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SuperSpot

Description

SuperSpot is an R package bringing metacells's concept (Baran et al., 2019, Ben-Kiki et al. 2022, Bilous et al., 2022 and Persad et al., 2022) and extending SuperCell to spatial transcriptomic data.

SuperSpot combines adjacent and transcriptionally similar spots into "metaspots". The process involves representing spots as nodes in a graph with edges connecting spots in spatial proximity and edge weights representing transcriptional similarity. Hierarchical clustering is used to aggregate spots into metaspots at a user-defined resolution.

Installation

Before installing SuperSpot, packages bluster and SuperCell are required. You can install them with the following commands:

if (!require("BiocManager", quietly=TRUE))
install.packages("BiocManager")
BiocManager::install("bluster")
if (!requireNamespace("remotes")) install.packages("remotes")
remotes::install_github("GfellerLab/SuperCell")

SuperSpot can be installed with the command:

if (!requireNamespace("remotes")) install.packages("remotes")
remotes::install_github("GfellerLab/SuperSpot")

Example

An example vignette is available (see example). The code used to produce the figures of the application note can be found here.

About

No description, website, or topics provided.

Resources

Readme
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3 stars

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1 watching

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GitHub - GfellerLab/SuperSpot · GitHub
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SuperSpot
Description
SuperSpot is an R package bringing metacells's concept (Baran et al., 2019, Ben-Kiki et al. 2022, Bilous et al., 2022 and Persad et al., 2022) and extending SuperCell to spatial transcriptomic data.
SuperSpot combines adjacent and transcriptionally similar spots into "metaspots". The process involves representing spots as nodes in a graph with edges connecting spots in spatial proximity and edge weights representing transcriptional similarity. Hierarchical clustering is used to aggregate spots into metaspots at a user-defined resolution.
Installation
Before installing SuperSpot, packages bluster and SuperCell are required. You can install them with the following commands:
if (!require("BiocManager", quietly=TRUE))
install.packages("BiocManager")
BiocManager::install("bluster")
if (!requireNamespace("remotes")) install.packages("remotes")
remotes::install_github("GfellerLab/SuperCell")
SuperSpot can be installed with the command:
if (!requireNamespace("remotes")) install.packages("remotes")
remotes::install_github("GfellerLab/SuperSpot")
Example
An example vignette is available (see example).
The code used to produce the figures of the application note can be found here.
About
No description, website, or topics provided.
Resources
Readme
Activity
Custom properties
Stars
3 stars
Watchers
1 watching
Forks
0 forks
Report repository
Releases
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Used by
Contributors
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, 'i');
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(function(){
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GitHub - GfellerLab/SuperSpot · GitHub
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SuperSpot
Description
SuperSpot is an R package bringing metacells's concept (Baran et al., 2019, Ben-Kiki et al. 2022, Bilous et al., 2022 and Persad et al., 2022) and extending SuperCell to spatial transcriptomic data.
SuperSpot combines adjacent and transcriptionally similar spots into "metaspots". The process involves representing spots as nodes in a graph with edges connecting spots in spatial proximity and edge weights representing transcriptional similarity. Hierarchical clustering is used to aggregate spots into metaspots at a user-defined resolution.
Installation
Before installing SuperSpot, packages bluster and SuperCell are required. You can install them with the following commands:
if (!require("BiocManager", quietly=TRUE))
install.packages("BiocManager")
BiocManager::install("bluster")
if (!requireNamespace("remotes")) install.packages("remotes")
remotes::install_github("GfellerLab/SuperCell")
SuperSpot can be installed with the command:
if (!requireNamespace("remotes")) install.packages("remotes")
remotes::install_github("GfellerLab/SuperSpot")
Example
An example vignette is available (see example).
The code used to produce the figures of the application note can be found here.
About
No description, website, or topics provided.
Resources
Readme
Activity
Custom properties
Stars
3 stars
Watchers
1 watching
Forks
0 forks
Report repository
Releases
Packages
Used by
Contributors
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(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '
GitHub - GfellerLab/SuperSpot · GitHub
Skip to content
BranchesTags
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SuperSpot
Description
SuperSpot is an R package bringing metacells's concept (Baran et al., 2019, Ben-Kiki et al. 2022, Bilous et al., 2022 and Persad et al., 2022) and extending SuperCell to spatial transcriptomic data.
SuperSpot combines adjacent and transcriptionally similar spots into "metaspots". The process involves representing spots as nodes in a graph with edges connecting spots in spatial proximity and edge weights representing transcriptional similarity. Hierarchical clustering is used to aggregate spots into metaspots at a user-defined resolution.
Installation
Before installing SuperSpot, packages bluster and SuperCell are required. You can install them with the following commands:
if (!require("BiocManager", quietly=TRUE))
install.packages("BiocManager")
BiocManager::install("bluster")
if (!requireNamespace("remotes")) install.packages("remotes")
remotes::install_github("GfellerLab/SuperCell")
SuperSpot can be installed with the command:
if (!requireNamespace("remotes")) install.packages("remotes")
remotes::install_github("GfellerLab/SuperSpot")
Example
An example vignette is available (see example).
The code used to produce the figures of the application note can be found here.
About
No description, website, or topics provided.
Resources
Readme
Activity
Custom properties
Stars
3 stars
Watchers
1 watching
Forks
0 forks
Report repository
Releases
Packages
Used by
Contributors
Languages

, 'i');
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(function(){
try {
var __m = "youtube.com";
var __re = new RegExp('^' + "youtube\\.com" + '
GitHub - GfellerLab/SuperSpot · GitHub
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SuperSpot
Description
SuperSpot is an R package bringing metacells's concept (Baran et al., 2019, Ben-Kiki et al. 2022, Bilous et al., 2022 and Persad et al., 2022) and extending SuperCell to spatial transcriptomic data.
SuperSpot combines adjacent and transcriptionally similar spots into "metaspots". The process involves representing spots as nodes in a graph with edges connecting spots in spatial proximity and edge weights representing transcriptional similarity. Hierarchical clustering is used to aggregate spots into metaspots at a user-defined resolution.
Installation
Before installing SuperSpot, packages bluster and SuperCell are required. You can install them with the following commands:
if (!require("BiocManager", quietly=TRUE))
install.packages("BiocManager")
BiocManager::install("bluster")
if (!requireNamespace("remotes")) install.packages("remotes")
remotes::install_github("GfellerLab/SuperCell")
SuperSpot can be installed with the command:
if (!requireNamespace("remotes")) install.packages("remotes")
remotes::install_github("GfellerLab/SuperSpot")
Example
An example vignette is available (see example).
The code used to produce the figures of the application note can be found here.
About
No description, website, or topics provided.
Resources
Readme
Activity
Custom properties
Stars
3 stars
Watchers
1 watching
Forks
0 forks
Report repository
Releases
Packages
Used by
Contributors
Languages

, 'i');
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(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '
GitHub - GfellerLab/SuperSpot · GitHub
Skip to content
BranchesTags
Repository files navigation
SuperSpot
Description
SuperSpot is an R package bringing metacells's concept (Baran et al., 2019, Ben-Kiki et al. 2022, Bilous et al., 2022 and Persad et al., 2022) and extending SuperCell to spatial transcriptomic data.
SuperSpot combines adjacent and transcriptionally similar spots into "metaspots". The process involves representing spots as nodes in a graph with edges connecting spots in spatial proximity and edge weights representing transcriptional similarity. Hierarchical clustering is used to aggregate spots into metaspots at a user-defined resolution.
Installation
Before installing SuperSpot, packages bluster and SuperCell are required. You can install them with the following commands:
if (!require("BiocManager", quietly=TRUE))
install.packages("BiocManager")
BiocManager::install("bluster")
if (!requireNamespace("remotes")) install.packages("remotes")
remotes::install_github("GfellerLab/SuperCell")
SuperSpot can be installed with the command:
if (!requireNamespace("remotes")) install.packages("remotes")
remotes::install_github("GfellerLab/SuperSpot")
Example
An example vignette is available (see example).
The code used to produce the figures of the application note can be found here.
About
No description, website, or topics provided.
Resources
Readme
Activity
Custom properties
Stars
3 stars
Watchers
1 watching
Forks
0 forks
Report repository
Releases
Packages
Used by
Contributors
Languages

, 'i');
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GitHub - GfellerLab/SuperSpot · GitHub
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SuperSpot
Description
SuperSpot is an R package bringing metacells's concept (Baran et al., 2019, Ben-Kiki et al. 2022, Bilous et al., 2022 and Persad et al., 2022) and extending SuperCell to spatial transcriptomic data.
SuperSpot combines adjacent and transcriptionally similar spots into "metaspots". The process involves representing spots as nodes in a graph with edges connecting spots in spatial proximity and edge weights representing transcriptional similarity. Hierarchical clustering is used to aggregate spots into metaspots at a user-defined resolution.
Installation
Before installing SuperSpot, packages bluster and SuperCell are required. You can install them with the following commands:
if (!require("BiocManager", quietly=TRUE))
install.packages("BiocManager")
BiocManager::install("bluster")
if (!requireNamespace("remotes")) install.packages("remotes")
remotes::install_github("GfellerLab/SuperCell")
SuperSpot can be installed with the command:
if (!requireNamespace("remotes")) install.packages("remotes")
remotes::install_github("GfellerLab/SuperSpot")
Example
An example vignette is available (see example).
The code used to produce the figures of the application note can be found here.
About
No description, website, or topics provided.
Resources
Readme
Activity
Custom properties
Stars
3 stars
Watchers
1 watching
Forks
0 forks
Report repository
Releases
Packages
Used by
Contributors
Languages