OSTA
This is the released version of OSTA; for the devel version, see OSTA.
Orchestrating Spatial Transcriptomics Analysis with Bioconductor
Bioconductor version: Release (3.23)
This package contains source files for the "Orchestrating Spatial Transcriptomics Analysis with Bioconductor" online book. This book provides interactive examples and discussion on key principles of computational analysis workflows for spatial transcriptomics data using Bioconductor in R. The book contains chapters describing individual analysis steps as well as extended workflows, each with examples including R code and datasets.
Author: Helena L. Crowell [aut] 
, Mark D. Robinson [aut] , Stephanie C. Hicks [aut] , Lukas M. Weber [aut, cre]
Maintainer: Lukas M. Weber <weberlm3 at gmail.com>
citation("OSTA")):Helena L. Crowell, Mark D. Robinson, Stephanie C. Hicks, Lukas M. Weber. OSTA: Orchestrating Spatial Transcriptomics Analysis with Bioconductor. doi:10.18129/B9.bioc.OSTA, R package version 1.2.2, https://bioconductor.org/packages/OSTA.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("OSTA")For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
| No vignettes available | |
| Reference Manual | |
| NEWS | Text |
Details
| biocViews | GeneExpression, SingleCell, Software, Spatial, Transcriptomics |
| Version | 1.2.2 |
| In Bioconductor since | BioC 3.23 (R-4.6) (< 6 months) |
| License | CC BY 4.0 |
| Depends | R (>= 4.5) |
| Imports | anndataR, AUCell, Banksy, basilisk, BayesSpace, BiocFileCache, BiocParallel, CARDspa, DESpace, doMC, dplyr, DropletUtils, EBImage, ExperimentHub, GenomeInfoDb, ggfortify, ggplot2, ggrepel, ggspavis, harmony, hoodscanR, igraph, imcdatasets, imcRtools, jsonlite, lme4, lmerTest, msigdbr, muSpaData, nnSVG, openxlsx, osfr, OSTA.data, pals, patchwork, pheatmap, RANN, RColorBrewer, reticulate, rtracklayer, scales, scater, scider, scrapper, scran, scuttle, scRNAseq, sf, SFEData, SingleR, sosta, SpaceTrooper, spacexr, SpatialExperiment, SpatialExperimentIO, spatialFDA, SpatialFeatureExperiment, spatialLIBD, spatstat, spdep, spicyR, SpotSweeper, STexampleData, tidyr, VisiumIO, Voyager, zoo |
| System Requirements | quarto |
| URL | https://github.com/lmweber/OSTA |
| Bug Reports | https://github.com/lmweber/OSTA/issues |
See More
| Suggests | BiocManager, BiocPkgTools, BiocStyle, BiocVersion, CCPlotR, downlit, glue, knitr, markdown, quarto, scrapper, sessioninfo, Statial, xml2 |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (sonoma-arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/OSTA |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/OSTA |
| Package Short Url | https://bioconductor.org/packages/OSTA/ |
| Package Downloads Report | Download Stats |