jazzPanda
This is the development version of jazzPanda; for the stable release version, see jazzPanda.
Finding spatially relevant marker genes in image based spatial transcriptomics data
Bioconductor version: Development (3.24)
This package contains the function to find marker genes for image-based spatial transcriptomics data. There are functions to create spatial vectors from the cell and transcript coordiantes, which are passed as inputs to find marker genes. Marker genes are detected for every cluster by two approaches. The first approach is by permtuation testing, which is implmented in parallel for finding marker genes for one sample study. The other approach is to build a linear model for every gene. This approach can account for multiple samples and backgound noise.
Maintainer: Melody Jin <jin.m at wehi.edu.au>
citation("jazzPanda")):
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")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("jazzPanda")
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("jazzPanda")| jazzPanda example | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | DifferentialExpression, GeneExpression, Software, Spatial, StatisticalMethod, Transcriptomics |
| Version | 1.5.0 |
| In Bioconductor since | BioC 3.21 (R-4.5) (1.5 years) |
| License | GPL-3 |
| Depends | R (>= 4.5.0) |
| Imports | spatstat.geom, dplyr, glmnet, caret, foreach, stats, magrittr, doParallel, BiocParallel, methods, BumpyMatrix, SpatialExperiment |
| System Requirements | |
| URL | https://github.com/phipsonlab/jazzPanda https://bhuvad.github.io/jazzPanda/ |
| Bug Reports | https://github.com/phipsonlab/jazzPanda/issues |
See More
| Suggests | BiocStyle, knitr, rmarkdown, spatstat, Seurat, statmod, corrplot, ggplot2, ggraph, ggrepel, gridExtra, reshape2, igraph, jsonlite, vdiffr, patchwork, ggpubr, tidyr, SpatialFeatureExperiment, ExperimentHub, TENxXeniumData, SingleCellExperiment, SFEData, Matrix, data.table, scran, scater, grid, GenomeInfoDb, testthat (>= 3.0.0) |
| 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 | jazzPanda_1.5.0.tar.gz |
| Windows Binary (x86_64) | jazzPanda_1.5.0.zip |
| macOS Binary (big-sur-x86_64) | jazzPanda_1.5.0.tgz |
| macOS Binary (sonoma-arm64) | jazzPanda_1.5.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/jazzPanda |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/jazzPanda |
| Bioc Package Browser | https://code.bioconductor.org/browse/jazzPanda/ |
| Package Short Url | https://bioconductor.org/packages/jazzPanda/ |
| Package Downloads Report | Download Stats |