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README.md

hocuspocus

hocuspocus provides an easy-to-use and intuitive workflow for basic analysis of single-cell RNA-Seq data. It combines custom functions with functions from available packages. Particular emphasis is placed on data presentation and visualization, with a variety of options for controlling the appearance of plots. Currently, tools include selection of important expressed genes based on variance and PCA, heatmaps with color bars, blot plots, 1D, 2D, and 3D PCA plots, clustering analysis, gap statistic caclulation, and all of the temporal ordering and differential expression analysis tools from monocle.

First installation

To install hocuspocus and run it for the first time, open a new R or RStudio session and type the following commands:

install.packages("devtools")
source("https://bioconductor.org/biocLite.R")
biocLite("sva")
devtools::install_github("satijalab/seurat")
devtools::install_github("joeburns06/hocuspocus")
library(hocuspocus)

Subsequent R sessions

After this initial installation, you should only need the following command to load and attach hocuspocus in subsequent R sessions:

library(hocuspocus)

Getting the latest version of hocuspocus

To obtain the latest version of hocuspocus, type the following commands:

devtools::install_github("joeburns06/hocuspocus")
library(hocuspocus)

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