Introduction

The upload tab is the first tab displayed when the singleCellTK is loaded. Here, you can upload a matrix of data along with annotation information to explore within the toolkit.

Under the hood, the SCTK created a SCtkExperiment object which stores one or more matrix of data along with a column annotation data frame and a row annotation data frame. The SCtkExperiment is an extension of the SingleCellExperiment object.

Input Data Format

The SCTK accepts tab-delimited files on the upload tab. You must provide a matrix of count data, and you can optionally provide both sample and feature annotation files as well. All files must have the same cells or genes and must be in the same order.

Assay

The input assay should be a matrix with genes as rows and samples (cells) as columns. For most users, the input assay will be a matrix of counts, but if the assay data being uploaded is not a count matrix, you can change the input assay type with the “Input Assay Type” drop-down. Download an example count file here.

Gene Cell1 Cell2 CellN
Gene1 0 0 0
Gene2 5 6 0
Gene3 4 3 8
GeneM 10 10 10

Sample Annotations (optional)

Sample annotations should be a table with samples (cells) as rows and annotations as columns. Download an example annotation file here.

Cell Annot1
Cell1 a
Cell2 a
Cell3 b
CellN b

Feature Annotations (optional)

Feature annotations should be a table with genes as rows and gene annotations as columns. Download an example feature file here.

Gene Annot2
Gene1 a
Gene2 a
Gene3 b
GeneM b

Example Data

You can also load example data sets on the upload tab for testing, see the package documentation for details about the available datasets.

Session info

## R version 3.6.0 (2019-04-26)
## Platform: x86_64-apple-darwin15.6.0 (64-bit)
## Running under: macOS Mojave 10.14.4
## 
## Matrix products: default
## BLAS:   /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib
## 
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] BiocStyle_2.12.0
## 
## loaded via a namespace (and not attached):
##  [1] Rcpp_1.0.1         rstudioapi_0.10    knitr_1.22        
##  [4] xml2_1.2.0         magrittr_1.5       roxygen2_6.1.1    
##  [7] MASS_7.3-51.4      R6_2.4.0           rlang_0.3.4       
## [10] stringr_1.4.0      tools_3.6.0        xfun_0.6          
## [13] htmltools_0.3.6    commonmark_1.7     yaml_2.2.0        
## [16] digest_0.6.18      assertthat_0.2.1   rprojroot_1.3-2   
## [19] bookdown_0.9       pkgdown_1.3.0      crayon_1.3.4      
## [22] BiocManager_1.30.4 fs_1.3.0           memoise_1.1.0     
## [25] evaluate_0.13      rmarkdown_1.12     stringi_1.4.3     
## [28] compiler_3.6.0     desc_1.2.0         backports_1.1.4