Bioinformatics Tools
Bioinformatics Tools & Software
The Guda Lab has developed or maintains these tools and software.
Currently Supported Tools
- scATACseq – Single-Cell Genomics Analysis with RAPIDS
- StrainIQ – StrainIQ is an n-gram based method to identify and quantify microbial communities in metagenomics samples.
- ChimeRScope – a novel alignment-free algorithm for fusion transcript prediction using paired-end RNA-Seq data
- NBBttest – is R package for implementing negative binomial beta t-test
- mintRULS – is a machine learning-based tool developed in python environment to predict interactions between miRNA and gene target sites
- red_panda – A tool for identifying variants in scRNA-seq
- LocSigDB -A catalog of protein sorting signals
- ngLOC – A Bayesian method for predicting protein subcellular localization
- ECemble – an ensemble machine learning method to predict enzyme and enzyme classes from unannotated protein sequences
Discontinued Tools
- pTARGET – A Prediction Server for Protein Subcellular Localization
- CE-MC – Multiple Protein Structure Alignment Server
- MITOPRED: a web server for the prediction of mitochondrial proteins
- SledgeHMMER: A web server for batch searching of Pfam database
- DMAPS: A Database of Multiple Alignments for Protein Structures
Other Databases Developed
- LIPID MAPS – Lipid Metabolites and Pathways Strategy
- MitoProteome – Human Mitochondrial Proteome Database
Licensed Bioinformatics Tools & Software
We provide the following software tools:
- Ingenuity Pathway Analysis (IPA): A web-based knowledge base and software for analyzing complex biological and chemical systems. It offers a variety of tools to analyze gene expression data and identify affected biological pathways, networks with literature supported evidence. Also contains tools to predict upstream or downstream interacting genes, building networks for hypothesis generation, and visualization of results. IPA is currently available only for UNMC users.
- GraphPad PPRISM The preferred analysis and graphing solution purpose-built for scientific research. The world’s leading scientists and discover how you can use Prism to save time, make more appropriate analysis choices, and elegantly graph and present your scientific research.
- CLC Genomics Workbench: A software suite for the analysis, visualization, and comparison of next-generation sequencing data. It can also be used for other data, please add the other features. We are working on making it available for all investigators.
- Statistical Analysis System (SAS) is a software suite for advanced data analysis, storage, and retrieval, with a graphical user interface. Third-party members of the INBRE consortium should purchase a license at a regular price on the SAS website. An institutional license is available for UNMC through ITS and OntheHub. A free SAS University version is also available, but not all modules are included.
- MATLAB: A high-level language and graphical environment which allows data exploration and analysis possible. A license can be obtained through RITO.