https://github.com/lpantano/seqclusterviz

visualization of seqcluster output, try at:
https://github.com/lpantano/seqclusterviz

mirna smallrna smallrna-seq trna-derived-small-rna visualization

Last synced: 2 months ago
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visualization of seqcluster output, try at:

• Host: GitHub
• URL: https://github.com/lpantano/seqclusterviz
• Owner: lpantano
• License: mit
• Created: 2015-06-23T16:33:16.000Z (almost 10 years ago)
• Default Branch: master
• Last Pushed: 2019-06-19T15:23:49.000Z (almost 6 years ago)
• Last Synced: 2025-03-25T07:41:30.558Z (3 months ago)
• Topics: mirna, smallrna, smallrna-seq, trna-derived-small-rna, visualization
• Language: JavaScript
• Homepage: http://lpantano.github.io/seqclusterViz/
• Size: 5.43 MB
• Stars: 6
• Watchers: 3
• Forks: 3
• Open Issues: 5
• Metadata Files:
  • Readme: README.md
  • Changelog: HISTORY.md
  • License: LICENSE

Awesome Lists containing this project

README

        
# seqclusterViz

Visualization of small RNAseq data 

Any question? chat here: [![chat](https://badges.gitter.im/Join%20Chat.svg)](https://gitter.im/lpantano/seqcluster)

    

[![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active)

[![DOI](https://img.shields.io/badge/DOI-10.7490%2Ff1000research.1114055.1-lightgrey.svg?style=flat-square)](https://f1000research.com/posters/6-673)

[![DOI](https://zenodo.org/badge/37931015.svg)](https://zenodo.org/badge/latestdoi/37931015)

   

**cite:**

Pantano Rubino L, Chapman B, Kirchner R et al. Characterization of the small RNA transcriptome using the bcbio-nextgen python framework [version 1; not peer reviewed]. F1000Research 2016, 5(ISCB Comm J):1627 (slides) (doi: 10.7490/f1000research.1112526.1)

Pantano L, Pantano Rubino F, Marti E and Ho Sui S. Visualization of the small RNA transcriptome using seqclusterViz [version 1; not peer reviewed]. F1000Research 2017, 6(ISCB Comm J):673 (poster) [doi: 10.7490/f1000research.1114055.1](https://f1000research.com/posters/6-673)

**How to:**

Visualization of [seqcluster output for small RNA data](https://github.com/lpantano/seqcluster). You can run seqcluster or bcbio-nextgen to get the output. With [bcbio-nextgen](https://bcbio-nextgen.readthedocs.io/en/latest/) the full analysis is much easier and you get plenty of other outputs. See an example of bcbio output [here](https://github.com/lpantano/small-RNA-analysis/tree/master/reanalysis_parkinson). This is the re-analysis of [small RNA from patients with Parkinson's disease](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE97285) published in [bioinformatics](https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/btv632). Use the [seqcluster.db](https://github.com/lpantano/small-RNA-analysis/blob/master/reanalysis_parkinson/final/2017-03-31_srna/seqclusterViz/seqcluster.db) to visualize this data with the tool.

Download [this repo](https://github.com/lpantano/seqclusterViz/archive/master.zip), unzip it, open `index.html` and use the tiny data `data/example.db` to test it!

See video: https://youtu.be/Zjzte8n2-Sg

[![IMAGE ALT TEXT](http://i.makeagif.com/media/7-03-2016/M0GjW2.gif)](https://youtu.be/Zjzte8n2-Sg "Example")