blase
This is thereleased version of blase; for the devel version, seeblase.
Bulk Linking Analysis for Single-cell Experiments
Bioconductor version: Release (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]
ORCID: 0009-0004-4187-799X, Toby Kettlewell [aut] ORCID: 0009-0001-1225-3318, Adrian M. Smith [aut] ORCID: 0000-0001-8833-2330, Rhiannon Kundu [aut] ORCID: 0000-0003-3970-5860, David A. Gunn [aut] ORCID: 0000-0001-9866-3221, Thomas D. Otto [aut, ths] ORCID: 0000-0002-1246-7404
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")BiocManager::install("blase")For older versions of R, please refer to the appropriateBioconductor 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 | 1.0.0 |
| In Bioconductor since | BioC 3.22 (R-4.5) (< 6 months) |
| 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
FollowInstallation instructions to use this package in your R session.
| Source Package | blase_1.0.0.tar.gz |
| Windows Binary (x86_64) | blase_1.0.0.zip |
| macOS Binary (x86_64) | blase_1.0.0.tgz |
| macOS Binary (arm64) | blase_1.0.0.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 |