To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("spade")
In most cases, you don't need to download the package archive at all.
spade
SPADE -- An analysis and visualization tool for Flow Cytometry
Bioconductor version: 3.0
SPADE, or Spanning tree Progression of Density normalized Events, is an analysis and visualization tool for high dimensional flow cytometry data that organizes cells into hierarchies of related phenotypes.
Author: M. Linderman, P. Qiu, E. Simonds, Z. Bjornson
Maintainer: Zach Bjornson <bjornson at stanford.edu>
Citation (from within R,
enter citation("spade")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("spade")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("spade")
| R Script | spade package | |
| Reference Manual | ||
| Text | LICENSE |
Details
| biocViews | Clustering, FlowCytometry, GUI, GraphAndNetwork, Software, Visualization |
| Version | 1.14.0 |
| In Bioconductor since | BioC 2.10 (R-2.15) |
| License | GPL-2 |
| Depends | R (>= 2.11), igraph, Rclusterpp |
| Imports | Biobase, flowCore |
| LinkingTo | |
| Suggests | flowViz |
| SystemRequirements | |
| Enhances | |
| URL | http://cytospade.org |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | spade_1.14.0.tar.gz |
| Windows Binary | spade_1.14.0.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | spade_1.14.0.tgz |
| Mac OS X 10.9 (Mavericks) | |
| Browse/checkout source | (username/password: readonly) |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Counting Reads for Differential Expression (parathyroideSE vignette)
- Annotation
- Annotating Variants
- Annotating Ranges
- Flow Cytometry and other assays
- Candidate Binding Sites for Known Transcription Factors
- Cloud-enabled cis-eQTL search and annotation
- RNA-Seq workflow: gene-level exploratory analysis and differential expression
- Changing genomic coordinate systems with rtracklayer::liftOver
- Mass spectrometry and proteomics data analysis
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