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https://github.com/neuropoly/qMRLab
Software for quantitative MR image analysis, simulation, and protocol optimization. It aims to provide the community with a tool for data fitting, plotting, simulation and protocol optimization for a variety of different quantitative models.
Proper citation: qMRLab (RRID:SCR_016256) Copy
Center that is part of the NIH Library of Integrated Network-based Cellular Signatures (LINCS) Program. Its goals are to collect and disseminate data and analytical tools needed to understand how human cells respond to perturbation by drugs, the environment, and mutation.
Proper citation: HMS LINCS Center (RRID:SCR_016370) Copy
https://www.med.upenn.edu/cbica/captk/
Software platform for analysis of radiographic cancer images. Used as quantitative imaging analytics for precision diagnostics and predictive modeling of clinical outcome.
Proper citation: Cancer Imaging Phenomics Toolkit (RRID:SCR_017323) Copy
Software toolbox for quantitative MRI in neuroscience and clinical research. Open source and flexible tool for qMRI data handling and processing. Allows estimation of high quality multi parameter qMRI maps followed by spatial registration in common space for statistical analysis.
Proper citation: hMRI-toolbox (RRID:SCR_017682) Copy
https://www.mbfbioscience.com/stereo-investigator-cleared-tissue-edition
Software tool for unbiased stereology to be used on cleared tissue. Used to analyze intact, cleared tissue specimens imaged with light sheet or confocal microscopes. Includes number, length, area and volume analyses.
Proper citation: Stereo Investigator - Cleared Tissue Edition (RRID:SCR_017668) Copy
https://edspace.american.edu/openbehavior/project/argus/
Portal provides software tool for analysis and quantification of both single and socially interacting zebrafish. Software data extraction and analysis tool built in open source R language for tracking zebrafish behavior.
Proper citation: Argus (RRID:SCR_021585) Copy
GenMAPP is a free computer application designed to visualize gene expression and other genomic data on maps representing biological pathways and groupings of genes. Integrated with GenMAPP are programs to perform a global analysis of gene expression or genomic data in the context of hundreds of pathway MAPPs and thousands of Gene Ontology Terms (MAPPFinder), import lists of genes/proteins to build new MAPPs (MAPPBuilder), and export archives of MAPPs and expression/genomic data to the web. The main features underlying GenMAPP are: *Draw pathways with easy to use graphics tools *Color genes on MAPP files based on user-imported genomic data *Query data against MAPPs and the GeneOntology Enhanced features include the simultaneous view of multiple color sets, expanded species-specific gene databases and custom database options.
Proper citation: Gene Map Annotator and Pathway Profiler (RRID:SCR_005094) Copy
A Web-based Tool for High-throughput Primer and Probe Design. The program has its different utilities available on its web server. A standalone version is also available. Algorithms: * SSPD - Sequence Specific Primer Design: to design primers for each of the specific sequences given by the user in the query input file against any alternate potential hybridization with any of the sequences given in the database input file. * PSPD - Probe Specific Primer Design: to design primers it selects the gene-specific fragments (probes) to design primer pairs for their PCR amplification. * FSPD Fragment Specific Primer Design: primer design algorithm used when there is a very long query sequence for which multiple primers are required for its amplification. * Check Binding Specificity * Probe Design Only: Probe design algorithm could be used to find sequence-specific probes, which doesn''t show any blast hit against database. Such probe design has been used for targeted sequencing like agilent sure-select technology with next-generation sequencing.
Proper citation: PRIMEGENS (RRID:SCR_005474) Copy
http://bowtie-bio.sourceforge.net/index.shtml
Software ultrafast memory efficient tool for aligning sequencing reads. Bowtie is short read aligner.
Proper citation: Bowtie (RRID:SCR_005476) Copy
https://www.mirion.com/products/genie-2000-basic-spectroscopy-software
Software tool as comprehensive environment for data acquisition, display and analysis of gamma and alpha spectrometry data.
Proper citation: Genie 2000 Basic (RRID:SCR_021933) Copy
A tool for performing multi-cluster gene functional enrichment analyses on large scale data (microarray experiments with many time-points, cell-types, tissue-types, etc.). It facilitates co-analysis of multiple gene lists and yields as output a rich functional map showing the shared and list-specific functional features. The output can be visualized in tabular, heatmap or network formats using built-in options as well as third-party software. It uses the hypergeometric test to obtain functional enrichment achieved via the gene list enrichment analysis option available in ToppGene.
Proper citation: ToppCluster (RRID:SCR_001503) Copy
Freely accessible phenotype-centered database with integrated analysis and visualization tools. It combines diverse data sets from multiple species and experiment types, and allows data sharing across collaborative groups or to public users. It was conceived of as a tool for the integration of biological functions based on the molecular processes that subserved them. From these data, an empirically derived ontology may one day be inferred. Users have found the system valuable for a wide range of applications in the arena of functional genomic data integration.
Proper citation: Gene Weaver (RRID:SCR_003009) Copy
https://github.com/QMICodeBase/TORTOISEV4
An integrated and flexible software package for processing of DTI data, and in general for the correction of diffusion weighted images to be used for DTI and potentially for high angular resolution diffusion imaging (HARDI) analysis. It can be run on both Linux and Mac platforms. It is composed of two modules named DIFF PREP and DIFF CALC. * DIFF_PREP - software for image resampling, motion, eddy current distortion and susceptibility induced EPI distortion corrections, and for re-orientation of data to a common space * DIFF_CALC - software for tensor fitting, error analysis, color map visualization and ROI analysis In addition, TORTOISE contains additional Utilities, such as a tool for the analysis of multi-center phantom data.
Proper citation: TORTOISE (RRID:SCR_001645) Copy
http://seer.cancer.gov/resources/
Portal provides SEER research data and software SEER*Stat and SEER*Prep. SEER incidence and population data associated by age, sex, race, year of diagnosis, and geographic areas can be used to examine stage at diagnosis by race/ethnicity, calculate survival by stage at diagnosis, age at diagnosis, and tumor grade or size, determine trends and incidence rates for various cancer sites over time. SEER releases new research data every Spring based on the previous November’s submission of data.
Proper citation: SEER Datasets and Software (RRID:SCR_003293) Copy
Software library for time-series analysis of data from neuroscience experiments. It contains a core of numerical algorithms for time-series analysis both in the time and spectral domains, a set of container objects to represent time-series, and auxiliary objects that expose a high level interface to the numerical machinery and make common analysis tasks easy to express with compact and semantically clear code.
Proper citation: Nitime (RRID:SCR_002504) Copy
https://www.ncbi.nlm.nih.gov/geo/
Functional genomics data repository supporting MIAME-compliant data submissions. Includes microarray-based experiments measuring the abundance of mRNA, genomic DNA, and protein molecules, as well as non-array-based technologies such as serial analysis of gene expression (SAGE) and mass spectrometry proteomic technology. Array- and sequence-based data are accepted. Collection of curated gene expression DataSets, as well as original Series and Platform records. The database can be searched using keywords, organism, DataSet type and authors. DataSet records contain additional resources including cluster tools and differential expression queries.
Proper citation: Gene Expression Omnibus (GEO) (RRID:SCR_005012) Copy
http://vortex.cs.wayne.edu/projects.htm#Onto-Compare
Microarrays are at the center of a revolution in biotechnology, allowing researchers to screen tens of thousands of genes simultaneously. Typically, they have been used in exploratory research to help formulate hypotheses. In most cases, this phase is followed by a more focused, hypothesis driven stage in which certain specific biological processes and pathways are thought to be involved. Since a single biological process can still involve hundreds of genes, microarrays are still the preferred approach as proven by the availability of focused arrays from several manufacturers. Since focused arrays from different manufacturers use different sets of genes, each array will represent any given regulatory pathway to a different extent. We argue that a functional analysis of the arrays available should be the most important criterion used in the array selection. We developed Onto-Compare as a database that can provide this functionality, based on the GO nomenclature. Compare commercially available microarrays based on GO. User account required. Platform: Online tool
Proper citation: Onto-Compare (RRID:SCR_005669) Copy
Issue
Software package for analysis of brain imaging data sequences. Sequences can be a series of images from different cohorts, or time-series from same subject. Current release is designed for analysis of fMRI, PET, SPECT, EEG and MEG.
Proper citation: SPM (RRID:SCR_007037) Copy
Chem Service, Inc. offers the convenience, cost savings and reliability of 1,000 Certified Standards Grade Organic Chemicals at your fingertips with our Organic Mini Stockroom Kit. Whether your lab is big or small, disposal fees are a concern. The Organic Mini-stockroom offers you the ability to have 1000 different chemicals at quantities ranging from 100mg to 10gm; thus, reducing disposal costs. Over 95% of their neat Standards Grade materials have a purity of 98.0% or greater, and have been analyzed by three or more (where feasible) independent methods of analysis. These do not require purity corrections when preparing a solution for use with EPA methods. Their more than 13,000 organic and inorganic standards, and solutions, support EPA Methods, ASTM Methods, State UST Methods, Air monitoring Methods, and International Methods. They offer explosive residue standards, PCB congeners, petroleum hydrocarbon standards for the petrochemical industry, pesticide standards, FAME, and vitamin standards for food analysis. Suited for identification of unknowns, product screening, optimal chemical selection and small scale chemical reactions, the O-1000A Organic Ministockroom Kit was designed for laboratories with broad chemical classification and indentification needs. Chem Service, Inc. is registered by ABS Quality Evaluations, Inc., to the internationally recognized requirements of ISO 9001 for design, development, production, distribution and servicing of organic neat and synthetic reference materials.
Proper citation: Chem Service, Inc. (RRID:SCR_008380) Copy
http://www.clcbio.com/products/clc-genomics-workbench/
Commercially available software for visualization and analysis of next generation sequencing data. Used for viewing, exploring, and sharing of NGS analysis results. Complete toolkit for genomics, transcriptomics, epigenomics, and metagenomics in one program.
Proper citation: CLC Genomics Workbench (RRID:SCR_011853) Copy
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