A Bioconductor "Summarized Experiment" from the Patel et al. (2014) paper that performed single cell RNA-Seq analysis on human glioblastoma tissue.
Switch branches/tags
Nothing to show
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Type Name Latest commit message Commit time
Failed to load latest commit information.
data
inst
vignette
.Rbuildignore
.gitattributes
.gitignore
DESCRIPTION
NAMESPACE
README.md
patel2014gliohuman.Rproj

README.md

patel2014gliohuman

This package contains a Bioconductor Summarized Experiment from the Patel et al. (2014) paper that performed single cell RNA-Seq analysis on human glioblastoma tissue. There are also some cell line and bulk RNA-Seq samples included. Metadata was obtained from Gene Expression Omnibus and raw FASTQ files were downloaded from Sequence Read Archive. All samples were quantified using Kallisto. The data provided are the estimated counts for ENSEMBL genes for all samples, not just the ones that were included in the authors' analysis. There are two SummarizedExperiment objects: (1) estimated counts from Kallisto and (2) TPMs from Kallisto.

Installation

The R-package patel2014gliohuman can be installed from Github using the R package devtools.

library(devtools)
install_github("willtownes/patel2014gliohuman")

Load data

The data is provided as a SummarizedExperiment object can be loaded by running the following code in R. Note that the assays are sparse Matrix objects, which is memory efficient due to large numbers of zeros.

library(SummarizedExperiment)
library(patel2014gliohuman)
data(patel_counts)
data(patel_tpm) 

# Get the pheno data (same for counts and TPM)
pdata = colData(patel_counts)

# Get the expression data in the form of counts
patel_counts = as.data.frame(as.matrix(assay(patel_counts)))

# Get the expression data in the form of TPMs
patel_tpm = as.data.frame(as.matrix(assay(patel_tpm)))

Bug reports

Report bugs as issues on the GitHub repository

Contributors