https://github.com/joeburns06/hocuspocus

hocuspocus
https://github.com/joeburns06/hocuspocus

Last synced: 23 days ago
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hocuspocus

• Host: GitHub
• URL: https://github.com/joeburns06/hocuspocus
• Owner: joeburns06
• Created: 2015-11-02T17:51:24.000Z (over 8 years ago)
• Default Branch: master
• Last Pushed: 2016-06-22T12:07:46.000Z (about 8 years ago)
• Last Synced: 2024-02-24T13:31:08.364Z (4 months ago)
• Language: R
• Size: 63.5 KB
• Stars: 0
• Watchers: 2
• Forks: 2
• Open Issues: 1
• Metadata Files:
  • Readme: README.md

Lists

• awesome_single_cell - HocusPocus - [R] - Basic PCA-based workflow for analysis and plotting of single cell RNA-seq data. (Software packages / RNA-seq)
• awesome-single-cell - HocusPocus - [R] - Basic PCA-based workflow for analysis and plotting of single cell RNA-seq data. (Software packages / RNA-seq)
• awesome-single-cell - HocusPocus - [R] - Basic PCA-based workflow for analysis and plotting of single cell RNA-seq data. (Software packages / RNA-seq)
• roryk-awesome-single-cell - HocusPocus - [R] - Basic PCA-based workflow for analysis and plotting of single cell RNA-seq data. (Software packages)

README

        
# 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)

```