README.md

In kendomaniac/BCsctutorial:

BCsc Tutorial

Supporting material for the manuscript: Bray Curtis for single cell RNAseq data integration (BCsc). PIacenti G, Alessandri L, Cordero F, Beccuti M, and Calogero RA

Introduction

This vignette provides support to use Bray Curtis for single cell RNAseq data integration (BCsc). BCsc analysis was added as extention of rCASC.

Installation

To simplify usage and to guarantee reproducibility the tools required for the BCs workflow are embedded in docker containers stored at docker.io/repbioinfo. For more info on the computational approaches used in BCsc tutorial please see Kulkarni et al. BMC Bioinformatics 2018

An extensive description of how rCASC works is provided at rCASC vignette. Installation of rCASC including the SCA modules requires:

• A workstation/server running 64 bits Linux.

• Docker daemon installed on the machine, for more info see this document:

  https://docs.docker.com/engine/install/.

• The functions in rCASC package require that user belongs to a group with the rights to execute docker. See the following document for more info:

  https://docs.docker.com/engine/install/linux-postinstall/

To install the BCsctutorial, write in an R session:

install.packages("devtools")
library(devtools)
install_github("kendomaniac/BCsctutorial", ref="master")

Then, after package installation, execute in R:

library(SCAtutorial)
#check if docker daemon is  running and install rCASC package from github.
installing.rcasc()

This step checks that dockert daemon is running and downloads the dockert containers required for the tutorial. It might require sometime, between minutes to hours, depending on the available internet bandwidth.

Web site

The vignette of the BCsc tutorial is available at vignette

The vignette is located in the folder BCsctutorial/docs/articles. The vignette was built using the following command:

pkgdown::build_site()

Data are instead located in BCsctutorial/vignettes/data folder.

kendomaniac/BCsctutorial documentation built on Jan. 23, 2021, 9:42 p.m.