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]

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SignacX.pdf |SignacX.html✨
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:

Genes_Of_Interest - Genes of interest for drug discovery / disease biology research

On CRAN:

cellular-phenotypes seurat single-cell-rna-seq

20 exports 23 stars 2.15 score 154 dependencies 26 scripts 246 downloads

Last updated 2 years agofrom:11e872c292. Checks:OK: 1 WARNING: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Aug 21 2024
R-4.5-win	WARNING	Aug 21 2024
R-4.5-linux	WARNING	Aug 21 2024
R-4.4-win	WARNING	Aug 21 2024
R-4.4-mac	WARNING	Aug 21 2024
R-4.3-win	WARNING	Aug 21 2024
R-4.3-mac	WARNING	Aug 21 2024

Exports:CID.entropy CID.GetDistMat CID.IsUnique CID.LoadData CID.LoadEdges CID.Louvain CID.Normalize CID.smooth CID.writeJSON GenerateLabels get_colors GetModels_HPCA GetTrainingData_HPCA KSoftImpute MASC ModelGenerator SaveCountsToH5 Signac SignacBoot SignacFast

Dependencies:abind askpass base64enc BH bitops boot bslib cachem caTools cli cluster codetools colorspace commonmark cowplot cpp11 crayon crosstalk curl data.table deldir Deriv digest dotCall64 dplyr dqrng evaluate fansi farver fastDummies fastmap fitdistrplus FNN fontawesome fs future future.apply generics ggplot2 ggrepel ggridges globals glue goftest gplots gridExtra gtable gtools here highr htmltools htmlwidgets httpuv httr ica igraph irlba isoband jquerylib jsonlite KernSmooth knitr labeling later lattice lazyeval leiden lifecycle listenv lme4 lmtest magrittr MASS Matrix matrixStats memoise mgcv mime miniUI minqa munsell neuralnet nlme nloptr openssl parallelly patchwork pbapply pbmcapply pillar pkgconfig plotly plyr png polyclip progressr promises purrr R6 RANN rappdirs RColorBrewer Rcpp RcppAnnoy RcppArmadillo RcppEigen RcppHNSW RcppProgress RcppTOML reshape2 reticulate RJSONIO rlang rmarkdown ROCR rprojroot RSpectra Rtsne sass scales scattermore sctransform Seurat SeuratObject shiny sitmo sourcetools sp spam spatstat.data spatstat.explore spatstat.geom spatstat.random spatstat.sparse spatstat.univar spatstat.utils stringi stringr survival sys tensor tibble tidyr tidyselect tinytex utf8 uwot vctrs viridisLite withr xfun xtable yaml zoo

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

Rendered fromsignac-Seurat_CITE-seq.Rmdusingknitr::rmarkdown_notangleon Aug 21 2024.

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 Aug 21 2024.

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 Aug 21 2024.

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 Aug 21 2024.

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 Aug 21 2024.

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

Learning CD56 NK cells from CITE-seq PBMCs

Rendered fromsignac-SPRING_Learning.Rmdusingknitr::rmarkdown_notangleon Aug 21 2024.

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

Mapping homologous gene symbols

Rendered fromCrabeating_vignette.Rmdusingknitr::rmarkdown_notangleon Aug 21 2024.

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Normalized Shannon entropy-based "unclassified" assignment	CID.entropy
Computes distance matrix from edge list	CID.GetDistMat
Extracts unique elements	CID.IsUnique
Load data file from directory	CID.LoadData
Load edges from edge list for single cell network	CID.LoadEdges
Detects community substructure by Louvain community detection	CID.Louvain
Library size normalize	CID.Normalize
Smoothing function	CID.smooth
Writes JSON file for SPRING integration	CID.writeJSON
Generates cellular phenotype labels	GenerateLabels
Genes of interest for drug discovery / disease biology research	Genes_Of_Interest
Loads neural network models from GitHub	GetModels_HPCA
Loads bootstrapped HPCA training data from GitHub	GetTrainingData_HPCA
KNN-based imputation	KSoftImpute
Mixed effect modeling	MASC
Generates an ensemble of neural network models.	ModelGenerator
Save count_matrix.h5 files for SPRING integration	SaveCountsToH5
Classification of cellular phenotypes in single cell data	Signac
Generates bootstrapped single cell data	SignacBoot
Fast classification of cellular phenotypes	SignacFast