Other packages > Find by keyword >

iCellR  

Analyzing High-Throughput Single Cell Sequencing Data
View on CRAN: Click here


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

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

Install by package version:
library("remotes")
install_version("iCellR", "1.6.7")



Attach the package and use:
library("iCellR")
Maintained by
Alireza Khodadadi-Jamayran
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2019-08-02
Latest Update: 2021-10-09
Description:
A toolkit that allows scientists to work with data from single cell sequencing technologies such as scRNA-seq, scVDJ-seq, scATAC-seq, CITE-Seq and Spatial Transcriptomics (ST). Single (i) Cell R package ('iCellR') provides unprecedented flexibility at every step of the analysis pipeline, including normalization, clustering, dimensionality reduction, imputation, visualization, and so on. Users can design both unsupervised and supervised models to best suit their research. In addition, the toolkit provides 2D and 3D interactive visualizations, differential expression analysis, filters based on cells, genes and clusters, data merging, normalizing for dropouts, data imputation methods, correcting for batch differences, pathway analysis, tools to find marker genes for clusters and conditions, predict cell types and pseudotime analysis. See Khodadadi-Jamayran, et al (2020) and Khodadadi-Jamayran, et al (2020) for more details.
How to cite:
Alireza Khodadadi-Jamayran (2019). iCellR: Analyzing High-Throughput Single Cell Sequencing Data. R package version 1.6.7, https://cran.r-project.org/web/packages/iCellR. Accessed 22 Dec. 2024.
Previous versions and publish date:
1.0.0 (2019-08-02 12:50), 1.1.2 (2019-09-10 21:20), 1.1.4 (2019-09-26 19:30), 1.2.0 (2019-10-15 07:20), 1.2.2 (2019-10-22 23:00), 1.2.5 (2019-11-04 23:00), 1.2.7 (2019-12-04 20:50), 1.2.9 (2020-01-17 00:10), 1.3.0 (2020-01-24 22:50), 1.3.1 (2020-02-26 13:50), 1.3.3 (2020-03-14 18:00), 1.4.0 (2020-04-03 16:10), 1.4.5 (2020-04-10 09:20), 1.5.0 (2020-05-08 10:40), 1.5.1 (2020-06-17 11:40), 1.5.4 (2020-07-03 18:30), 1.5.5 (2020-07-16 23:20), 1.5.8 (2020-10-09 06:40), 1.5.9 (2021-01-21 06:30), 1.6.0 (2021-01-30 07:00), 1.6.1 (2021-03-04 06:20), 1.6.4 (2021-04-27 19:10), 1.6.5 (2021-10-09 17:00)
Other packages that cited iCellR R package
View iCellR citation profile
Other R packages that iCellR depends, imports, suggests or enhances
Complete documentation for iCellR
Functions, R codes and Examples using the iCellR R package
Some associated functions: Rphenograph . add.10x.image . add.adt . add.vdj . adt.rna.merge . bubble.gg.plot . capture.image.10x . cc . cell.cycle . cell.filter . cell.gating . cell.type.pred . change.clust . clono.plot . clust.avg.exp . clust.cond.info . clust.ord . clust.rm . clust.stats.plot . cluster.plot . data.aggregation . data.scale . down.sample . find.dim.genes . findMarkers . find_neighbors . g2m.phase . gate.to.clust . gene.plot . gene.stats . gg.cor . heatmap.gg.plot . hto.anno . i.score . iba . iclust . load.h5 . load10x . make.bed . make.gene.model . makej . myImp . norm.adt . norm.data . opt.pcs.plot . prep.vdj . pseudotime.knetl . pseudotime . pseudotime.tree . qc.stats . run.anchor . run.cca . run.clustering . run.diff.exp . run.diffusion.map . run.impute . run.knetl . run.mnn . run.pc.tsne . run.pca . run.phenograph . run.tsne . run.umap . s.phase . spatial.plot . stats.plot . top.markers . vdj.stats . volcano.ma.plot . 
Some associated R codes: F0001.R . F0002.R . F0003.R . F0004.R . F0005.R . F0006.R . F0007.R . F0008.R . F0009.R . F0010.R . F0011.R . F0012.R . F0013.R . F0014.R . F0015.R . F0016.R . F0017.R . F0018.R . F0019.R . F0020.R . F0021.R . F0022.R . F0023.R . F0024.R . F0025.R . F0026.R . F0027.R . F0028.R . F0029.R . F0030.R . F0031.R . F0032.R . F0033.R . F0034.R . F0035.R . F0036.R . F0037.R . F0038.R . F0039.R . F0040.R . F0041.R . F0042.R . F0043.R . F0044.R . F0045.R . F0046.R . F0047.R . F0048.R . F0049.R . F0050.R . F0051.R . F0052.R . F0053.R . F0054.R . F0055.R . F0057.R . F0058.R . F0059.R . F0060.R . F0061.R . F0062.R . F0063.R . F0064.R . F0065.R . F0066.R . F0067.R . F0068.R . F0069.R . F0070.R . F0071.R . F0072.R . F0100.R . RcppExports.R .  Full iCellR package functions and examples
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

composits  
Compositional, Multivariate and Univariate Time Series Outlier Ensemble
A compositional multivariate and univariate time series outlier ensemble.It uses the four R packages ...
Download / Learn more Package Citations See dependency  
LOGANTree  
Tree-Based Models for the Analysis of Log Files from Computer-Based Assessments
Enables researchers to model log-file data from computer-based assessments using machine-learning te ...
Download / Learn more Package Citations See dependency  
Maintainer: Qi Qin (view profile)
elect  
Estimation of Life Expectancies Using Multi-State Models
Functions to compute state-specific and marginal life expectancies. The computation is based on a fi ...
Download / Learn more Package Citations See dependency  
dmlalg  
Double Machine Learning Algorithms
Implementation of double machine learning (DML) algorithms in R, based on Emmenegger and Buehlmann ...
Download / Learn more Package Citations See dependency  
Rfast2  
A Collection of Efficient and Extremely Fast R Functions II
A collection of fast statistical and utility functions for data analysis. Functions for regression, ...
Download / Learn more Package Citations See dependency  
quickcode  
Quick and Essential 'R' Tricks for Better Scripts
The NOT functions, 'R' tricks and a compilation of some simple quick plus often used 'R' codes to im ...
Download / Learn more Package Citations See dependency  

23,394

R Packages

201,798

Dependencies

63,416

Author Associations

23,395

Publication Badges

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