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http://www.biotech.uconn.edu/resources/biophysics
Software for analyzing sedimentation equilibrium (SE) data from analytical ultracentrifugation experiments. It uses a model-dependent simulation of data for matching data in order to determine when equilibrium has been achieved.
Proper citation: HeteroAnalysis (RRID:SCR_014991) Copy
Software Python package for simulation and analysis of neuronal networks using the NEURON simulator.Used to facilitate development, parallel simulation, analysis, and optimization of biological neuronal networks.
Proper citation: NetPyNE (RRID:SCR_014758) Copy
https://aceabio.com/product/rtca-dp/
Data acquisition and analysis software used for xCELLigence Real Time Cell Analysis SP, DP and MP instruments. The software is used to program and execute experiments and analyze data.
Proper citation: RTCA Software (RRID:SCR_014821) Copy
Web server for statistical, functional and integrative analysis of metabolomics data. Web based tool suite used for metabolomic data processing, normalization, multivariate statistical analysis, and data annotation, biomarker discovery and classification.
Proper citation: MetaboAnalyst (RRID:SCR_015539) Copy
https://github.com/sanger-pathogens/ariba
Analysis software that identifies antibiotic resistance genes by running local assemblies. It can also be used for MLST calling.
Proper citation: Ariba (RRID:SCR_015976) Copy
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 23,2023.Software for automated docking analysis to precalculate the set of grids describing the target protein. It is a part of automated molecular modeling simulation software AutoDock.
Proper citation: Autogrid (RRID:SCR_015982) Copy
Alignment analysis software tool for comparative mapping between two genome assemblies or between two different genomes. It can cache intermediate results to speed a comparisons of multiple sequences.
Proper citation: Atac (RRID:SCR_015980) Copy
https://github.com/kdmurray91/axe
Software for sequencing data analysis and demultiplexing. It can be used in situations where sequence reads contain the barcodes that uniquely distinguish samples.
Proper citation: Axe (RRID:SCR_015984) Copy
https://github.com/pezmaster31/bamtools/wiki
Software that provides both a C++ API and a command-line toolkit for reading, writing, and manipulating genome sequence alignment files in the BAM and SAM formats. It is used for research analysis and management of data produced by sequencing technologies.
Proper citation: Bamtools (RRID:SCR_015987) Copy
https://www.nitrc.org/projects/mrtool
Software toolkit for analysis of MR brain imaging data. MRTool runs on Apple computers and PCs and requires SPM12.
Proper citation: MRTool (RRID:SCR_015956) Copy
https://bioconductor.org/packages/release/bioc/html/scater.html
Software toolkit for doing various analyses of single-cell RNA-seq gene expression data, with a focus on quality control. This package facilitates pre-processing, quality control, normalization and visualization of scRNA-seq data.
Proper citation: scater (RRID:SCR_015954) Copy
A Web-based Analysis Tool for Indirect Calorimetry Experiments which measure physiological energy balance. It is a web application for indirect calorimetry analysis which generates customizable time, bar and regression plots for calorimetry data using two-, three-, and four-group templates.
Proper citation: CalR (RRID:SCR_015849) Copy
https://www.biacore.com/lifesciences/service/downloads/software_licenses/biaevaluation/
Analysis software for life science data. This software package is for presentation and evaluation of sensorgram data from real-time BIA analyses.
Proper citation: BIAevaluation Software (RRID:SCR_015936) Copy
https://github.com/jdiedrichsen/pcm_toolbox
Software for a Bayesian approach for evaluating representational models that specify how complex patterns of neural activity relate to visual stimuli, motor actions, or abstract thoughts. PCM evaluates the ability of models to predict novel brain activity patterns and integrates over all possible activity profiles and computes the marginal likelihood of the data under the activity profile distribution specified by the representational model.
Proper citation: Pattern Component Modelling Toolbox (RRID:SCR_015891) Copy
https://github.com/markmikkelsen/Gannet
Free, open-source MATLAB-based software toolkit for analyzing edited 1H magnetic resonance spectroscopy (MRS) data.
Proper citation: Gannet (RRID:SCR_016049) Copy
https://gitlab.com/SimonHTausch/HiLive
Software tool for performing read mapping that maps Illumina HiSeq sequencer read alignments when they are produced. Used in Next Generation Sequencing in time critical, clinical applications.
Proper citation: HiLive (RRID:SCR_016134) Copy
Software for statistical analysis and spreadsheet editing that is built on top of the R statistical language. It encourages a “community driven” philosophy, where users can develop and publish their analyses to make them available to a wide audience.
Proper citation: jamovi (RRID:SCR_016142) Copy
https://github.com/Ashod/garli
Software application for inferring phylogenetic trees and analysis of molecular sequence data using the maximum-likelihood criterion. It implements nucleotide, amino acid and codon-based models of sequence evolution.
Proper citation: GARLI (RRID:SCR_016117) Copy
https://github.com/nvalimak/fsm-lite
Software application as a single-core implementation of frequency-based substring mining. It can be used in bioinformatics to extract substrings that discriminate two (or more) datasets inside high-throughput sequencing data.
Proper citation: Fsm-lite (RRID:SCR_016115) Copy
https://github.com/bbuchfink/diamond
Software that performs sequence alignment for protein and translated DNA searches and functions. Used for high performance analysis of big sequence data, protein-protein search, and DNA-protein search.
Proper citation: DIAMOND (RRID:SCR_016071) Copy
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