Software Development

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On this page you will find links to software developed by BIAS members, in alphabetical order, and a short explanation of each package. 

Software Development

  • baseline package in R

    This package is a collection of baseline correction algorithms, along with a framework and a GUI for optimising baseline algorithm parameters. This package is used, e.g., to remove background effects from spectra originating from various types of spectroscopy and spectrometry. 

  • CNOGpro package in R 

    The CNOGpro package encompasses methods for assigning copy number states and breakpoints in resequencing experiments of prokaryotic organisms. 

  • Familias

    Familias is a free software for probability calculations when inferring paternity and identification based on DNA data, and allows for multiple alternative pedigrees to be handled. 

  • FamLink

    FamLink is a free software that provides functions for likelihood calculation for family relationships/pedigrees using pairwise linked DNA marker data. 

  • FamLinkX

    FamLinkX is a free software that provides functions for likelihood calculation for family relationships/pedigrees using X-chromosomal genetic marker data. 

  • microclass package in R

    The microclass package has functions for assigning 16S sequence data to a taxonomic level in the tree-of-life for prokaryotes.

  • microcontax package in R

    The microcontax package is a consensus taxonomy for prokaryotes that employs a set of datasets for best possible taxonomic classification based on 16S rRNA sequence data.

  • micropan package in R

    The micropan package is a collection of functions for computations and visualizations of microbial pan-genomes.

  • microRMS

    The microRMS package provides tools for handling and analyzing quantitative data on microbiota generated by Reduced Metagenome Sequencing (RMS).  

  • microseq package in R

    The microseq package provides basic functions for microbial sequence data analysis.

  • NMBU/UMB R repository

    At BIAS, we are heavily engaged in teaching courses in statistics and bioinformatics to students (for a list of courses see our master's program page). The NMBU/UMB repository contains R-packages and documentation for students taking courses at NMBU that use R or R Commander. 

  • PlantGenIE

    The Plant Genome Integrative Explorer (PlantGenIE) is a collection of interoperable web resources for searching, visualizing and analyzing genomics and transcriptomics data for different plant species.

  • pls package in R 

    The pls package encompasses various multivariate regression methods such as Partial Least Squares Regression (PLSR), Principal Component Regression (PCR), and Canonical Powered Partial Least Squares (CPPLS).

  • SalMotifDB

     SalMotifDB is a cis-regulatory motif database for salmonid species. 

  • simrel package in R 

    The simrel package allows users to simulate multi-response linear model data. It can be used as a tool for model comparison, and educational purposes.
Published 1. November 2019 - 13:38 - Updated 1. February 2020 - 13:11