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")):
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
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 |