https://github.com/drisso/archive-scrnaseq
Archived version of the scRNAseq Bioconductor package. All future development will be done at https://github.com/LTLA/scRNAseq
https://github.com/drisso/archive-scrnaseq
Last synced: 9 months ago
JSON representation
Archived version of the scRNAseq Bioconductor package. All future development will be done at https://github.com/LTLA/scRNAseq
- Host: GitHub
- URL: https://github.com/drisso/archive-scrnaseq
- Owner: drisso
- Created: 2016-03-01T20:11:54.000Z (over 10 years ago)
- Default Branch: master
- Last Pushed: 2019-06-09T16:40:20.000Z (almost 7 years ago)
- Last Synced: 2024-12-17T13:51:38.434Z (over 1 year ago)
- Language: R
- Homepage:
- Size: 143 MB
- Stars: 4
- Watchers: 9
- Forks: 3
- Open Issues: 3
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
README
# scRNAseq
## Gene-level summaries of public single-cell RNA-seq datasets
This package contains a collection of three publicly available single-cell RNA-seq datasets. The data were downloaded from NCBI's SRA or from EBI's ArrayExpress (see below for Accession numbers) and pre-processed with a standardized pipeline (see vignette). For each dataset, the package provides gene-level read counts obtained from Tophat + featureCounts, gene-level FPKMs obtained from Cufflinks, and gene-level read counts and TPMs from RSEM.
The dataset _fluidigm_ contains 65 cells from Pollen et al. (2014), each sequenced at high and low coverage (SRA: SRP041736).
The dataset _th2_ contains 96 T helper cells from Mahata et al. (2014) (ArrayExpress: E-MTAB-2512).
The dataset _allen_ contains 379 cells from the mouse visual cortex. This is a subset of the data published in Tasic et al. (2016) (SRA: SRP061902).
## To install
You can download the latest release [here](https://github.com/drisso/scRNAseq/releases). Once dowloaded, type in R
```{r}
install.packages("scRNAseq_0.99.0.tar.gz", repos=NULL)
```
to install the package, where `scRNAseq_0.99.0.tar.gz` is the name of the file downloaded (note that the name could change reflecting the release of a new version of the package).
Note that this package depends on the Bioconductor package `SummarizedExperiment`, which can be installed in R by typing
```{r}
source("https://bioconductor.org/biocLite.R")
biocLite("SummarizedExperiment")
```
## References
Pollen, Nowakowski, Shuga, Wang, Leyrat, Lui, Li, Szpankowski, Fowler, Chen, Ramalingam, Sun, Thu, Norris, Lebofsky, Toppani, Kemp II, Wong, Clerkson, Jones, Wu, Knutsson, Alvarado, Wang, Weaver, May, Jones, Unger, Kriegstein, West. Low-coverage single-cell mRNA sequencing reveals cellular heterogeneity and activated signaling pathways in developing cerebral cortex. _Nature Biotechnology_, __32__, 1053-1058 (2014).
Mahata, Zhang, Kolodziejczyk, Proserpio, Haim-Vilmovsky, Taylor, Hebenstreit, Dingler, Moignard, Gottgens, Arlt, McKenzie, Teichmann. Single-Cell RNA Sequencing Reveals T Helper Cells Synthesizing Steroids De Novo to Contribute to Immune Homeostasis. _Cell Reports_, __7__(4): 1130–1142 (2014).
Tasic, Menon, Nguyen, Kim, Jarsky, Yao, Levi, Gray, Sorensen, Dolbeare, Bertagnolli, Goldy, Shapovalova, Parry, Lee, Smith, Bernard, Madisen, Sunkin, Hawrylycz, Koch, Zeng. Adult mouse cortical cell taxonomy revealed by single cell transcriptomics. _Nature Neuroscience_, __19__, 335–346 (2016).
## Disclaimer
The data were downloaded from NCBI's SRA or from EBI's ArrayExpress. See the following disclaimers for copyright / license policies.
http://www.insdc.org/policy.html
http://www.ncbi.nlm.nih.gov/geo/info/disclaimer.html