GloScope
This is the released version of GloScope; for the devel version, see GloScope.
Population-level Representation on scRNA-Seq data
Bioconductor version: Release (3.23)
This package aims at representing and summarizing the entire single-cell profile of a sample. It allows researchers to perform important bioinformatic analyses at the sample-level such as visualization and quality control. The main functions Estimate sample distribution and calculate statistical divergence among samples, and visualize the distance matrix through MDS plots.
Author: Elizabeth Purdom [aut, cre], William Torous [aut]
, Hao Wang [aut]
, Boying Gong [aut]
Maintainer: Elizabeth Purdom <epurdom at stat.berkeley.edu>
citation("GloScope")):
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("GloScope")
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("GloScope")| GloScope | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DataRepresentation, QualityControl, RNASeq, Sequencing, SingleCell, Software |
| Version | 2.2.0 |
| In Bioconductor since | BioC 3.18 (R-4.3) (3 years) |
| License | Artistic-2.0 |
| Depends | R (>= 4.4.0) |
| Imports | utils, stats, MASS, mclust, ggplot2, RANN, FNN, BiocParallel, mvnfast, SingleCellExperiment, rlang, RColorBrewer, pheatmap, vegan, cluster, boot, permute |
| System Requirements | |
| URL | |
| Bug Reports | https://github.com/epurdom/GloScope/issues |
See More
| Suggests | BiocStyle, testthat (>= 3.0.0), knitr, rmarkdown, zellkonverter |
| 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 | GloScope_2.2.0.tar.gz |
| Windows Binary (x86_64) | GloScope_2.2.0.zip |
| macOS Binary (big-sur-x86_64) | GloScope_2.2.0.tgz |
| macOS Binary (sonoma-arm64) | GloScope_2.2.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/GloScope |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/GloScope |
| Bioc Package Browser | https://code.bioconductor.org/browse/GloScope/ |
| Package Short Url | https://bioconductor.org/packages/GloScope/ |
| Package Downloads Report | Download Stats |