# Seurat-Local - Other

**Pages:** 9

---

## Tools for Single Cell Genomics • Seurat

**URL:** http://127.0.0.1:9173/seurat/license/index.html

**Contents:**
- MIT License
- Contents

Copyright (c) 2021 Seurat authors

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the “Software”), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

Developed by Rahul Satija, Satija Lab and Collaborators.

Site built with pkgdown 2.0.7.

---

## Tools for Single Cell Genomics • Seurat

**URL:** http://127.0.0.1:9173/code_of_conduct.html

**Contents:**
- Contributor Covenant Code of Conduct
- Our Pledge
- Our Standards
- Our Responsibilities
- Scope
- Enforcement
- Attribution
- Contents

In the interest of fostering an open and welcoming environment, we as contributors and maintainers pledge to making participation in our project and our community a harassment-free experience for everyone, regardless of age, body size, disability, ethnicity, sex characteristics, gender identity and expression, level of experience, education, socio-economic status, nationality, personal appearance, race, religion, or sexual identity and orientation.

Examples of behavior that contributes to creating a positive environment include:

Examples of unacceptable behavior by participants include:

Project maintainers are responsible for clarifying the standards of acceptable behavior and are expected to take appropriate and fair corrective action in response to any instances of unacceptable behavior.

Project maintainers have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this Code of Conduct, or to ban temporarily or permanently any contributor for other behaviors that they deem inappropriate, threatening, offensive, or harmful.

This Code of Conduct applies both within project spaces and in public spaces when an individual is representing the project or its community. Examples of representing a project or community include using an official project e-mail address, posting via an official social media account, or acting as an appointed representative at an online or offline event. Representation of a project may be further defined and clarified by project maintainers.

Instances of abusive, harassing, or otherwise unacceptable behavior may be reported by contacting the project team at rsatija@nygenome.org. All complaints will be reviewed and investigated and will result in a response that is deemed necessary and appropriate to the circumstances. The project team is obligated to maintain confidentiality with regard to the reporter of an incident. Further details of specific enforcement policies may be posted separately.

Project maintainers who do not follow or enforce the Code of Conduct in good faith may face temporary or permanent repercussions as determined by other members of the project’s leadership.

This Code of Conduct is adapted from the Contributor Covenant, version 1.4, available at https://www.contributor-covenant.org/version/1/4/code-of-conduct.html

For answers to common questions about this code of conduct, see https://www.contributor-covenant.org/faq

Developed by Rahul Satija, Satija Lab and Collaborators.

Site built with pkgdown 2.0.7.

---

## Tools for Single Cell Genomics • Seurat

**URL:** http://127.0.0.1:9173/authors.html

**Contents:**
- Authors
- Citation

Andrew Butler. Contributor.

Saket Choudhary. Contributor.

Charlotte Darby. Contributor.

Jeff Farrell. Contributor.

Isabella Grabski. Contributor.

Christoph Hafemeister. Contributor.

Yuhan Hao. Contributor.

Austin Hartman. Contributor.

Paul Hoffman. Contributor.

Jaison Jain. Contributor.

Longda Jiang. Contributor.

Madeline Kowalski. Contributor.

Skylar Li. Contributor.

Gesmira Molla. Contributor.

Efthymia Papalexi. Contributor.

Patrick Roelli. Contributor.

Rahul Satija. Author, maintainer.

Karthik Shekhar. Contributor.

Avi Srivastava. Contributor.

Tim Stuart. Contributor.

Kristof Torkenczy. Contributor.

Shiwei Zheng. Contributor.

Satija Lab and Collaborators. Funder.

Hao et al. Dictionary learning for integrative, multimodal and scalable single-cell analysis. Nature Biotechnology (2023) [Seurat V5]

Hao and Hao et al. Integrated analysis of multimodal single-cell data. Cell (2021) [Seurat V4]

Stuart and Butler et al. Comprehensive Integration of Single-Cell Data. Cell (2019) [Seurat V3]

Butler et al. Integrating single-cell transcriptomic data across different conditions, technologies, and species. Nat Biotechnol (2018) [Seurat V2]

Satija and Farrell et al. Spatial reconstruction of single-cell gene expression data. Nat Biotechnol (2015) [Seurat V1]

Developed by Rahul Satija, Satija Lab and Collaborators.

Site built with pkgdown 2.0.7.

**Examples:**

Example 1 (unknown):
```unknown
inst/CITATION
```

Example 2 (unknown):
```unknown
@Article{,
  author = {Yuhan Hao and Tim Stuart and Madeline H Kowalski and Saket Choudhary and Paul Hoffman and Austin Hartman and Avi Srivastava and Gesmira Molla and Shaista Madad and Carlos Fernandez-Granda and Rahul Satija},
  title = {Dictionary learning for integrative, multimodal and scalable single-cell analysis},
  journal = {Nature Biotechnology},
  year = {2023},
  doi = {10.1038/s41587-023-01767-y},
  url = {https://doi.org/10.1038/s41587-023-01767-y},
}
```

Example 3 (unknown):
```unknown
@Article{,
  author = {Yuhan Hao and Stephanie Hao and Erica Andersen-Nissen and William M. Mauck III and Shiwei Zheng and Andrew Butler and Maddie J. Lee and Aaron J. Wilk and Charlotte Darby and Michael Zagar and Paul Hoffman and Marlon Stoeckius and Efthymia Papalexi and Eleni P. Mimitou and Jaison Jain and Avi Srivastava and Tim Stuart and Lamar B. Fleming and Bertrand Yeung and Angela J. Rogers and Juliana M. McElrath and Catherine A. Blish and Raphael Gottardo and Peter Smibert and Rahul Satija},
  title = {Integrated analysis of multimodal single-cell data},
  journal = {Cell},
  year = {2021},
  doi = {10.1016/j.cell.2021.04.048},
  url = {https://doi.org/10.1016/j.cell.2021.04.048},
}
```

Example 4 (unknown):
```unknown
@Article{,
  author = {Tim Stuart and Andrew Butler and Paul Hoffman and Christoph Hafemeister and Efthymia Papalexi and William M Mauck III and Yuhan Hao and Marlon Stoeckius and Peter Smibert and Rahul Satija},
  title = {Comprehensive Integration of Single-Cell Data},
  journal = {Cell},
  year = {2019},
  volume = {177},
  pages = {1888-1902},
  doi = {10.1016/j.cell.2019.05.031},
  url = {https://doi.org/10.1016/j.cell.2019.05.031},
}
```

Example 5 (unknown):
```unknown
@Article{,
  author = {Andrew Butler and Paul Hoffman and Peter Smibert and Efthymia Papalexi and Rahul Satija},
  title = {Integrating single-cell transcriptomic data across different conditions, technologies, and species},
  journal = {Nature Biotechnology},
  year = {2018},
  volume = {36},
  pages = {411-420},
  doi = {10.1038/nbt.4096},
  url = {https://doi.org/10.1038/nbt.4096},
}
```

Example 6 (unknown):
```unknown
@Article{,
  author = {Rahul Satija and Jeffrey A Farrell and David Gennert and Alexander F Schier and Aviv Regev},
  title = {Spatial reconstruction of single-cell gene expression data},
  journal = {Nature Biotechnology},
  year = {2015},
  volume = {33},
  pages = {495-502},
  doi = {10.1038/nbt.3192},
  url = {https://doi.org/10.1038/nbt.3192},
}
```

---

## Tools for Single Cell Genomics • Seurat

**URL:** http://127.0.0.1:9173/seurat/authors/index.html

**Contents:**
- Authors
- Citation

Andrew Butler. Contributor.

Saket Choudhary. Contributor.

Charlotte Darby. Contributor.

Jeff Farrell. Contributor.

Isabella Grabski. Contributor.

Christoph Hafemeister. Contributor.

Yuhan Hao. Contributor.

Austin Hartman. Contributor.

Paul Hoffman. Contributor.

Jaison Jain. Contributor.

Longda Jiang. Contributor.

Madeline Kowalski. Contributor.

Skylar Li. Contributor.

Gesmira Molla. Contributor.

Efthymia Papalexi. Contributor.

Patrick Roelli. Contributor.

Rahul Satija. Author, maintainer.

Karthik Shekhar. Contributor.

Avi Srivastava. Contributor.

Tim Stuart. Contributor.

Kristof Torkenczy. Contributor.

Shiwei Zheng. Contributor.

Satija Lab and Collaborators. Funder.

Hao et al. Dictionary learning for integrative, multimodal and scalable single-cell analysis. Nature Biotechnology (2023) [Seurat V5]

Hao and Hao et al. Integrated analysis of multimodal single-cell data. Cell (2021) [Seurat V4]

Stuart and Butler et al. Comprehensive Integration of Single-Cell Data. Cell (2019) [Seurat V3]

Butler et al. Integrating single-cell transcriptomic data across different conditions, technologies, and species. Nat Biotechnol (2018) [Seurat V2]

Satija and Farrell et al. Spatial reconstruction of single-cell gene expression data. Nat Biotechnol (2015) [Seurat V1]

Developed by Rahul Satija, Satija Lab and Collaborators.

Site built with pkgdown 2.0.7.

**Examples:**

Example 1 (unknown):
```unknown
inst/CITATION
```

Example 2 (unknown):
```unknown
@Article{,
  author = {Yuhan Hao and Tim Stuart and Madeline H Kowalski and Saket Choudhary and Paul Hoffman and Austin Hartman and Avi Srivastava and Gesmira Molla and Shaista Madad and Carlos Fernandez-Granda and Rahul Satija},
  title = {Dictionary learning for integrative, multimodal and scalable single-cell analysis},
  journal = {Nature Biotechnology},
  year = {2023},
  doi = {10.1038/s41587-023-01767-y},
  url = {https://doi.org/10.1038/s41587-023-01767-y},
}
```

Example 3 (unknown):
```unknown
@Article{,
  author = {Yuhan Hao and Stephanie Hao and Erica Andersen-Nissen and William M. Mauck III and Shiwei Zheng and Andrew Butler and Maddie J. Lee and Aaron J. Wilk and Charlotte Darby and Michael Zagar and Paul Hoffman and Marlon Stoeckius and Efthymia Papalexi and Eleni P. Mimitou and Jaison Jain and Avi Srivastava and Tim Stuart and Lamar B. Fleming and Bertrand Yeung and Angela J. Rogers and Juliana M. McElrath and Catherine A. Blish and Raphael Gottardo and Peter Smibert and Rahul Satija},
  title = {Integrated analysis of multimodal single-cell data},
  journal = {Cell},
  year = {2021},
  doi = {10.1016/j.cell.2021.04.048},
  url = {https://doi.org/10.1016/j.cell.2021.04.048},
}
```

Example 4 (unknown):
```unknown
@Article{,
  author = {Tim Stuart and Andrew Butler and Paul Hoffman and Christoph Hafemeister and Efthymia Papalexi and William M Mauck III and Yuhan Hao and Marlon Stoeckius and Peter Smibert and Rahul Satija},
  title = {Comprehensive Integration of Single-Cell Data},
  journal = {Cell},
  year = {2019},
  volume = {177},
  pages = {1888-1902},
  doi = {10.1016/j.cell.2019.05.031},
  url = {https://doi.org/10.1016/j.cell.2019.05.031},
}
```

Example 5 (unknown):
```unknown
@Article{,
  author = {Andrew Butler and Paul Hoffman and Peter Smibert and Efthymia Papalexi and Rahul Satija},
  title = {Integrating single-cell transcriptomic data across different conditions, technologies, and species},
  journal = {Nature Biotechnology},
  year = {2018},
  volume = {36},
  pages = {411-420},
  doi = {10.1038/nbt.4096},
  url = {https://doi.org/10.1038/nbt.4096},
}
```

Example 6 (unknown):
```unknown
@Article{,
  author = {Rahul Satija and Jeffrey A Farrell and David Gennert and Alexander F Schier and Aviv Regev},
  title = {Spatial reconstruction of single-cell gene expression data},
  journal = {Nature Biotechnology},
  year = {2015},
  volume = {33},
  pages = {495-502},
  doi = {10.1038/nbt.3192},
  url = {https://doi.org/10.1038/nbt.3192},
}
```

---

## Satija Lab

**URL:** http://127.0.0.1:9173/index.html

**Contents:**
- Satija Lab
- Welcome to the Satija Lab
    - Recent News

Our goal is to understand how cellular heterogeneity encodes the molecular structure, function, and regulation of complex biological systems. Primarily using single cell genomics, we analyze systems by profiling their most fundamental units individually - a ‘bottom-up’ approach that allows us to study how diverse groups of cells work together to drive biological processes and behaviors.We’re located at the New York Genome Center in Lower Manhattan, a short walk from our joint appointment at the NYU Center for Genomics and Systems Biology .

---

## Tools for Single Cell Genomics • Seurat

**URL:** http://127.0.0.1:9173/license.html

**Contents:**
- MIT License
- Contents

Copyright (c) 2021 Seurat authors

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the “Software”), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

Developed by Rahul Satija, Satija Lab and Collaborators.

Site built with pkgdown 2.0.7.

---

## Tools for Single Cell Genomics • Seurat

**URL:** http://127.0.0.1:9173/license-text.html

**Contents:**
- License
- Contents

Developed by Rahul Satija, Satija Lab and Collaborators.

Site built with pkgdown 2.0.7.

**Examples:**

Example 1 (unknown):
```unknown
YEAR: 2021
COPYRIGHT HOLDER: Seurat authors
```

---

## Tools for Single Cell Genomics • Seurat

**URL:** http://127.0.0.1:9173/seurat/code_of_conduct/index.html

**Contents:**
- Contributor Covenant Code of Conduct
- Our Pledge
- Our Standards
- Our Responsibilities
- Scope
- Enforcement
- Attribution
- Contents

In the interest of fostering an open and welcoming environment, we as contributors and maintainers pledge to making participation in our project and our community a harassment-free experience for everyone, regardless of age, body size, disability, ethnicity, sex characteristics, gender identity and expression, level of experience, education, socio-economic status, nationality, personal appearance, race, religion, or sexual identity and orientation.

Examples of behavior that contributes to creating a positive environment include:

Examples of unacceptable behavior by participants include:

Project maintainers are responsible for clarifying the standards of acceptable behavior and are expected to take appropriate and fair corrective action in response to any instances of unacceptable behavior.

Project maintainers have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this Code of Conduct, or to ban temporarily or permanently any contributor for other behaviors that they deem inappropriate, threatening, offensive, or harmful.

This Code of Conduct applies both within project spaces and in public spaces when an individual is representing the project or its community. Examples of representing a project or community include using an official project e-mail address, posting via an official social media account, or acting as an appointed representative at an online or offline event. Representation of a project may be further defined and clarified by project maintainers.

Instances of abusive, harassing, or otherwise unacceptable behavior may be reported by contacting the project team at rsatija@nygenome.org. All complaints will be reviewed and investigated and will result in a response that is deemed necessary and appropriate to the circumstances. The project team is obligated to maintain confidentiality with regard to the reporter of an incident. Further details of specific enforcement policies may be posted separately.

Project maintainers who do not follow or enforce the Code of Conduct in good faith may face temporary or permanent repercussions as determined by other members of the project’s leadership.

This Code of Conduct is adapted from the Contributor Covenant, version 1.4, available at https://www.contributor-covenant.org/version/1/4/code-of-conduct.html

For answers to common questions about this code of conduct, see https://www.contributor-covenant.org/faq

Developed by Rahul Satija, Satija Lab and Collaborators.

Site built with pkgdown 2.0.7.

---

## Tools for Single Cell Genomics • Seurat

**URL:** http://127.0.0.1:9173/seurat/license-text/index.html

**Contents:**
- License
- Contents

Developed by Rahul Satija, Satija Lab and Collaborators.

Site built with pkgdown 2.0.7.

**Examples:**

Example 1 (unknown):
```unknown
YEAR: 2021
COPYRIGHT HOLDER: Seurat authors
```

---
