blase
This is the released version of blase; for the devel version, see blase.
Bulk Linking Analysis for Single-cell Experiments
Bioconductor version: Release (3.23)
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")):
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("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 | ||
| NEWS | Text |
Details
| biocViews | CellBasedAssays, CellBiology, GeneExpression, RNASeq, Sequencing, SingleCell, Software, TimeCourse, Transcription, Transcriptomics |
| Version | 1.2.0 |
| In Bioconductor since | BioC 3.22 (R-4.5) (1 year) |
| 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), lsa |
| 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_1.2.0.tar.gz |
| Windows Binary (x86_64) | blase_1.2.0.zip |
| macOS Binary (big-sur-x86_64) | blase_1.2.0.tgz |
| macOS Binary (sonoma-arm64) | blase_1.2.0.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 |