq

6.59 score 27 stars 41 scripts 268 downloads 20 exports 153 dependencies

Last updated from:11e872c292. Checks:7 WARNING, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64WARNING198
source / vignettesOK259
linux-release-x86_64WARNING184
macos-release-arm64WARNING167
macos-oldrel-arm64WARNING186
windows-develWARNING128
windows-releaseWARNING113
windows-oldrelWARNING110
wasm-releaseOK165

Exports:CID.entropyCID.GetDistMatCID.IsUniqueCID.LoadDataCID.LoadEdgesCID.LouvainCID.NormalizeCID.smoothCID.writeJSONGenerateLabelsget_colorsGetModels_HPCAGetTrainingData_HPCAKSoftImputeMASCModelGeneratorSaveCountsToH5SignacSignacBootSignacFast

Dependencies:abindaskpassbase64encBHbitopsbootbslibcachemcaToolscliclustercodetoolscommonmarkcowplotcpp11crosstalkcurldata.tabledeldirDerivdigestdotCall64dplyrdqrngevaluatefarverfastDummiesfastmapfitdistrplusFNNfontawesomefsfuturefuture.applygenericsggplot2ggrepelggridgesglobalsgluegoftestgplotsgridExtragtablegtoolsherehighrhtmltoolshtmlwidgetshttpuvhttricaigraphirlbaisobandjquerylibjsonliteKernSmoothknitrlabelinglaterlatticelazyevallifecyclelistenvlme4lmtestmagrittrMASSMatrixmatrixStatsmemoisemimeminiUIminqaneuralnetnlmenloptropensslotelparallellypatchworkpbapplypbmcapplypillarpkgconfigplotlyplyrpngpolyclipprogressrpromisespurrrR6RANNrappdirsrbibutilsRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppHNSWRcppProgressRcppTOMLRdpackreformulasreshape2reticulateRJSONIOrlangrmarkdownROCRrprojrootRSpectraRtsneS7sassscalesscattermoresctransformSeuratSeuratObjectshinysitmosourcetoolsspspamspatstat.dataspatstat.explorespatstat.geomspatstat.randomspatstat.sparsespatstat.univarspatstat.utilsstringistringrsurvivalsystensortibbletidyrtidyselecttinytexutf8uwotvctrsviridisLitewithrxfunxtableyamlzoo

Cell type classification with SignacX: CITE-seq PBMCs from 10X Genomics

Rendered fromsignac-Seurat_CITE-seq.Rmdusingknitr::rmarkdown_notangleon May 26 2026.

Last update: 2021-03-01
Started: 2021-02-25

SignacX, Seurat and MASC: Analysis of kidney cells from AMP

Rendered fromsignac-Seurat_AMP.Rmdusingknitr::rmarkdown_notangleon May 26 2026.

Last update: 2021-03-01
Started: 2021-02-04

Cell type classification with SignacX: 1k PBMCs from 10X Genomics

Rendered fromsignac-Seurat_pbmcs.Rmdusingknitr::rmarkdown_notangleon May 26 2026.

Last update: 2021-03-01
Started: 2021-02-25

Benchmarking SignacFast with single cell flow-sorted data

Rendered fromSignacFast-Seurat_AMP_RA.Rmdusingknitr::rmarkdown_notangleon May 26 2026.

Last update: 2021-03-01
Started: 2021-02-18

Benchmarking SignacX and SingleR with synovial flow cytometry data

Rendered fromsignac-Seurat_AMP_RA.Rmdusingknitr::rmarkdown_notangleon May 26 2026.

Last update: 2021-03-01
Started: 2021-02-11

Learning CD56 NK cells from CITE-seq PBMCs

Rendered fromsignac-SPRING_Learning.Rmdusingknitr::rmarkdown_notangleon May 26 2026.

Last update: 2021-03-01
Started: 2021-02-11

Mapping homologous gene symbols

Rendered fromCrabeating_vignette.Rmdusingknitr::rmarkdown_notangleon May 26 2026.

Last update: 2021-03-01
Started: 2021-02-10