Skip to main content
bioRxiv
  • Home
  • About
  • Submit
  • ALERTS / RSS
Advanced Search
New Results

UBiT2: a client-side web-application for gene expression data analysis

View ORCID ProfileJean Fan, View ORCID ProfileDavid Fan, View ORCID ProfileKamil Slowikowski, View ORCID ProfileNils Gehlenborg, Peter Kharchenko
doi: https://doi.org/10.1101/118992
Jean Fan
Department of Biomedical Informatics, Harvard Medical School, 10 Shattuck St. Boston, MA 02130Bioinformatics and Integrative Genomics, Harvard University, Cambridge, MA 02138
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Jean Fan
David Fan
Department of Computer Science, Princeton University, 35 Olden Street Princeton, NJ 08540
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for David Fan
Kamil Slowikowski
Department of Biomedical Informatics, Harvard Medical School, 10 Shattuck St. Boston, MA 02130Bioinformatics and Integrative Genomics, Harvard University, Cambridge, MA 02138
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Kamil Slowikowski
Nils Gehlenborg
Department of Biomedical Informatics, Harvard Medical School, 10 Shattuck St. Boston, MA 02130
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Nils Gehlenborg
Peter Kharchenko
Department of Biomedical Informatics, Harvard Medical School, 10 Shattuck St. Boston, MA 02130
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Supplementary material
  • Preview PDF
Loading

ABSTRACT

We present a purely client-side web-application, UBiT2 (User-friendly BioInformatics Tools), that provides installation-free, offline alignment, analysis, and visualization of RNA-sequencing as well as qPCR data. Analysis modules were designed with single cell transcriptomic analysis in mind. Using just a browser, users can perform standard analyses such as quality control, filtering, hierarchical clustering, principal component analysis, differential expression analysis, gene set enrichment testing, and more, all with interactive visualizations and exportable publication-quality figures. We apply UBiT2 to recapitulate findings from single cell RNA-seq and Fluidigm Biomark™ multiplex RT-qPCR gene expression datasets. UBiT2 is available at http://pklab.med.harvard.edu/jean/ubit2/index.html with open-source code available at https://github.com/JEFworks/ubit2.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.
Back to top
PreviousNext
Posted March 22, 2017.
Download PDF

Supplementary Material

Email

Thank you for your interest in spreading the word about bioRxiv.

NOTE: Your email address is requested solely to identify you as the sender of this article.

Enter multiple addresses on separate lines or separate them with commas.
UBiT2: a client-side web-application for gene expression data analysis
(Your Name) has forwarded a page to you from bioRxiv
(Your Name) thought you would like to see this page from the bioRxiv website.
Share
UBiT2: a client-side web-application for gene expression data analysis
Jean Fan, David Fan, Kamil Slowikowski, Nils Gehlenborg, Peter Kharchenko
bioRxiv 118992; doi: https://doi.org/10.1101/118992
Digg logo Reddit logo Twitter logo CiteULike logo Facebook logo Google logo Mendeley logo
Citation Tools
UBiT2: a client-side web-application for gene expression data analysis
Jean Fan, David Fan, Kamil Slowikowski, Nils Gehlenborg, Peter Kharchenko
bioRxiv 118992; doi: https://doi.org/10.1101/118992

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
  • Tweet Widget
  • Facebook Like
  • Google Plus One

Subject Area

  • Bioinformatics
Subject Areas
All Articles
  • Animal Behavior and Cognition (1524)
  • Biochemistry (2479)
  • Bioengineering (1731)
  • Bioinformatics (9670)
  • Biophysics (3897)
  • Cancer Biology (2968)
  • Cell Biology (4190)
  • Clinical Trials (135)
  • Developmental Biology (2624)
  • Ecology (4098)
  • Epidemiology (2031)
  • Evolutionary Biology (6894)
  • Genetics (5206)
  • Genomics (6498)
  • Immunology (2183)
  • Microbiology (6937)
  • Molecular Biology (2751)
  • Neuroscience (17262)
  • Paleontology (126)
  • Pathology (425)
  • Pharmacology and Toxicology (705)
  • Physiology (1056)
  • Plant Biology (2488)
  • Scientific Communication and Education (643)
  • Synthetic Biology (831)
  • Systems Biology (2687)
  • Zoology (429)