In krishan57gupta/DOSeq: Modeling expression drop-out for analysis of scRNA-Seq data

knitr::opts_chunk$set(
    collapse = TRUE,
    comment = "#>"
)

DOSeq

Modeling expression drop-out for analysis of scRNA-Seq data

Introduction

DOSeq - Modeling expression drop-out for analysis of scRNA-Seq data. DOSeq takes read count matrix and factor for drop-out ratio as input and return the read count matrix with dropout. Here input parameter factor indicates drop-out ratio in expression matrix.

Installation

The developer's version of the R package can be installed with the following R commands:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("DOSeq")

The github's version of the R package can be installed with the following R commands:

library(devtools)
install_github('krishan57gupta/DOSeq')

Vignette tutorial

This vignette uses the Tung dataset, which is already inbuilt in the package, to demonstrate a standard pipeline.

Example

Libraries need to be loaded before running.

library(DOSeq)

Loading tung dataset

samples<-DOSeq::L_Tung_single$NA19098_NA19101_count
samples[1:5,1:5]

DOSeq analysis.

Input: gene expression matrix with genes in rows and cells in columns.

output<-DOSeq(countData=samples, factor=.8)

Showing results are in the form of gene expression with drop out

Simulated gene expression matrix

output[1:5,1:5]

krishan57gupta/DOSeq documentation built on Feb. 17, 2021, 12:06 a.m.