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https://CRAN.R-project.org/package=caret

Software R package provides misc functions for training and plotting classification and regression models.Contains tools for data splitting, pre-processing, feature selection, model tuning using resampling, and variable importance estimation, as well as other functionality.

Proper citation: caret (RRID:SCR_021138) Copy   

•   Source: SciCrunch Registry

http://www.clcbio.com/products/clc-main-workbench/

A suite of software for DNA, RNA and protein sequence data analysis. The software allows for the analysis and visualization of Sanger sequencing data as well as gene expression analysis, molecular cloning, primer design, phylogenetic analyses, and sequence data management.

Proper citation: CLC Main Workbench (RRID:SCR_000354) Copy   

•   Source: SciCrunch Registry

http://www.mbfbioscience.com/stereo-investigator

Stereo Investigator system includes microscope, computer, and Stereo Investigator software. Software works with Brightfield, Multi-Channel Fluorescence, Confocal, and Structured Illumination Microscopes. System used to provide estimates of number, length, area, and volume of cells or biological structures in tissue specimen in areas of neuroscience including neurodegenerative diseases, neuropathy, memory, and behavior, pulmonary research, spinal cord research, and toxicology.

Proper citation: Stereo Investigator (RRID:SCR_002526) Copy   

•   Source: SciCrunch Registry

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https://reich.hms.harvard.edu/software

EIGENSOFT package combines functionality from our population genetics methods (Patterson et al. 2006) and our EIGENSTRAT stratification method (Price et al. 2006). The EIGENSTRAT method uses principal components analysis to explicitly model ancestry differences between cases and controls along continuous axes of variation; the resulting correction is specific to a candidate marker''s variation in frequency across ancestral populations, minimizing spurious associations while maximizing power to detect true associations. The EIGENSOFT package has a built-in plotting script and supports multiple file formats and quantitative phenotypes. Source code, documentation and executables for using EIGENSOFT 3.0 on a Linux platform can be downloaded. New features of EIGENSOFT 3.0 include supporting either 32-bit or 64-bit Linux machines, a utility to merge different data sets, a utility to identify related samples (accounting for population structure), and supporting multiple file formats for EIGENSTRAT stratification correction.

Proper citation: Eigensoft (RRID:SCR_004965) Copy   

•   Source: SciCrunch Registry

https://www.thermofisher.com/order/catalog/product/4363991

Software that allows users to manually or automatically design custom primers and probes for gene quantitation and allelic discrimination (SNP) real-time PCR applications. It supports assays based on TaqMan and SYBR Green I dye chemistries.

Proper citation: Primer Express (RRID:SCR_014326) Copy   

•   Source: SciCrunch Registry

https://CRAN.R-project.org/package=cluster

Software R package. Methods for Cluster analysis. Performs variety of types of cluster analysis and other types of processing on large microarray datasets.

Proper citation: Cluster (RRID:SCR_013505) Copy   

•   Source: SciCrunch Registry

https://www.iconplc.com/innovation/nonmem/

Software tool for nonlinear mixed effects modelling. Used for population pharmacokinetic and pharmacodynamic analysis and to simulate data and to fit data. Used in the development of new drugs. NONMEM versions up through 6 are the property of the Regents of the University of California, San Francisco, but ICON Development Solutions has exclusive rights to license their use. NONMEM 7 up to the current version is the property of ICON Development Solutions.

Proper citation: NONMEM (RRID:SCR_016986) Copy   

•   Source: SciCrunch Registry

http://www.malvern.com/en/products/technology/nanoparticle-tracking-analysis/

Software which utilizes the properties of both light scattering and Brownian motion to obtain the particle size distribution of samples in liquid suspension. The Nanoparticle Tracking Analysis software tracks many particles individually and calculates their hydrodynamic diameters using the Stokes Einstein equation.

Proper citation: Nanoparticle Tracking Analysis (RRID:SCR_014239) Copy   

•   Source: SciCrunch Registry

https://www.comsol.com/comsol-multiphysics

General-purpose software platform for modeling and simulating physics-based problems which accounts for coupled or multiphysics phenomena. The platform includes a set of core physics interfaces for common physics application areas such as structural analysis, laminar flow, pressure acoustics, transport of diluted species, electrostatics, electric currents, heat transfer, and Joule heating.

Proper citation: COMSOL Multiphysics (RRID:SCR_014767) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/release/bioc/html/oligo.html

Software package to analyze oligonucleotide arrays (expression/SNP/tiling/exon) at probe-level. It currently supports Affymetrix (CEL files) and NimbleGen arrays (XYS files).

Proper citation: oligo (RRID:SCR_015729) Copy   

•   Source: SciCrunch Registry

https://www.openclinica.com/

Web platform for electronic data capture by OpenClinica, LLC. Used as clinical trial management system.

Proper citation: OpenClinica (RRID:SCR_019223) Copy   

•   Source: SciCrunch Registry

https://www.schrodinger.com/glide

Software package which approximates a complete search of the conformational, orientational, and positional space of the ligand in a given receptor. Used in drug development for predicting protein ligand binding modes and ranking ligands via high throughput virtual screening.

Proper citation: Glide (RRID:SCR_000187) Copy   

•   Source: SciCrunch Registry

http://www.mediacy.com/imageproplus

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 18,2023. Software package to capture, process, measure, analyze and share images and data.

Proper citation: Image Pro Plus (RRID:SCR_007369) Copy   

•   Source: SciCrunch Registry

http://qiime.org/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 23,2023.Software package for comparison and analysis of microbial communities, primarily based on high-throughput amplicon sequencing data, but also supporting analysis of other types of data. QIMME analyzes and transforms raw sequencing data generated on Illumina or other platforms to publication quality graphics and statistics.

Proper citation: QIIME (RRID:SCR_008249) Copy   

•   Source: SciCrunch Registry

http://tree.bio.ed.ac.uk/software/figtree

A graphical viewer of phylogenetic trees and a program for producing publication-ready figures. It is designed to display summarized and annotated trees produced by BEAST.

Proper citation: FigTree (RRID:SCR_008515) Copy   

•   Source: SciCrunch Registry

http://bioinf.uni-greifswald.de/augustus/

Software for gene prediction in eukaryotic genomic sequences. Serves as a basis for further steps in the analysis of sequenced and assembled eukaryotic genomes.

Proper citation: Augustus (RRID:SCR_008417) Copy   

•   Source: SciCrunch Registry

http://www.randomizer.org

This site is designed for researchers and students who want a quick way to generate random numbers or assign participants to experimental conditions. Research Randomizer can be used in a wide variety of situations, including psychology experiments, medical trials, and survey research. The program uses a JavaScript random number generator to produce customized sets of random numbers. Since its release in 1997, Research Randomizer has been used to generate number sets over 10.7 million times. This service is part of Social Psychology Network and is fast, free, and runs with any recent web browser as long as JavaScript isn''t disabled. Research Randomizer is a free service offered to students and researchers interested in conducting random assignment and random sampling. By using this service, you agree to abide by the SPN User Policy and to hold Research Randomizer and its staff harmless in the event that you experience a problem with the program or its results. Although every effort has been made to develop a useful means of generating random numbers, Research Randomizer and its staff do not guarantee the quality or randomness of numbers generated. Any use to which these numbers are put remains the sole responsibility of the user who generated them. What are the system requirements needed to run Research Randomizer? This program works best with Firefox and other recent web browsers. If you''re using a browser that came with America Online, or older browsers made prior to 2003, you may experience some difficulties with Research Randomizer. You may also not be able to use Research Randomizer with some limited-function browsers that do not fully support JavaScript, such as the Opera broswer used on certain game consoles. We would suggest that you update to a fairly recent, fully- functional stand-alone browser. How do I know what browser I am using? The easiest way to find this out is to click Help on the pulldown menu at the top of the screen. One of the options should be About Mozilla Firefox, About Internet Explorer, About Netscape, or something similar. Selecting this option will open a window that displays the name, version number, and copyright date of your browser. How does Research Randomizer generate its numbers? Research Randomizer uses the Math.random method within the JavaScript programming language to generate its random numbers for all modern web browsers. If you are using an older version of Microsoft Internet Explorer or Netscape Navigator (that is prior to version 4.0 of either), Research Randomizer uses an adaptation of the Central Randomizer by Paul Houle. Note that Research Randomizer no longer supports much-older browsers by other vendors (e.g., Mosaic). Who designed Research Randomizer? The original idea and programming for Research Randomizer came from Geoffrey C. Urbaniak in 1997. Research Randomizer was then jointly developed with Scott Plous, webmaster of Social Psychology Network, and online tutorials were added to the main program. In 1999 the site was redesigned with the assistance of Mike Lestik, in 2003 Mike Lestik added the download function, and in 2007 Mike Lestik and Scott Plous redesigned the site and added new content.

Proper citation: Research Randomizer (RRID:SCR_008563) Copy   

•   Source: SciCrunch Registry

http://salilab.org/modeller/modeller.html

Software tool as Program for Comparative Protein Structure Modelling by Satisfaction of Spatial Restraints. Used for homology or comparative modeling of protein three dimensional structures. User provides alignment of sequence to be modeled with known related structures and MODELLER automatically calculates model containing all non hydrogen atoms.

Proper citation: MODELLER (RRID:SCR_008395) Copy   

•   Source: SciCrunch Registry

https://pypi.org/project/jcvi/

Software tool as collection of Python libraries to parse bioinformatics files, or perform computation related to assembly, annotation, and comparative genomics.

Proper citation: jcvi (RRID:SCR_021641) Copy   

•   Source: SciCrunch Registry

http://treebase.org/treebase-web/

Repository of phylogenetic information, specifically user-submitted phylogenetic trees and the data used to generate them. TreeBASE accepts all kinds of phylogenetic data (e.g., trees of species, trees of populations, trees of genes) representing all biotic taxa. Data in TreeBASE are exposed to the public if they are used in a publication that is in press or published in a peer-reviewed scientific journal, book, conference proceedings, or thesis. Data used in publications that are in preparation or in review can be submitted to TreeBASE but will not be available to the public until they have passed peer review.

Proper citation: TreeBASE (RRID:SCR_005688) Copy   

•   Source: SciCrunch Registry