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To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("monocle")
In most cases, you don't need to download the package archive at all.
monocle
Analysis tools for single-cell expression experiments.
Bioconductor version: 3.0
Monocle performs differential expression and time-series analysis for single-cell expression experiments. It orders individual cells according to progress through a biological process, without knowing ahead of time which genes define progress through that process. Monocle also performs differential expression analysis, clustering, visualization, and other useful tasks on single cell expression data. It is designed to work with RNA-Seq and qPCR data, but could be used with other types as well.
Author: Cole Trapnell
Maintainer: Cole Trapnell <coletrap at uw.edu>
Citation (from within R,
enter citation("monocle")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("monocle")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("monocle")
| R Script | Monocle: Differential expression and time-series analysis for single-cell RNA-Seq and qPCR experiments. | |
| Reference Manual | ||
| Text | README | |
| Text | NEWS |
Details
| biocViews | Clustering, DataImport, DataRepresentation, DifferentialExpression, GeneExpression, Infrastructure, MultipleComparison, QualityControl, RNASeq, Sequencing, Software, Visualization |
| Version | 1.0.0 |
| In Bioconductor since | BioC 3.0 (R-3.1) |
| License | Artistic-2.0 |
| Depends | R (>= 2.7.0), HSMMSingleCell, Biobase, ggplot2 (>= 0.9.3.1), splines, VGAM (>= 0.9-4), igraph (>= 0.7.0), plyr |
| Imports | BiocGenerics, cluster, combinat, fastICA, grid, irlba, matrixStats, methods, parallel, reshape2, stats, utils, limma |
| LinkingTo | |
| Suggests | knitr, Hmisc |
| SystemRequirements | |
| Enhances | |
| URL | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | monocle_1.0.0.tar.gz |
| Windows Binary | monocle_1.0.0.zip |
| Mac OS X 10.6 (Snow Leopard) | monocle_1.0.0.tgz |
| Mac OS X 10.9 (Mavericks) | monocle_1.0.0.tgz |
| 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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