README.md

In gongx030/scDatasets: Single cell RNA-seq datasets

scDatasets

Processed single cell sequencing datasets

1. Installation

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.

2. Datasets

The scRNA-seq dataset could be loaded in this way:

library(scDatasets)
library(SummarizedExperiment)
data(pollen)
pollen

Here 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). |

gongx030/scDatasets documentation built on May 29, 2019, 12:37 p.m.