blase
This is the development version of blase; to use it, please install the devel version of Bioconductor.
Bulk Linking Analysis for Single-cell Experiments
Bioconductor version: Development (3.22)
BLASE is a method for finding where bulk RNA-seq data lies on a single-cell pseudotime trajectory. It uses a fast and understandable approach based on Spearman correlation, with bootstrapping to provide confidence. BLASE can be used to "date" bulk RNA-seq data, annotate cell types in scRNA-seq, and help correct for developmental phenotype differences in bulk RNA-seq experiments.
Author: Andrew McCluskey [aut, cre]
, Toby Kettlewell [aut]
, Adrian M. Smith [aut]
, Rhiannon Kundu [aut]
, David A. Gunn [aut]
, Thomas D. Otto [aut, ths]
Maintainer: Andrew McCluskey <2117532m at student.gla.ac.uk>
citation("blase")):
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("blase")
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("blase")| Assigning bulk RNA-seq to pseudotime | HTML | R Script |
| BLASE for annotating scRNA-seq | HTML | R Script |
| BLASE for excluding developmental genes from bulk RNA-seq | HTML | R Script |
| Reference Manual |
Details
| biocViews | CellBasedAssays, CellBiology, GeneExpression, RNASeq, Sequencing, SingleCell, Software, TimeCourse, Transcription, Transcriptomics |
| Version | 0.99.3 |
| In Bioconductor since | BioC 3.22 (R-4.5) |
| License | GPL (>= 3) |
| Depends | R (>= 4.5.0) |
| Imports | SummarizedExperiment, SingleCellExperiment, ggplot2, viridis, patchwork, Matrix, scater, methods, rlang, BiocParallel, boot, dplyr, mgcv, stats, MatrixGenerics, Seurat (>= 4.0.0) |
| System Requirements | |
| URL | https://andrewmccluskey-uog.github.io/blase/ |
| Bug Reports | https://andrewmccluskey-uog.github.io/blase/issues |
See More
| Suggests | knitr, rmarkdown, testthat (>= 3.2.3), covr, tradeSeq, scran, slingshot, tools, ami, reshape2, plyr, fs, sparseMatrixStats, ggVennDiagram, uwot, BiocStyle, DelayedMatrixStats, limma |
| 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 | blase_0.99.3.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | blase_0.99.3.tgz |
| macOS Binary (arm64) | blase_0.99.3.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/blase |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/blase |
| Bioc Package Browser | https://code.bioconductor.org/browse/blase/ |
| Package Short Url | https://bioconductor.org/packages/blase/ |
| Package Downloads Report | Download Stats |