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.
The R-package patel2014gliohuman can be installed from Github using the R package devtools.
library(devtools)
install_github("willtownes/patel2014gliohuman")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)))Report bugs as issues on the GitHub repository