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BayesSpace

Bayesian model for clustering and enhancing the resolution of spatial gene expression experiments.

https://github.com/edward130603/bayesspace

Science Score: 36.0%

This score indicates how likely this project is to be science-related based on various indicators:

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    CITATION.cff file
  • ✓
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    DOI references
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    Academic publication links
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    Committers with academic emails
    1 of 10 committers (10.0%) from academic institutions
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  • ○
    Scientific vocabulary similarity
    Low similarity (16.7%) to scientific vocabulary

Keywords from Contributors

bioconductor-packages gene shiny ontology
Last synced: 10 months ago · JSON representation

Repository

Bayesian model for clustering and enhancing the resolution of spatial gene expression experiments.

Basic Info
Statistics
  • Stars: 150
  • Watchers: 3
  • Forks: 26
  • Open Issues: 52
  • Releases: 1
Created about 6 years ago · Last pushed 12 months ago
Metadata Files
Readme Changelog License

README.md

BayesSpace

<!-- badges: start --> Bioconductor build status <!-- badges: end -->

Overview

BayesSpace provides tools for clustering and enhancing the resolution of spatial gene expression experiments.

BayesSpace clusters a low-dimensional representation of the gene expression matrix, incorporating a spatial prior to encourage neighboring spots to cluster together. The method can enhance the resolution of the low-dimensional representation into "sub-spots", for which features such as gene expression or cell type composition can be imputed.

System requirements

Operating system

BayesSpace has been built and tested on the following operating systems:

  • Linux: Ubuntu 18.04.4 LTS (Bionic Beaver)
  • macOS: 10.14.6 (Mojave), 10.15.6 (Catalina)
  • Windows: 10, Server 2012 R2 Standard

Software dependencies

BayesSpace requires R 4.0+ and Bioconductor 3.12+. Specific package dependencies are defined in the package DESCRIPTION and are managed by the Bioconductor and devtools installers.

Installation

BayesSpace is available through Bioconductor.

```

Install the Bioconductor package manager, if necessary

if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")

BiocManager::install("BayesSpace") ```

The development version can be installed via Bioconductor (see instructions on using the devel branch) or from github with devtools.

```

Install devtools, if necessary

if (!requireNamespace("devtools", quietly = TRUE)) install.packages("devtools")

devtools::install_github("edward130603/BayesSpace") ```

Installation, including compilation, should take no more than one minute.

Installing from source on macOS

Installing from source on macOS (such as when installing via devtools::install_github()) requires Fortran to compile the Rcpp code.

Download links for the appropriate macOS versions can be found here: * Mojave (10.14) and Catalina (10.15) - gfortran8.2 * Sierra (10.12) and High Sierra (10.13) - gfortran6.3

Additional details on installing the R compiler tools for Rcpp on macOS can be found in this blog post.

Note about homebrew: While gfortran is available via homebrew, we've encountered issues linking to its libraries after installation. We recommend installing directly from the GNU Fortran repo.

Demonstration

For an example of typical BayesSpace usage, please see our package vignette for a demonstration and overview of the functions included in BayesSpace.

Running the entire vignette takes approximately 5m30s on a Macbook Pro with a 2.0 GHz quad-core processor and 16 GB of RAM.

Owner

  • Name: Edward Zhao
  • Login: edward130603
  • Kind: user

GitHub Events

Total
  • Issues event: 14
  • Watch event: 40
  • Delete event: 1
  • Issue comment event: 27
  • Member event: 1
  • Push event: 21
  • Pull request event: 7
  • Fork event: 4
  • Create event: 4
Last Year
  • Issues event: 14
  • Watch event: 40
  • Delete event: 1
  • Issue comment event: 27
  • Member event: 1
  • Push event: 21
  • Pull request event: 7
  • Fork event: 4
  • Create event: 4

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 244
  • Total Committers: 10
  • Avg Commits per committer: 24.4
  • Development Distribution Score (DDS): 0.676
Past Year
  • Commits: 14
  • Committers: 3
  • Avg Commits per committer: 4.667
  • Development Distribution Score (DDS): 0.357
Top Committers
Name Email Commits
Matt Stone m****2@g****m 79
Edward Zhao z****e@u****u 78
Matt Stone m****e@f****g 60
Senbai Kang s****g@g****m 9
Nitesh Turaga n****a@g****m 6
edward130603 e****3@g****m 5
Your Name y****u@e****m 4
lshep l****d@r****g 1
Zhao e****o@f****g 1
Kang Senbai s****4@h****v 1
Committer Domains (Top 20 + Academic)
fredhutch.org: 2 hos73185.wifi.intranet.chuv: 1 roswellpark.org: 1 uw.edu: 1

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 116
  • Total pull requests: 11
  • Average time to close issues: about 1 month
  • Average time to close pull requests: 3 months
  • Total issue authors: 95
  • Total pull request authors: 4
  • Average comments per issue: 2.55
  • Average comments per pull request: 0.64
  • Merged pull requests: 7
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 13
  • Pull requests: 6
  • Average time to close issues: about 1 month
  • Average time to close pull requests: 3 minutes
  • Issue authors: 12
  • Pull request authors: 3
  • Average comments per issue: 0.77
  • Average comments per pull request: 0.0
  • Merged pull requests: 4
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • BinDuan (4)
  • meaksu (3)
  • CromitDolores0808 (3)
  • zqsha (3)
  • lcolladotor (3)
  • rue1996 (2)
  • PIR015 (2)
  • lmweber (2)
  • jessielam415 (2)
  • jleechung (2)
  • astrid12345 (2)
  • ivykos (2)
  • edward130603 (2)
  • alberto-valdeolivas (2)
  • briglo (2)
Pull Request Authors
  • senbaikang (6)
  • edward130603 (3)
  • msto (2)
  • xander-p (2)
Top Labels
Issue Labels
documentation (1)
Pull Request Labels

Packages

  • Total packages: 3
  • Total downloads:
    • bioconductor 23,181 total
  • Total dependent packages: 1
    (may contain duplicates)
  • Total dependent repositories: 0
    (may contain duplicates)
  • Total versions: 10
  • Total maintainers: 1
proxy.golang.org: github.com/edward130603/bayesspace
  • Versions: 1
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent packages count: 5.4%
Average: 5.6%
Dependent repos count: 5.8%
Last synced: 10 months ago
proxy.golang.org: github.com/edward130603/BayesSpace
  • Versions: 1
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent packages count: 5.4%
Average: 5.6%
Dependent repos count: 5.8%
Last synced: 10 months ago
bioconductor.org: BayesSpace

Clustering and Resolution Enhancement of Spatial Transcriptomes

  • Versions: 8
  • Dependent Packages: 1
  • Dependent Repositories: 0
  • Downloads: 23,181 Total
Rankings
Dependent repos count: 0.0%
Dependent packages count: 0.0%
Average: 20.5%
Downloads: 61.6%
Maintainers (1)
senbai.kang@chuv.ch
Last synced: 10 months ago

Dependencies

DESCRIPTION cran
  • R >= 4.0.0 depends
  • SingleCellExperiment * depends
  • BiocFileCache * imports
  • BiocSingular * imports
  • DirichletReg * imports
  • Matrix * imports
  • RCurl * imports
  • Rcpp >= 1.0.4.6 imports
  • S4Vectors * imports
  • SummarizedExperiment * imports
  • assertthat * imports
  • coda * imports
  • ggplot2 * imports
  • mclust * imports
  • purrr * imports
  • rhdf5 * imports
  • scales * imports
  • scater * imports
  • scran * imports
  • stats * imports
  • utils * imports
  • xgboost * imports
  • RColorBrewer * suggests
  • Seurat * suggests
  • dplyr * suggests
  • igraph * suggests
  • knitr * suggests
  • patchwork * suggests
  • rmarkdown * suggests
  • spatialLIBD * suggests
  • testthat * suggests
  • viridis * suggests