Omicsbox Apps – BioBam

Extend the functionalities of OmicsBox

OmicsBox Apps and our Developer SDK can be used to extend the functionalities of OmicsBox. With OmicsBox Apps you are able to:

Share your own bioinformatics tools or visualizations with the BioBam Community.
Create a tool by wrapping a popular command line program to ease your or your colleagues’ research.
Connect your software/system with a OmicsBox App that integrates OmicsBox into your existing environment.

Interested in making your own App?

You are more than welcome! Please write us an email to dev@biobam.com and we will provide you with a login to our developer zone and a developer licence key for OmicsBox. Looking forward to getting in touch with you.

Access to the Developer Zone allows you to use all the resources needed to develop OmicsBox Apps.

App Directory

Find here a list of already available tools developed by the BioBam Community and us shortly.

App		Type	Manual
	sc-RNAseq Clustering Perform the clustering of cells coming from single-cell RNA sequencing (scRNA-seq) data. Show More	Transcriptomics Module
This tool aims to find groups of cells that share similar expression patterns, which should correspond to the same cell type or state. Prior to the clustering, this tool allows filtering and preprocessing the data in order to make it suitable for the clustering algorithm. This application is based on the widely-used Seurat package.		Author: BioBam Bioinformatics S.L. Version: Release Date: 2021-06-22

	MLST Multi-Locus Sequence Typing (MLST) Show More	Genome Analysis Module
Multilocus Species Typing (MLST) is a nucleotide sequence-based approach of an unambiguous procedure of characterizing isolates of bacterial species using the sequences of internal fragments of (usually) seven house-keeping genes.		Author: BioBam Bioinformatics S.L. Version: Release Date: 2019-07-15

	Psortb A prediction tool for bacterial protein subcellular localization Show More	Functional Analysis Module
If you use this tool for your research please cite: PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes. N.Y. Yu, J.R. Wagner, M.R. Laird, G. Melli, S. Rey, R. Lo, P. Dao, S.C. Sahinalp, M. Ester, L.J. Foster, and F.S.L. Brinkman (2010) Bioinformatics 26(13):1608-1615. For more information please visit: http://www.psort.org		Author: BioBam Bioinformatics S.L. Version: Release Date: 2016-05-14

	Coding Potential Assesement Tool This App allow to calculate the coding potential probability for RNA sequences. Show More	Genome Analysis Module
This App allow to use prebuild models or to build new species-specific models from files or from the NCBI datbase in order to assign to each RNA sequence a coding probability score.		Author: BioBam Bioinformatics S.L. Version: Release Date: 2017-03-16

Extend the functionalities of OmicsBox

Interested in making your own App?

App Directory

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