DAssemble
This is the development version of DAssemble; to use it, please install the devel version of Bioconductor.
Ensemble Models for Differential Analysis
Bioconductor version: Development (3.24)
The DAssemble package implements an ensemble framework for differential-abundance and differential-expression analysis across bulk RNA-seq, single-cell RNA-seq, and microbiome studies. It wraps a collection of popular DA/DE methods as core methods and combines them via Cauchy Combination Tests (CCT), optionally augmented by simple enhancers such as Wilcoxon, Kolmogorov–Smirnov, and presence–absence logistic regression.
Author: Himel Mallick [aut], Ziyu Liu [aut], Nalin Arora [aut, cre]
Maintainer: Nalin Arora <naa4050 at med.cornell.edu>
citation("DAssemble")):
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")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("DAssemble")
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("DAssemble")| DAssemble: Ensemble Differential Analysis | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | DifferentialExpression, Microbiome, Normalization, RNASeq, Regression, SingleCell, Software, StatisticalMethod |
| Version | 0.99.3 |
| In Bioconductor since | BioC 3.24 (R-4.6) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.6.0) |
| Imports | stats, utils, dplyr, MultiAssayExperiment, SummarizedExperiment |
| System Requirements | |
| URL | https://github.com/himelmallick/DAssemble |
| Bug Reports | https://github.com/himelmallick/DAssemble/issues |
See More
| Suggests | DESeq2, edgeR, limma, dearseq, metagenomeSeq, MAST, cplm, dfadjust, glmmTMB, logging, MASS, pbapply, preprocessCore, Maaslin2, maaslin3, LOCOM2, MicrobiomeStat, ANCOMBC, ALDEx2, parallel, airway, scran, SingleCellExperiment, knitr, rmarkdown, BiocStyle, phyloseq, Seurat, S4Vectors, testthat (>= 3.0.0), TreeSummarizedExperiment, KernSmooth, foreign, nnet, rpart, spatial, boot, class |
| Linking To | |
| Enhances | |
| Depends On Me | |
| 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 | DAssemble_0.99.3.tar.gz |
| Windows Binary (x86_64) | DAssemble_0.99.3.zip |
| macOS Binary (big-sur-x86_64) | DAssemble_0.99.3.tgz |
| macOS Binary (sonoma-arm64) | DAssemble_0.99.3.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/DAssemble |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/DAssemble |
| Bioc Package Browser | https://code.bioconductor.org/browse/DAssemble/ |
| Package Short Url | https://bioconductor.org/packages/DAssemble/ |
| Package Downloads Report | Download Stats |