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

Software package to perform Granger mediation analysis for time series. Includes single level GMA model and two-level GMA model, for time series with hierarchically nested structure.

Proper citation: GMA (RRID:SCR_009212) Copy   

•   Source: SciCrunch Registry

http://www.readout.info

Matlab toolbox that makes it easy to apply decoding analyses to neural data. The design of the toolbox revolves around four abstract object classes which enables users to interchange particular modules in order to try different analyses while keeping the rest of the processing stream intact. The toolbox is capable of analyzing data from many different types of recording modalities, and examples are given on how it can be used to decode basic visual information from neural spiking activity and how it can be used to examine how invariant the activity of a neural population is to stimulus transformations.

Proper citation: Neural Decoding Toolbox (RRID:SCR_009012) Copy   

•   Source: SciCrunch Registry

http://www.arrayserver.com/wiki/index.php?title=ArrayStudio_Online_Help

Software package which provides statistics and visualization for analysis of high dimensional quantification data including microarray or RTPCR data or Taqman data, genotype data including SNP or Copy Number data and Next Generation Sequencing data. Provides integrated environment for analyzing and visualizing high dimensional data.

Proper citation: Array Studio (RRID:SCR_010970) Copy   

•   Source: SciCrunch Registry

http://bioinf.wehi.edu.au/limma/

Software package for the analysis of gene expression microarray data, especially the use of linear models for analyzing designed experiments and the assessment of differential expression.

Proper citation: LIMMA (RRID:SCR_010943) Copy   

•   Source: SciCrunch Registry

http://www.moleculardevices.com/products/software/pclamp.html

Software suite for electrophysiology data acquisition and analysis by Molecular Devices. Used for the control and recording of voltage clamp, current clamp, and patch clamp experiments. The software suite consists of Clampex 11 Software for data acquisition, AxoScope 11 Software for background recording, Clampfit 11 Software for data analysis, and optional Clampfit Advanced Analysis Module for sophisticated and streamlined analysis.

Proper citation: pClamp (RRID:SCR_011323) Copy   

•   Source: SciCrunch Registry

http://homer.ucsd.edu/

Software tools for Motif Discovery and next-gen sequencing analysis. Used for analyzing ChIP-Seq, GRO-Seq, RNA-Seq, DNase-Seq, Hi-C and numerous other types of functional genomics sequencing data sets. Collection of command line programs for unix style operating systems written in Perl and C++.

Proper citation: HOMER (RRID:SCR_010881) Copy   

•   Source: SciCrunch Registry

http://www.geenivaramu.ee/en/tools/gwama

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software tool for meta analysis of whole genome association data.

Proper citation: GWAMA (RRID:SCR_006624) Copy   

•   Source: SciCrunch Registry

http://www.leaddiscovery.co.uk/

LeadDiscovery was founded by life scientists to expedite drug discovery and pharmaceutical development. Based on a solid background of experience from within the pharmaceutical research and development sector, the aim of this resource is to help companies optimize drug discovery and product pipelines through the identification of breaking research and the in depth and expert evaluation of selected therapeutic areas. At the same time it also provides a showcase for pharmaceutical, biotechnology and academic organizations wishing to increase the exposure of their research to the drug development community. LeadDiscovery sits at the center of this sector helping companies to identify commercially viable R&D options from within small biotechs and the public sector. Additionally, it supports the drug discovery and pharmaceutical development community through three key services: DailyUpdates, UpdatesPlus and PharmaReports - DailyUpdates: Launched in 2002 this popular e-mail alert service delivers information on breaking research, new clinical trials, drug development news and recently published market research and pipeline analysis reports. Registration to receive the service is available here - UpdatesPlus: Developed in 2007 as an extension of DailyUpdates, UpdatesPlus provides a monthly in depth analysis of breaking research and development activity in high profile therapeutic areas. - PharmaReports: LeadDiscovery offers a wide range of in depth pharmaceutical reports. It''s reports include market research reports and pipeline analyses. You can search our entire portfolio using LeadDiscovery''s search engine. Alternatively as it are one of the few information providers that has extensive research and development experience, LeadDiscovery occupys a unique position of being able to source reports that accurately meet your needs. If we don''t have a report that fits your requirements, it can produce one through its pharmaceutical consultancy services. LeadDiscovery offers full reports in selected areas of the pharmaceutical and biotech sector. Each of the reports below has been especially selected by LeadDiscovery and categorized into relevant areas: - Oncology - Cancer Immunotherapy - Immunology & Inflammatory Diseases - Infectious Diseases - Psychiatric, Addictive & Sleep Disorders - Pain - Neurodegenerative & Neuroelectrophysiological Disorders - Metabolic & Hormonal Disorders - Cardiovascular Disorders - GenitoUrinary Tract Disorders - Technology - Diagnostics & Devices - Other Theraputic Areas, Pharmaceutical Strategy and Development

Proper citation: LeadDiscovery: Providing Information to the Drug Discovery Sector (RRID:SCR_006464) Copy   

•   Source: SciCrunch Registry

http://bioconductor.org/packages/bioc/html/GeneAnswers.html

GeneAnswers provide an integrated tool for given genes biological or medical interpretation. It includes statistical test of given genes and specified categories. Microarray techniques have been widely employed in genomic scale studies for more than one decade. The standard analysis of microarray data is to filter out a group of genes from thousands of probes by certain statistical criteria. These genes are usually called significantly differentially expressed genes. Recently, next generation sequencing (NGS) is gradually adopted to explore gene transcription, methylation, etc. Also a gene list can be obtained by NGS preliminary data analysis. However, this type of information is not enough to understand the potential linkage between identified genes and interested functions. The integrated functional and pathway analysis with gene expression data would be very helpful for researchers to interpret the relationship between the identified genes and proposed biological or medical functions and pathways. The GeneAnswers package provides an integrated solution for a group of genes and specified categories (biological or medical functions, such as Gene Ontology, Disease Ontology, KEGG, etc) to reveal the potential relationship between them by means of statistical methods, and make user-friendly network visualization to interpret the results. Besides the package has a function to combine gene expression profile and category analysis together by outputting concept-gene cross tables, keywords query on NCBI Entrez Gene and application of human based Disease ontology analysis of given genes from other species can help people to understand or discover potential connection between genes and functions. Sponsors: This project was supported in part by Award Number UL1RR025741 from the National Center for Research Resources.

Proper citation: GeneAnswers (RRID:SCR_006498) Copy   

•   Source: SciCrunch Registry

http://www.physionet.org/physiotools/

Growing library of software for physiologic signal processing and analysis, detection of physiologically significant events using both classical techniques and novel methods based on statistical physics and nonlinear dynamics, interactive display and characterization of signals, creation of new databases, simulation of physiologic and other signals, quantitative evaluation and comparison of analysis methods, and analysis of nonequilibrium and nonstationary processes. A unifying theme of the research projects that contribute software to PhysioToolkit is the extraction of hidden information from biomedical signals, information that may have diagnostic or prognostic value in medicine, or explanatory or predictive power in basic research. Contributions of software to PhysioToolkit are welcome, http://physionet.org/guidelines.shtml#software-contributions

Proper citation: PhysioToolkit (RRID:SCR_006868) Copy   

•   Source: SciCrunch Registry

http://scicrunch.org

THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 27, 2019.

Database for those interested in the consequences of Factor VIII genetic variation at the DNA and protein level, it provides access to data on the molecular pathology of haemophilia A. The database presents a review of the structure and function of factor VIII and the molecular genetics of haemophilia A, a real time update of the biostatistics of each parameter in the database, a molecular model of the A1, A2 and A3 domains of the factor VIII protein (based on the crystal structure of caeruloplasmin) and a bulletin board for discussion of issues in the molecular biology of factor VIII. The database is completely updated with easy submission of point mutations, deletions and insertions via e-mail of custom-designed forms. A methods section devoted to mutation detection is available, highlighting issues such as choice of technique and PCR primer sequences. The FVIII structure section now includes a download of a FVIII A domain homology model in Protein Data Bank format and a multiple alignment of the FVIII amino-acid sequences from four species (human, murine, porcine and canine) in addition to the virtual reality simulations, secondary structural data and FVIII animation already available. Finally, to aid navigation across this site, a clickable roadmap of the main features provides easy access to the page desired. Their intention is that continued development and updating of the site shall provide workers in the fields of molecular and structural biology with a one-stop resource site to facilitate FVIII research and education. To submit your mutants to the Haemophilia A Mutation Database email the details. (Refer to Submission Guidelines)

Proper citation: HAMSTeRS - The Haemophilia A Mutation Structure Test and Resource Site (RRID:SCR_006883) Copy   

•   Source: SciCrunch Registry

http://geneontology.org/docs/tools-overview/

Collection of tools developed by GO Consortium and by third parties. Tools are listed by category or alphabetically and continue to be improved and expanded.

Proper citation: Gene Ontology Tools (RRID:SCR_006941) Copy   

•   Source: SciCrunch Registry

http://microbetracker.org/

THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone. Software for bacterial microscopy image analysis. It is designed to detect and outline bacterial cells in microscopy images and to analyze fluorescence signal inside them.

Proper citation: MicrobeTracker (RRID:SCR_015939) Copy   

•   Source: SciCrunch Registry

https://github.com/harry-thorpe/piggy

Pipeline for analyzing intergenic regions in bacteria. It is designed to be used in conjunction with Roary (https://github.com/sanger-pathogens/Roary).

Proper citation: Piggy (RRID:SCR_015941) Copy   

•   Source: SciCrunch Registry

http://molevol.cmima.csic.es/castresana/Gblocks_server.html

Software that eliminates poorly aligned positions and divergent regions of a DNA or protein alignment so that it becomes more suitable for phylogenetic analysis., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Gblocks (RRID:SCR_015945) Copy   

•   Source: SciCrunch Registry

http://www.fsm.ethz.ch/publications-list/software.html

Software for tracking and analysis based on algorithms describing structural and topological features of fiber-like objects. The program operates on images from any microscopic source (atomic force or transmission electron microscopy, optical, fluorescence, confocal, etc.), acquiring the spatial coordinates of objects.

Proper citation: FiberApp (RRID:SCR_015826) Copy   

•   Source: SciCrunch Registry

https://genome.tugraz.at/genesisclient/genesisclient_description.shtml

Software for cluster analysis of microarray data. Genesis is a platform independent Java package of tools to simultaneously visualize and analyze a whole set of gene expression experiments.

Proper citation: Genesis (RRID:SCR_015775) Copy   

•   Source: SciCrunch Registry

https://github.com/ABCD-STUDY/DEAP

Web service for data exploration and analysis of the ABCD Study - the largest long-term study of brain development and child health in the United States.

Proper citation: DEAP - Data Exploration and Analysis Portal (RRID:SCR_016158) Copy   

•   Source: SciCrunch Registry

http://hyphy.org/

Open source software package for comparative sequence analysis using stochastic evolutionary models. Used for analysis of genetic sequence data in particular the inference of natural selection using techniques in phylogenetics, molecular evolution, and machine learning.

Proper citation: HyPhy (RRID:SCR_016162) Copy   

•   Source: SciCrunch Registry

https://sanger-pathogens.github.io/gubbins/

Software application as an algorithm that iteratively identifies loci containing elevated densities of base substitutions while concurrently constructing a phylogeny based on the putative point mutations outside of these regions. It is used for phylogenetic analysis of genome sequences and generating highly accurate reconstructions under realistic models of short-term bacterial evolution., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Gubbins (RRID:SCR_016131) Copy   

•   Source: SciCrunch Registry