pagoda2
R package for analyzing and interactively exploring large-scale single-cell RNA-seq datasets
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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✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
○DOI references
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○Academic publication links
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✓Committers with academic emails
3 of 16 committers (18.8%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (14.3%) to scientific vocabulary
Keywords
Repository
R package for analyzing and interactively exploring large-scale single-cell RNA-seq datasets
Basic Info
Statistics
- Stars: 234
- Watchers: 15
- Forks: 47
- Open Issues: 1
- Releases: 17
Topics
Metadata Files
README.md
pagoda2
pagoda2: Rapid Processing and Interactive Analysis of Large Datasets
Pagoda2 is an R package for analyzing and interactively exploring large-scale single-cell RNA-seq datasets. The methods were optimized to rapidly process modern scRNAseq datasets, which are both large (approximately 1e6 cells or greater) and sparse. The package provides methods for quality control, filtering, clustering, visualization, differential expression, cross-cutting aspects/states, and geneset/pathway overdispersion analysis. The companion frontend application allows users to figure out which gene expression patterns give rise to different subpopulations within the data. The application allows users to inspect the gene expression patterns of subpopulations through annotated gene sets and pathways, including Gene Ontology (GO) categories. Users may also highlight certain clusters and perform differential expression from their browsers via the frontend application.
Note that pagoda2 is an R package developed for analyzing standalone scRNAseq datasets. For joint analysis of multiple datasets, please see the package conos. (The package pagoda2 is primarily used to preprocess input datasets for conos.)
Several methods within this package were developed based on the originals implemented within SCDE and PAGODA1.
Tutorials
Basic Walkthrough * HTML version * Markdown version
Web Demo of Application
Installation
To install the stable version from CRAN, use:
r
install.packages('pagoda2')
To install the latest version of pagoda2, use:
r
install.packages('devtools')
devtools::install_github('kharchenkolab/pagoda2')
Installing Linux dependencies
Installation for Debian-based distributions (e.g. Ubuntu):
sh
sudo apt-get update
sudo apt-get -y install libcurl4-openssl-dev libssl-dev
Installation for Red-Hat-based distributions (e.g. CentOS or Fedora)
sh
yum install openssl-devel libcurl-devel
Installing with Mac OS
We recommend the Homebrew package manager to install require dependencies on Mac OS. Please run the following commands in the terminal:
sh
brew update
brew install curl openssl wget
As of version 0.1.3, pagoda2 should sucessfully install on Mac OS. Furthermore, we encourage Mac OS users to install the package via the binaries on CRAN. However, if there are issues, please refer to the following wiki page for further instructions on installing pagoda2 with Mac OS: Installing pagoda2 for Mac OS
Pagoda2 via Docker
If you are having trouble setting up pagoda2 on your system, an alternative approach to work with pagoda2 is via a Docker container. To use the Docker container, first install docker on your platform and then run the pagoda2 image with the following command in the shell:
docker run -p 8787:8787 -e PASSWORD=pass pkharchenkolab/pagoda2:latest
The first time you run this command, it will pull/download several images---please make sure that you have reliable internet access. You can then point your browser to http://localhost:8787/ to access an Rstudio environment with pagoda2 installed (please log in using credentials username=rstudio, password=pass). Explore the Docker --mount option to allow the Docker image to access your local files.
Citation
If you find pagoda2 useful for your publication, please cite:
Nikolas Barkas, Viktor Petukhov, Peter Kharchenko, Simon Steiger,
Rasmus Rydbirk, and Evan Biederstedt (2021). pagoda2: Single Cell
Analysis and Differential Expression. R package version 1.0.13.
Owner
- Name: Kharchenko Lab
- Login: kharchenkolab
- Kind: organization
- Website: http://pklab.org
- Twitter: KharchenkoLab
- Repositories: 21
- Profile: https://github.com/kharchenkolab
GitHub Events
Total
- Create event: 1
- Release event: 1
- Issues event: 1
- Watch event: 23
- Issue comment event: 1
- Push event: 5
Last Year
- Create event: 1
- Release event: 1
- Issues event: 1
- Watch event: 23
- Issue comment event: 1
- Push event: 5
Committers
Last synced: over 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| barkasn | N****s@o****m | 580 |
| evanbiederstedt | e****t@g****m | 287 |
| Redspecialist | b****e@l****m | 105 |
| Peter Kharchenko | p****o@g****m | 80 |
| evanbiederstedt | e****t | 54 |
| Nikolas Barkas | n****s@o****m | 49 |
| viktor_petukhov | v****v@y****u | 41 |
| Nikolas Barkas | N****s@h****u | 38 |
| Simontuk | s****r@g****m | 34 |
| Nikolaos Barkas | b****n@g****m | 22 |
| Nikolaos Barkas | b****n@o****m | 4 |
| Nikolas Barkas | b****n@N****l | 3 |
| Jean Fan | j****n@f****u | 2 |
| rrydbirk | r****k@b****k | 2 |
| Kamil Slowikowski | k****i@g****m | 1 |
| Nikolas Barkas | b****n@n****u | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 78
- Total pull requests: 29
- Average time to close issues: about 1 year
- Average time to close pull requests: 24 days
- Total issue authors: 59
- Total pull request authors: 5
- Average comments per issue: 3.26
- Average comments per pull request: 1.03
- Merged pull requests: 24
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 4
- Pull requests: 0
- Average time to close issues: 12 days
- Average time to close pull requests: N/A
- Issue authors: 3
- Pull request authors: 0
- Average comments per issue: 1.75
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- barkasn (10)
- VPetukhov (4)
- JEFworks (3)
- haircell (2)
- rrydbirk (2)
- katkatrach (2)
- airfan0 (2)
- markdunning (2)
- wJDKnight (1)
- mzhibo (1)
- chrisley90 (1)
- PavelnZ (1)
- xiongyichun (1)
- KabitaBaral1 (1)
- wresch (1)
Pull Request Authors
- evanbiederstedt (23)
- rrydbirk (2)
- barkasn (2)
- VPetukhov (1)
- Simontuk (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 2
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Total downloads:
- cran 661 last-month
- Total docker downloads: 618
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Total dependent packages: 3
(may contain duplicates) -
Total dependent repositories: 12
(may contain duplicates) - Total versions: 15
- Total maintainers: 1
cran.r-project.org: pagoda2
Single Cell Analysis and Differential Expression
- Homepage: https://github.com/kharchenkolab/pagoda2
- Documentation: http://cran.r-project.org/web/packages/pagoda2/pagoda2.pdf
- License: GPL-3
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Latest release: 1.0.13
published 6 months ago
Rankings
Maintainers (1)
conda-forge.org: r-pagoda2
- Homepage: https://github.com/kharchenkolab/pagoda2
- License: GPL-3.0-only
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Latest release: 1.0.10
published almost 4 years ago
Rankings
Dependencies
- Matrix * depends
- R >= 3.5.0 depends
- igraph * depends
- MASS * imports
- N2R * imports
- R.utils * imports
- R6 * imports
- RMTstat * imports
- Rcpp * imports
- Rook * imports
- Rtsne * imports
- dendsort * imports
- drat * imports
- fastcluster * imports
- grDevices * imports
- graphics * imports
- irlba * imports
- magrittr * imports
- methods * imports
- mgcv * imports
- parallel * imports
- plyr * imports
- rjson * imports
- rlang * imports
- sccore >= 0.1.1 imports
- stats * imports
- urltools * imports
- utils * imports
- AnnotationDbi * suggests
- BiocGenerics * suggests
- BiocParallel * suggests
- GO.db * suggests
- KernSmooth * suggests
- base64enc * suggests
- colorRamps * suggests
- data.table * suggests
- dbscan * suggests
- dplyr * suggests
- ggplot2 * suggests
- gridExtra * suggests
- knitr * suggests
- org.Dr.eg.db * suggests
- org.Hs.eg.db * suggests
- org.Mm.eg.db * suggests
- pcaMethods * suggests
- pheatmap * suggests
- rgl * suggests
- rmarkdown * suggests
- robustbase * suggests
- scde * suggests
- testthat * suggests
- uwot * suggests
- rocker/tidyverse 4.0.1 build