To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("gmapR")
In most cases, you don't need to download the package archive at all.
gmapR
Provides convenience methods to work with GMAP and GSNAP from within R
Bioconductor version: 3.0
GSNAP and GMAP are a pair of tools to align short-read data written by Tom Wu. This package provides convenience methods to work with GMAP and GSNAP from within R. In addition, it provides methods to tally alignment results on a per-nucleotide basis using the bam_tally tool.
Author: Cory Barr, Thomas Wu, Michael Lawrence
Maintainer: Michael Lawrence <lawrence.michael at gene.com>
Citation (from within R,
enter citation("gmapR")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("gmapR")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("gmapR")
| R Script | gmapR | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | Alignment, Software |
| Version | 1.8.0 |
| In Bioconductor since | BioC 2.11 (R-2.15) |
| License | Artistic-2.0 |
| Depends | R (>= 2.15.0), methods, GenomeInfoDb(>= 1.1.3), GenomicRanges(>= 1.17.12) |
| Imports | S4Vectors, IRanges, Rsamtools(>= 1.17.8), rtracklayer(>= 1.25.5), GenomicFeatures(>= 1.17.13), Biostrings, VariantAnnotation(>= 1.11.4), tools, Biobase, BSgenome, GenomicAlignments(>= 1.1.9), BiocParallel |
| LinkingTo | |
| Suggests | RUnit, BSgenome.Dmelanogaster.UCSC.dm3, BSgenome.Scerevisiae.UCSC.sacCer3, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19, LungCancerLines |
| SystemRequirements | |
| Enhances | |
| URL | |
| Depends On Me | HTSeqGenie |
| Imports Me | VariantTools |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | gmapR_1.8.0.tar.gz |
| Windows Binary | |
| Mac OS X 10.6 (Snow Leopard) | |
| 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
Post questions about Bioconductor packages to our mailing lists. Read the posting guide before posting!
Contact us: support.bioconductor.org
Hosting provided by Fred Hutchinson Cancer Research Center
Copyright © 2003 - 2015, Bioconductor
