ZEB1CRC Data Package

Installation

The data package can be installed as follows:

install.packages("remotes")
remotes::install_github("cubida/ZEB1CRC")

Exploring SCE data

The Single Cell Experiment objects can be accessed as follows:

Load library

library("ZEB1CRC")

AOM/DSS KO

#
aomdss_ko <- system.file("extdata", "aomdss.ko.sce.data.RData", package = "ZEB1CRC")
aomdss_ko <- load(aomdss_ko)
aomdss_ko <- sce.data
aomdss_ko

## Loading required package: SingleCellExperiment

## Loading required package: SummarizedExperiment

## Loading required package: MatrixGenerics

## Loading required package: matrixStats

## 
## Attaching package: 'MatrixGenerics'

## The following objects are masked from 'package:matrixStats':
## 
##     colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
##     colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
##     colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
##     colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
##     colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
##     colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
##     colWeightedMeans, colWeightedMedians, colWeightedSds,
##     colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
##     rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
##     rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
##     rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
##     rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
##     rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
##     rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
##     rowWeightedSds, rowWeightedVars

## Loading required package: GenomicRanges

## Loading required package: stats4

## Loading required package: BiocGenerics

## 
## Attaching package: 'BiocGenerics'

## The following objects are masked from 'package:stats':
## 
##     IQR, mad, sd, var, xtabs

## The following objects are masked from 'package:base':
## 
##     anyDuplicated, aperm, append, as.data.frame, basename, cbind,
##     colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
##     get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
##     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
##     Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort,
##     table, tapply, union, unique, unsplit, which.max, which.min

## Loading required package: S4Vectors

## 
## Attaching package: 'S4Vectors'

## The following object is masked from 'package:utils':
## 
##     findMatches

## The following objects are masked from 'package:base':
## 
##     expand.grid, I, unname

## Loading required package: IRanges

## Loading required package: GenomeInfoDb

## Loading required package: Biobase

## Welcome to Bioconductor
## 
##     Vignettes contain introductory material; view with
##     'browseVignettes()'. To cite Bioconductor, see
##     'citation("Biobase")', and for packages 'citation("pkgname")'.

## 
## Attaching package: 'Biobase'

## The following object is masked from 'package:MatrixGenerics':
## 
##     rowMedians

## The following objects are masked from 'package:matrixStats':
## 
##     anyMissing, rowMedians

## class: SingleCellExperiment 
## dim: 14016 834 
## metadata(2): merge.info pca.info
## assays(3): reconstructed counts logcounts
## rownames(14016): 0610007N19Rik__chr15 0610007P14Rik__chr12 ...
##   mtNd5__chrM mtNd6__chrM
## rowData names(1): rotation
## colnames(834): sce.MS002_X001 sce.MS002_X002 ... sce.MS006_X383
##   sce.MS006_X384
## colData names(20): batch sample ... sizeFactor label

## Loading required package: BiocSingular

## reducedDimNames(2): corrected TSNE
## mainExpName: NULL
## altExpNames(1): ERCC

AOM/DSS WT

#
aomdss_wt <- system.file("extdata", "aomdss.wt.sce.data.RData", package = "ZEB1CRC")
aomdss_wt <- load(aomdss_wt)
aomdss_wt <- sce.data
aomdss_wt

## class: SingleCellExperiment 
## dim: 13941 817 
## metadata(2): merge.info pca.info
## assays(3): reconstructed counts logcounts
## rownames(13941): 0610007N19Rik__chr15 0610007P14Rik__chr12 ...
##   mtNd5__chrM mtNd6__chrM
## rowData names(1): rotation
## colnames(817): sce.MS001_X001 sce.MS001_X002 ... sce.MS004_X381
##   sce.MS004_X384
## colData names(20): batch sample ... sizeFactor label
## reducedDimNames(2): corrected TSNE
## mainExpName: NULL
## altExpNames(1): ERCC

Orthotropic KO

#
orthotropic_ko <- system.file("extdata", "orthotropic.ko.sce.data.RData", package = "ZEB1CRC")
orthotropic_ko <- load(orthotropic_ko)
orthotropic_ko <- sce.data
orthotropic_ko

## class: SingleCellExperiment 
## dim: 14562 94 
## metadata(2): merge.info pca.info
## assays(3): reconstructed counts logcounts
## rownames(14562): 0610007N19Rik__chr15 0610007P14Rik__chr12 ...
##   mtNd5__chrM mtNd6__chrM
## rowData names(1): rotation
## colnames(94): sce.MS002_X002 sce.MS002_X004 ... sce.MS010_X252
##   sce.MS010_X336
## colData names(23): batch sample ... sizeFactor label
## reducedDimNames(2): corrected TSNE
## mainExpName: NULL
## altExpNames(1): ERCC

Orthotropic WT

#
orthotropic_wt <- system.file("extdata", "orthotropic.wt.sce.data.RData", package = "ZEB1CRC")
orthotropic_wt <- load(orthotropic_wt)
orthotropic_wt <- sce.data
orthotropic_wt

## class: SingleCellExperiment 
## dim: 13580 124 
## metadata(2): merge.info pca.info
## assays(3): reconstructed counts logcounts
## rownames(13580): 0610007N19Rik__chr15 0610007P14Rik__chr12 ...
##   mtNd5__chrM mtNd6__chrM
## rowData names(1): rotation
## colnames(124): sce.MS003_X001 sce.MS003_X003 ... sce.MS007_X335
##   sce.MS007_X336
## colData names(23): batch sample ... sizeFactor label
## reducedDimNames(2): corrected TSNE
## mainExpName: NULL
## altExpNames(1): ERCC

Integrated AOM/DSS

#
integrated_aomdss <- system.file("extdata", "merged.rescaled2.RData", package = "ZEB1CRC")
integrated_aomdss <- load(integrated_aomdss)
integrated_aomdss <- merged.rescaled2
integrated_aomdss

## class: SingleCellExperiment 
## dim: 13207 1651 
## metadata(2): merge.info pca.info
## assays(3): reconstructed counts logcounts
## rownames(13207): 0610007N19Rik__chr15 0610007P14Rik__chr12 ...
##   mtNd5__chrM mtNd6__chrM
## rowData names(3): rotation symbol ensemble
## colnames(1651): sce.MS001_X001 sce.MS001_X002 ... sce.MS006_X383
##   sce.MS006_X384
## colData names(5): batch sample condition sizeFactor label
## reducedDimNames(5): corrected PCA TSNE UMAP force
## mainExpName: NULL
## altExpNames(1): ERCC