Processed single cell sequencing datasets
The recommended installation method for scDatasets is using install_github command from devtools library. You will first have to have devtools package installed.
library(devtools)
install_github('gongx030/scDatasets')A number of needed packages are installed in this process.
The scRNA-seq dataset could be loaded in this way:
library(scDatasets)
library(SummarizedExperiment)
data(pollen)
pollenHere summarizes the name, data type, expression unit and source of included datasets:
| Name | Data_Type | Expression_Unit | Source |
|---|---|---|---|
| guo | scPCR | exp(-Ct) | Guo et al. Resolution of cell fate decisions revealed by single-cell gene expression analysis from zygote to blastocyst. Dev Cell. 2010 Apr 20;18(4):675-85. (20412781). |
| guo2 | scRNA-seq | count | Guo et al. The Transcriptome and DNA Methylome Landscapes of Human Primordial Germ Cells. Cell. 2015 Jun 4;161(6):1437-52. (26046443). |
| loh | scRNA-seq | count | Loh et al. Mapping the Pairwise Choices Leading from Pluripotency to Human Bone, Heart, and Other Mesoderm Cell Types. Cell. 2016 Jul 14;166(2):451-467. (27419872) |
| pollen | scRNA-seq | count | Pollen et al. Low-coverage single-cell mRNA sequencing reveals cellular heterogeneity and activated signaling pathways in developing cerebral cortex. Nat Biotechnol. 2014 Oct;32(10):1053-8. (25086649). |
| trapnell | scRNA-seq | FPKM | Trapnell et al. The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells. Nat Biotechnol. 2014 Apr;32(4):381-386. (24658644). |
| usoskin | scRNA-seq | FPKM | Usoskin et al. Unbiased classification of sensory neuron types by large-scale single-cell RNA sequencing. Nat Neurosci. 2015 Jan;18(1):145-53. (25420068). |
| blakeley | scRNA-seq | count | Blakeley et al. Defining the three cell lineages of the human blastocyst by single-cell RNA-seq. Development. 2015 Oct 15;142(20):3613. (26487783). |
| iPSC | scRNA-seq | count | Single-Cell RNA-seq of iPSC-CM differentiations at iPSC stage (D0), differentiation day 6 (D6), D10, D30 and D60. |
| petropoulos | scRNA-seq | count | Single-Cell RNA-Seq Reveals Lineage and X Chromosome Dynamics in Human Preimplantation Embryos. Cell. 2016 May 5;165(4):1012-26. (27062923). |
| deng | scRNA-seq | count | Deng et al. Single-cell RNA-seq reveals dynamic, random monoallelic gene expression in mammalian cells. Science. 2014 Jan 10;343(6167):193-6. (24408435). |