Package: scClassify 1.17.0

Yingxin Lin

scClassify: scClassify: single-cell Hierarchical Classification

scClassify is a multiscale classification framework for single-cell RNA-seq data based on ensemble learning and cell type hierarchies, enabling sample size estimation required for accurate cell type classification and joint classification of cells using multiple references.

Authors:Yingxin Lin

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NEWS

# Install 'scClassify' in R:

install.packages('scClassify', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/sydneybiox/scclassify/issues

Datasets:

scClassify_example - Example data used in scClassify package
trainClassExample_wang - Subset of pretrained model of Wang et al.
trainClassExample_xin - Subset of pretrained model of Xin et al.

On BioConductor:scClassify-1.17.0(bioc 3.20)scClassify-1.16.0(bioc 3.19)

bioconductor-package

16 exports 1.45 score 147 dependencies 3 mentions

Last updated 2 months agofrom:97c7d77ef6

Exports:cellTypeTrain cellTypeTree features getN learningCurve model modelweights name plotCellTypeTree predict_scClassify predict_scClassifyJoint runHOPACH runSampleCal scClassify scClassifyTrainModelList train_scClassify

Dependencies:abind annotate AnnotationDbi askpass base64enc BH Biobase BiocGenerics BiocParallel Biostrings bit bit64 blob bslib cachem Cepo cli cluster codetools colorspace cpp11 crayon crosstalk curl data.table DBI DelayedArray DelayedMatrixStats digest diptest dplyr evaluate fansi farver fastmap fontawesome formatR fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicRanges ggforce ggplot2 ggraph ggrepel glue graph graphlayouts gridExtra GSEABase gtable HDF5Array highr hopach htmltools htmlwidgets httr igraph IRanges isoband jquerylib jsonlite KEGGREST kernlab knitr labeling lambda.r later lattice lazyeval lifecycle limma magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime minpack.lm mixtools munsell nlme openssl patchwork pillar pkgconfig plogr plotly plyr png polyclip promises proxy proxyC purrr R6 rappdirs RColorBrewer Rcpp RcppArmadillo RcppEigen reshape2 rhdf5 rhdf5filters Rhdf5lib rlang rmarkdown RSQLite S4Arrays S4Vectors sass scales segmented SingleCellExperiment snow SparseArray sparseMatrixStats statmod stringi stringr SummarizedExperiment survival sys systemfonts tibble tidygraph tidyr tidyselect tinytex tweenr UCSC.utils utf8 vctrs viridis viridisLite withr xfun XML xtable XVector yaml zlibbioc

Performing scClassify using pretrained model

Yingxin Lin

Rendered frompretrainedModel.Rmdusingknitr::rmarkdownon Jul 02 2024.

Last update: 2020-04-20
Started: 2019-09-20

scClassify Model Building and Prediction

Yingxin Lin

Rendered fromscClassify.Rmdusingknitr::rmarkdownon Jul 02 2024.

Last update: 2020-04-20
Started: 2019-09-20

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
The scClassifyTrainModel class	.scClassifyTrainModel
Accessors of cellTypeTrain for scClassifyTrainModel	cellTypeTrain cellTypeTrain,scClassifyTrainModel-method
Accessors of cellTypeTree for scClassifyTrainModel	cellTypeTree cellTypeTree,scClassifyTrainModel-method
Accessors of features for scClassifyTrainModel	features features,scClassifyTrainModel-method
Function to get the required N given by the accuracy and the learning curve model	getN
Fit learning curve for accuracy matrix	learningCurve
Accessors of model for scClassifyTrainModel	model model,scClassifyTrainModel-method
Accessors of modelweights for scClassifyTrainModel	modelweights modelweights,scClassifyTrainModel-method
Accessors of name for scClassifyTrainModel	name name,scClassifyTrainModel-method
To plot cell type tree	plotCellTypeTree
Testing scClassify model	predict_scClassify
Testing scClassify model (joint training)	predict_scClassifyJoint
Create HOPACH tree	runHOPACH
Run sample size calculation for pilot data for reference dataset	runSampleCal
Train and test scClassify model	scClassify
Example data used in scClassify package	scClassify_example
An S4 class to stored training model for scClassify	scClassifyTrainModel-class
The scClassifyTrainModelList class	scClassifyTrainModelList
An S4 class to stored a list of training models from scClassify	scClassifyTrainModelList-class
Training scClassify model	train_scClassify
Subset of pretrained model of Wang et al.	trainClassExample_wang
Subset of pretrained model of Xin et al.	trainClassExample_xin

Package: scClassify 1.17.0

scClassify: scClassify: single-cell Hierarchical Classification

Performing scClassify using pretrained model

scClassify Model Building and Prediction

Citation

Development and contributors

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)