AIMS
This is the released version of AIMS; for the devel version, see AIMS.
AIMS : Absolute Assignment of Breast Cancer Intrinsic Molecular Subtype
Bioconductor version: Release (3.23)
This package contains the AIMS implementation. It contains necessary functions to assign the five intrinsic molecular subtypes (Luminal A, Luminal B, Her2-enriched, Basal-like, Normal-like). Assignments could be done on individual samples as well as on dataset of gene expression data.
Author: Eric R. Paquet, Michael T. Hallett
Maintainer: Eric R Paquet <eric.r.paquet at gmail.com>
citation("AIMS")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("AIMS")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("AIMS")| AIMS An Introduction (HowTo) | R Script | |
| Reference Manual | ||
| README | Text |
Details
| biocViews | Classification, GeneExpression, ImmunoOncology, Microarray, RNASeq, Software |
| Version | 1.44.0 |
| In Bioconductor since | BioC 3.1 (R-3.2) (11.5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 2.10), e1071, Biobase |
| Imports | |
| System Requirements | |
| URL | http://www.bci.mcgill.ca/AIMS |
See More
| Suggests | breastCancerVDX, hgu133a.db, RUnit, BiocGenerics |
| Linking To | |
| Enhances | |
| Depends On Me | genefu |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | AIMS_1.44.0.tar.gz |
| Windows Binary (x86_64) | AIMS_1.44.0.zip |
| macOS Binary (big-sur-x86_64) | AIMS_1.44.0.tgz |
| macOS Binary (sonoma-arm64) | AIMS_1.44.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/AIMS |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/AIMS |
| Bioc Package Browser | https://code.bioconductor.org/browse/AIMS/ |
| Package Short Url | https://bioconductor.org/packages/AIMS/ |
| Package Downloads Report | Download Stats |