iobio.io

What is it? · iobio

Iobio uses immediate visual feedback to make understanding complex genomic datasets more intuitive, and analysis more interactive. To view this video please enable JavaScript, and consider upgrading to a web browser that supports HTML5 video. Sign up to hear about new apps and when you can build your own. An alignment data inspector tool that quickly samples bam files and visualizes a series of metrics. A variant data inspector tool that quickly samples vcf files and visualizes a series of metrics. A dev...

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What is it? · iobio | iobio.io Reviews

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Iobio uses immediate visual feedback to make understanding complex genomic datasets more intuitive, and analysis more interactive. To view this video please enable JavaScript, and consider upgrading to a web browser that supports HTML5 video. Sign up to hear about new apps and when you can build your own. An alignment data inspector tool that quickly samples bam files and visualizes a series of metrics. A variant data inspector tool that quickly samples vcf files and visualizes a series of metrics. A dev...

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4 developers

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What is it? · iobio | iobio.io Reviews

https://iobio.io

Iobio uses immediate visual feedback to make understanding complex genomic datasets more intuitive, and analysis more interactive. To view this video please enable JavaScript, and consider upgrading to a web browser that supports HTML5 video. Sign up to hear about new apps and when you can build your own. An alignment data inspector tool that quickly samples bam files and visualizes a series of metrics. A variant data inspector tool that quickly samples vcf files and visualizes a series of metrics. A dev...

SUBDOMAINS

taxonomer.iobio.io

taxonomer.iobio

Based on 16S rRNA Gene Reads). Based on Viral and Unbinned Reads Classified as Viral). Based on Internal Transcribed Spacer (ITS) Reads). Hold shift to select 2 mate-pair files). Enter URL for FASTQ/FASTA(s). Enter SRA Run ID. Add URL to reads (fasta or fastq). Add Mate Pair (optional). Oops, there was an error analyzing your sample. Please make sure your file, url, or SRRid is valid and try agin.

gene.iobio.io

gene.iobio

Welcome to gene.iobio. An app for interrogating disease-causing variants. Type in the gene name BRCA2 and select from the drop down list. Click on next arrow to continue to next step. This shows the gene model for the canonical transcript. Select 'Single' to view variants for a single sample. Select 'Trio' when performing trio analysis with variants from proband, mother, and father. In this tour, we will be analyzing the variants from a single sample, so press the 'Single' button. Click the maximize butt...

INTERNAL PAGES

iobio.io

1

About us · iobio

http://iobio.io/about.html

We are a team of developers in the Marth lab at the Center for Genetic Discovery. At the University of Utah. If you'd like to give suggestions or collaborate on an app in your research area, contact us at iobioproject at gmail dot com. Developed in the Marth Lab by.

2

Developers · iobio

http://iobio.io/developers.html

Developed in the Marth Lab by.

3

Applications · iobio

http://iobio.io/applications.html

These are our full applications ready for use. Improvements? A web app for investigating potential disease-causing variants. An ultra fast metagenomics classification and analysis app. An alignment data inspector tool that quickly samples bam files and visualizes a series of metrics. An variant data inspector tool that quickly samples vcf files and visualizes a series of metrics. Here are some ideas we have explored but haven't turned into full polished apps. Developed in the Marth Lab by.

4

Pacbio Alignments In Bam.iobio · iobio

http://iobio.io/2015/04/15/pacbio-alignments-in-bam.iobio

Pacbio Alignments In Bam.iobio. The Schatz lab just posted some pacbio bam files. A quick look shows a few interesting things, such as the read length looks like it clusters below 5k, but has consistent longer reads all the way out to 30k. Check out the rest in bam.iobio. BY Alistair Ward ON Nov 3, 2016. What pathogenic variants do we know? BY Chase Miller ON Nov 2, 2016. IOBIO Now in Galaxy. Bamiobio and vcf.iobio have been integrated into galaxy. BY Alistair Ward ON Sep 22, 2016.

5

Blog · iobio

http://iobio.io/blog.html

BY Alistair Ward ON Nov 3, 2016. What pathogenic variants do we know? BY Chase Miller ON Nov 2, 2016. IOBIO Now in Galaxy. Bamiobio and vcf.iobio have been integrated into galaxy. BY Alistair Ward ON Sep 22, 2016. Geneiobio version 2.1. A new version of gene.iobio is now available. BY Alistair Ward ON Sep 20, 2016. Query the origin of sequencing data. BY Alistair Ward ON Aug 3, 2016. What are bookmarks and why should I use them? BY Alistair Ward ON Jun 29, 2016. Web dev position available. Why Am I Sick?

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taxonomer.iobio.io

taxonomer.iobio Sample Datasets

http://taxonomer.iobio.io/info.html

Taxonomer is a kmer-based ultrafast metagenomics tool for assigning taxonomy to sequencing reads from both clinical and environmental samples. Taxonomer enables simultaneous microbial detection and human transcript quantification within a clinically meaningful timeframe (i.e. minutes). Taxonomer supports nucleotide and protein-based pathogen detection and phylogenetic classification using DNA and RNA sequencing data in a single integrated algorithmic framework. Taxonomer results are i...RNA-Seq data of a...

ucgd.genetics.utah.edu

USTAR Center for Genetic Discovery » Gabor Marth

http://ucgd.genetics.utah.edu/gabor-marth

Gabor Marth, D.Sc. To visit the iobio. Dr Marth is Professor of Human Genetics at University of Utah and an internationally recognized expert in DNA sequence variation detection and analysis software development. He has served as:. SAB Chair for Ontario Institute of Cancer Research Program in Computational Biology. Chair of Exome Sequencing Group of the 1000 Genomes Project. Co-Director of USTAR Center for Genetic Discovery. IRB, RPPR, CITI. FML. Very nice plots showing progression of clones! Siddhartha ...

nightlylibrary.wordpress.com

Portals – NightlyArt Vault

https://nightlylibrary.wordpress.com/portals

There are several websites (online app/services) out there with the capability to make anyone’s day sucks less. This list is my attempt to keep tabs on them. Watch people codes (and for beginners, time to learn from pros or be confused by them). Textbooks are exorbitantly expensive. Let’s buy cheaper ones. Free lab management platform. I heard it is completely free. Those with paranoia about web security in the online world, this website has the resources for you. It looks like Trello on steroid. What I ...

ucgd.genetics.utah.edu

USTAR Center for Genetic Discovery » Software

http://ucgd.genetics.utah.edu/software

This page serves as an index for the applications written and distributed by the Yandell, Marth, and Quinlan labs. Each item may include links to: documentation, code, and publications. Software is listed with most recent releases first. VARPRISM (VARiant PRIoritization SuM). Annotates a VCF with any number of sorted and tabixed input BED, BAM, and VCF files in parallel. It does this by finding overlaps as it streams over the data and applying user-defined operations on the overlapping annotations. Genom...

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iobio.io

What is it? · iobio

Iobio uses immediate visual feedback to make understanding complex genomic datasets more intuitive, and analysis more interactive. To view this video please enable JavaScript, and consider upgrading to a web browser that supports HTML5 video. Sign up to hear about new apps and when you can build your own. An alignment data inspector tool that quickly samples bam files and visualizes a series of metrics. A variant data inspector tool that quickly samples vcf files and visualizes a series of metrics. A dev...

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