Other packages > Find by keyword >

singleCellHaystack  

A Universal Differential Expression Prediction Tool for Single-Cell and Spatial Genomics Data
View on CRAN: Click here


Download and install singleCellHaystack package within the R console
Install from CRAN:
install.packages("singleCellHaystack")

Install from Github:
library("remotes")
install_github("cran/singleCellHaystack")

Install by package version:
library("remotes")
install_version("singleCellHaystack", "1.0.3")



Attach the package and use:
library("singleCellHaystack")
Maintained by
Alexis Vandenbon
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2020-07-01
Latest Update: 2024-01-11
Description:
One key exploratory analysis step in single-cell genomics data analysis is the prediction of features with different activity levels. For example, we want to predict differentially expressed genes (DEGs) in single-cell RNA-seq data, spatial DEGs in spatial transcriptomics data, or differentially accessible regions (DARs) in single-cell ATAC-seq data. 'singleCellHaystack' predicts differentially active features in single cell omics datasets without relying on the clustering of cells into arbitrary clusters. 'singleCellHaystack' uses Kullback-Leibler divergence to find features (e.g., genes, genomic regions, etc) that are active in subsets of cells that are non-randomly positioned inside an input space (such as 1D trajectories, 2D tissue sections, multi-dimensional embeddings, etc). For the theoretical background of 'singleCellHaystack' we refer to our original paper Vandenbon and Diez (Nature Communications, 2020) <doi:10.1038/s41467-020-17900-3> and our update Vandenbon and Diez (Scientific Reports, 2023) <doi:10.1038/s41598-023-38965-2>.
How to cite:
Alexis Vandenbon (2020). singleCellHaystack: A Universal Differential Expression Prediction Tool for Single-Cell and Spatial Genomics Data. R package version 1.0.3, https://cran.r-project.org/web/packages/singleCellHaystack. Accessed 06 Jun. 2026.
Previous versions and publish date:
0.3.2 (2020-07-01 13:10), 0.3.3 (2020-09-18 16:40), 0.3.4 (2021-03-28 03:50), 1.0.0 (2022-12-20 11:00), 1.0.2 (2024-01-11 11:00)
Other packages that cited singleCellHaystack R package
View singleCellHaystack citation profile
Other R packages that singleCellHaystack depends, imports, suggests or enhances
Complete documentation for singleCellHaystack
Downloads during the last 30 days

Today's Hot Picks in Authors and Packages

odbc  
Connect to ODBC Compatible Databases (using the DBI Interface)
A DBI-compatible interface to ODBC databases. ...
Download / Learn more Package Citations See dependency  
BALLI  
Expression RNA-Seq Data Analysis Based on Linear Mixed Model
Analysis of gene expression RNA-seq data using Bartlett-Adjusted Likelihood-based LInear model (BALL ...
Download / Learn more Package Citations See dependency  
worrrd  
Generate Wordsearch and Crossword Puzzles
Generate wordsearch and crossword puzzles using custom lists of words (and clues).Make them easy or ...
Download / Learn more Package Citations See dependency  
rwavelet  
Wavelet Analysis
Perform wavelet analysis (orthogonal,translation invariant, tensorial, 1-2-3d transforms, thresholdi ...
Download / Learn more Package Citations See dependency  
r2resize  
In-Text Resize for Images, Tables and Fancy Resize Containers in 'shiny', 'rmarkdown' and 'quarto' Documents
Automatic resizing toolbar for containers, images and tables. Various resizable or expandable contai ...
Download / Learn more Package Citations See dependency  
IAPWS95  
Thermophysical Properties of Water and Steam
An implementation of the International Association for the Properties of Water (IAPWS) Formulation ...
Download / Learn more Package Citations See dependency  

27,268

R Packages

233,548

Dependencies

72,820

Author Associations

27,205

Publication Badges

© Copyright since 2022. All right reserved, rpkg.net.  Based in Cambridge, Massachusetts, USA