Main logo
?
tutorial arrow
×
Create your own tool library
Bookmark tools and put favorites into folders to find them easily.

SplicePlot | A utility for visualizing splicing quantitative trait loci

A package for visualizing alternative splicing and the effects of splicing quantitative trait loci (sQTLs) from RNA-seq data. SplicePlot takes mapped RNA sequencing reads and genotype data as input and outputs publication-quality Sashimi plots, hive plots and structure plots, enabling better investigation and understanding of the role of genetics on alternative splicing and transcript structure. Such visualizations take advantage of the high precision quantification of RNA-seq and enable a better understanding of the genetic effects behind alternative splicing in RNA-seq data.

User report

tutorial arrow
×
Vote up tools and offer feedback
Give value to tools and make your expertise visible
Give your feedback on this tool
Sign up for free to join and share with the community

0 user reviews

star_border star_border star_border star_border star_border
star star star star star

0 user reviews

star_border star_border star_border star_border star_border
star star star star star

No review has been posted.

SplicePlot forum

tutorial arrow
×
Communicate with other users
Participate in the forum to get support for using tools. Ask questions about technical specifications.
Take part in the discussion
Sign up for free to ask question and share your advices

No open topic.

SplicePlot classification

SplicePlot specifications

Unique identifier:
OMICS_02185
Interface:
Command line interface
Input data:
Gene sequence variations, exons and aligned RNA-seq data
Output data:
Plot setting file
Programming languages:
Python
Version:
1.1
Requirements:
Numpy, Scipy, Matploblib, Pandas, Pysam
Maintained:
Yes
Software type:
Package/Module
Restrictions to use:
None
Input format:
VCF, GTF, BAM, TXT
Operating system:
Unix/Linux, Mac OS, Windows
Computer skills:
Advanced
Stability:
Stable
Source code URL:
https://codeload.github.com/wueric/SplicePlot/zip/master

SplicePlot distribution

versioning

tutorial arrow
×
Upload and version your source code
Get a DOI for each update to improve tool traceability. Archive your releases so the community can easily visualize progress on your work.
Facilitate your tool traceability
Sign up for free to upload your code and get a DOI

No versioning.

Credits

tutorial arrow
×
Promote your skills
Define all the tasks you managed and assign your profile the appropriate badges. Become an active member.
Promote your work
Sign up for free to badge your contributorship

Publications

Institution(s)

Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA

Funding source(s)

Edward Mallinckrodt Jr. Foundation

By using OMICtools you acknowledge that you have read and accepted the terms of the end user license agreement.