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", "1.0.2")



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 1.0.2, https://cran.r-project.org/web/packages/singleCellHaystack
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)
Other packages that cited singleCellHaystack R package
View singleCellHaystack citation profile
Other R packages that singleCellHaystack depends, imports, suggests or enhances
Downloads during the last 30 days
Get rewarded with contribution points by helping add
Reviews / comments / questions /suggestions ↴↴↴

Today's Hot Picks in Authors and Packages

nextGenShinyApps  
Craft Exceptional 'R Shiny' Applications and Dashboards with Novel Responsive Tools
Nove responsive tools for designing and developing 'Shiny' dashboards and applications. The scripts ...
Download / Learn more Package Citations See dependency  
MatrixEQTL  
Matrix eQTL: Ultra Fast eQTL Analysis via Large Matrix Operations
Matrix eQTL is designed for fast eQTL analysis on large datasets. Matrix eQTL can test for associat ...
Download / Learn more Package Citations See dependency  
stagePop  
Modelling the Population Dynamics of a Stage-Structured Species in Continuous Time
Provides facilities to implement and run population models of stage-structured species... ...
Download / Learn more Package Citations See dependency  
gclus  
Clustering Graphics
Orders panels in scatterplot matrices and parallel coordinate displays by some merit index. Package ...
Download / Learn more Package Citations See dependency  
ismev  
An Introduction to Statistical Modeling of Extreme Values
Functions to support the computations carried out in `An Introduction to Statistical Modeling of Ex ...
Download / Learn more Package Citations See dependency  
multiocc  
Fits Multivariate Spatio-Temporal Occupancy Model
Spatio-temporal multivariate occupancy models can handle multiple species in occupancy models. This ...
Download / Learn more Package Citations See dependency  

22,114

R Packages

188,080

Dependencies

55,244

Author Associations

22,115

Publication Badges

© Copyright 2022 - present. All right reserved, rpkg.net. Contact Us / Suggestions / Concerns