looking4clusters
This is the development version of looking4clusters; to use it, please install the devel version of Bioconductor.
Interactive Visualization of scRNA-Seq
Bioconductor version: Development (3.22)
Enables the interactive visualization of dimensional reduction, clustering, and cell properties for scRNA-Seq results. It generates an interactive HTML page using either a numeric matrix, SummarizedExperiment, SingleCellExperiment or Seurat objects as input. The input data can be projected into two-dimensional representations by applying dimensionality reduction methods such as PCA, MDS, t-SNE, UMAP, and NMF. Displaying multiple dimensionality reduction results within the same interface, with interconnected graphs, provides different perspectives that facilitate accurate cell classification. The package also integrates unsupervised clustering techniques, whose results that can be viewed interactively in the graphical interface. In addition to visualization, this interface allows manual selection of groups, labeling of cell entities based on processed meta-information, generation of new graphs displaying gene expression values for each cell, sample identification, and visual comparison of samples and clusters.
Author: David Barrios [aut, cre]
, Angela Villaverde [aut]
, Carlos Prieto [aut]
Maintainer: David Barrios <metal at usal.es>
citation("looking4clusters")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("looking4clusters")
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("looking4clusters")| scRNA-Seq, Dimensional Reduction, Clustering and Visualization | HTML | R Script |
| Reference Manual |
Details
| biocViews | Classification, Clustering, DataRepresentation, GeneExpression, MultipleComparison, Software, Visualization |
| Version | 0.99.4 |
| In Bioconductor since | BioC 3.22 (R-4.5) |
| License | GPL-2 | GPL-3 |
| Depends | R (>= 4.5.0) |
| Imports | stats, utils, SummarizedExperiment, SingleCellExperiment, BiocBaseUtils, jsonlite |
| System Requirements | |
| URL | https://github.com/BioinfoUSAL/looking4clusters/ |
| Bug Reports | https://github.com/BioinfoUSAL/looking4clusters/issues/ |
See More
| Suggests | knitr, rmarkdown, Seurat, parallelDist, uwot, NMF, fpc, dendextend, cluster, Rtsne, scRNAseq, Matrix |
| 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 | looking4clusters_0.99.4.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | looking4clusters_0.99.4.tgz |
| macOS Binary (arm64) | looking4clusters_0.99.4.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/looking4clusters |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/looking4clusters |
| Bioc Package Browser | https://code.bioconductor.org/browse/looking4clusters/ |
| Package Short Url | https://bioconductor.org/packages/looking4clusters/ |
| Package Downloads Report | Download Stats |