CLAMP
This is the development version of CLAMP; to use it, please install the devel version of Bioconductor.
Curated Latent-variable Analysis with Molecular Priors
Bioconductor version: Development (3.24)
CLAMP performs prior-informed latent variable decomposition of high-dimensional transcriptomic data. It integrates curated gene sets to learn biologically interpretable latent variables, supports file-backed matrices for large datasets, and provides tools for preprocessing, normalization, projection, and evaluation of latent structures. CLAMP is designed to scale to tens of thousands of samples, making it suitable for large public resources such as recount3 and ARCHS4. It enables researchers to uncover biologically meaningful patterns that connect genes, pathways, and complex traits in transcriptomics studies.
Author: Marc Subirana-Granes [aut, cre]
, Maria Chikina [aut], National Human Genome Research Institute [fnd] (R00 HG011898 to M.P.; R01 HG009299-6A1 to M.C.), Eunice Kennedy Shriver National Institute of Child Health and Human Development [fnd] (R01 HD109765 to M.P.), National Science Foundation [fnd] (NSF 2238125 to M.C.), National Eye Institute [fnd] (NIH R01 EY030546-01A1 to M.C.)
Maintainer: Marc Subirana-Granes <mb2subi at gmail.com>
citation("CLAMP")):
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("CLAMP")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
| Reference Manual |
Details
| biocViews | DimensionReduction, GeneExpression, GenePrediction, GeneTarget, Normalization, Pathways, Preprocessing, RNASeq, Software, Transcriptomics, Visualization |
| Version | 0.99.3 |
| In Bioconductor since | BioC 3.24 (R-4.6) |
| License | GPL-3 |
| Depends | R (>= 4.6.0) |
| Imports | bigstatsr, circlize, ComplexHeatmap, dplyr, ggplot2, ggrepel, glmnet, grid, irlba, Matrix, matrixStats, methods, patchwork, Rcpp, rlang, rsvd, stats, utils |
| System Requirements | |
| URL | https://chikinalab.github.io/CLAMP/ https://github.com/chikinalab/CLAMP |
| Bug Reports | https://github.com/chikinalab/CLAMP/issues |
See More
| Suggests | AnnotationDbi, BiocStyle, CLAMPData, data.table, DiagrammeR, DT, rhdf5, here, knitr, org.Hs.eg.db, PCAtools, magick, rmarkdown, testthat (>= 3.0.0) |
| Linking To | Rcpp, RcppArmadillo |
| 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 | |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (sonoma-arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/CLAMP |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/CLAMP |
| Package Short Url | https://bioconductor.org/packages/CLAMP/ |
| Package Downloads Report | Download Stats |