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http://www.rnasoft.ca/sstrand

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A scientific community-crowdsourced database containing the RNA secondary structures of known types and organisms. It is meant to provide a simple and powerful way to analyze, search and update a shared repository of information.

Proper citation: RNA STRAND-The RNA secondary STRucture and statistical ANalysis Database (RRID:SCR_000086) Copy   

•   Source: SciCrunch Registry

http://neuralensemble.org/sumatra/

A software tool for managing and tracking projects based on numerical simulation or analysis to support reproducible research. It can be thought of as an automated electronic lab notebook for simulation/analysis projects. Sumatra consists of: a command-line interface, smt, for launching simulations/analyses with automatic recording of information about the context, annotating these records, linking to data files, etc.; a web interface with a built-in web-server, smtweb, for browsing and annotating simulation/analysis results; a LaTeX package and Sphinx extension for including Sumatra-tracked figures and links to provenance information in papers and other documents; and a Python API, on which smt and smtweb are based, that can be used in personalized scripts in place of using smt.

Proper citation: Sumatra (RRID:SCR_001381) Copy   

•   Source: SciCrunch Registry

http://dirt.projectbamboo.org/

Registry of digital research tools for scholarly use that makes it easy for digital humanists and others conducting digital research to find and compare resources ranging from content management systems to music OCR, statistical analysis packages to mindmapping software., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Bamboo DiRT (RRID:SCR_002556) Copy   

•   Source: SciCrunch Registry

http://analysis2.bio-x.cn/myAnalysis.php

A powerful web-based platform for analyses of linkage disequilibrium, haplotype construction, and genetic association at polymorphism loci.

Proper citation: SHEsis: Analysis Tools For Random Samples (RRID:SCR_002958) Copy   

•   Source: SciCrunch Registry

http://rfmri.org/DPARSF

A MATLAB toolbox forpipeline data analysis of resting-state fMRI that is based on Statistical Parametric Mapping (SPM) and a plug-in software within DPABI. After the user arranges the Digital Imaging and Communications in Medicine (DICOM) files and click a few buttons to set parameters, DPARSF will then give all the preprocessed (slice timing, realign, normalize, smooth) data and results for functional connectivity, regional homogeneity, amplitude of low-frequency fluctuation (ALFF), fractional ALFF, degree centrality, voxel-mirrored homotopic connectivity (VMHC) results. DPARSF can also create a report for excluding subjects with excessive head motion and generate a set of pictures for easily checking the effect of normalization. In addition, users can also use DPARSF to extract time courses from regions of interest. DPARSF basic edition is very easy to use while DPARSF advanced edition (alias: DPARSFA) is much more flexible and powerful. DPARSFA can parallel the computation for each subject, and can be used to reorient images interactively or define regions of interest interactively. Users can skip or combine the processing steps in DPARSF advanced edition freely.

Proper citation: DPARSF (RRID:SCR_002372) Copy   

•   Source: SciCrunch Registry

https://www.upf.edu/web/ntsa/downloads/-/asset_publisher/xvT6E4pczrBw/content/2012-nonrandomness-nonlinear-dependence-and-nonstationarity-of-electroencephalographic-recordings-from-epilepsy-patients

THIS RESOURCE IS NO LONGER IN SERVICE, documented November 23, 2020; EEG data set, source code, and results from 7500 signal pairs from 5 epilepsy patients analyzed in the manuscript, Andrzejak RG, Schindler K, Rummel C. Nonrandomness, nonlinear dependence, and nonstationarity of electroencephalographic recordings from epilepsy patients. Phys. Rev. E, 86, 046206, 2012. All Matlab source codes are included in the file ASR_Sources_2012_10_16.zip. The clinical purpose of these recordings was to delineate the brain areas to be surgically removed in each individual patient in order to achieve seizure control.

Proper citation: Bern-Barcelona EEG database (RRID:SCR_001582) Copy   

•   Source: SciCrunch Registry

http://www.genetrap.org/

Consortium represents all publicly available gene trap cell lines, which are available on non-collaborative basis for nominal handling fees. Researchers can search and browse IGTC database for cell lines of interest using accession numbers or IDs, keywords, sequence data, tissue expression profiles and biological pathways, can find trapped genes of interest on IGTC website, and order cell lines for generation of mutant mice through blastocyst injection. Consortium members include: BayGenomics (USA), Centre for Modelling Human Disease (Toronto, Canada), Embryonic Stem Cell Database (University of Manitoba, Canada), Exchangeable Gene Trap Clones (Kumamoto University, Japan), German Gene Trap Consortium provider (Germany), Sanger Institute Gene Trap Resource (Cambridge, UK), Soriano Lab Gene Trap Resource (Mount Sinai School of Medicine, New York, USA), Texas Institute for Genomic Medicine - TIGM (USA), TIGEM-IRBM Gene Trap (Naples, Italy).

Proper citation: International Gene Trap Consortium (RRID:SCR_002305) Copy   

•   Source: SciCrunch Registry

http://icatb.sourceforge.net/fusion/fusion_startup.php

A MATLAB toolbox which implements the joint Independent Component Analysis (ICA), parallel ICA and CCA with joint ICA methods. It is used to to extract the shared information across modalities like fMRI, EEG, sMRI and SNP data. * Environment: Win32 (MS Windows), Gnome, KDE * Operating System: MacOS, Windows, Linux * Programming Language: MATLAB * Supported Data Format: ANALYZE, NIfTI-1

Proper citation: Fusion ICA Toolbox (RRID:SCR_003494) Copy   

•   Source: SciCrunch Registry

http://gephi.org/

Open-source software for network visualization and analysis helping data analysts to intuitively reveal patterns and trends, highlight outliers and tells stories with their data. It uses a 3D render engine to display large graphs in real-time and to speed up the exploration. Gephi combines built-in functionalities and flexible architecture to: explore, analyze, spatialize, filter, cluterize, manipulate and export all types of networks. Gephi runs on Windows, Linux and Mac OS X. Gephi is based on a visualize-and-manipulate paradigm which allow any user to discover networks and data properties. Moreover, it is designed to follow the chain of a case study, from data file to nice printable maps. It is open-source and free (GNU General Public License). Applications: * Exploratory Data Analysis: intuition-oriented analysis by networks manipulations in real time. * Link Analysis: revealing the underlying structures of associations between objects, in particular in scale-free networks. * Social Network Analysis: easy creation of social data connectors to map community organizations and small-world networks. * Biological Network analysis: representing patterns of biological data. * Poster creation: scientific work promotion with hi-quality printable maps. Gephi 0.7 architecture is modular and therefore allows developers to add and extend functionalities with ease. New features like Metrics, Layout, Filters, Data sources and more can be easily packaged in plugins and shared. The built-in Plugins Center automatically gets the list of plugins available from the Gephi Plugin portal and takes care of all software updates. Download, comment, and rate plugins provided by community members and third-party companies, or post your own contributions!

Proper citation: Gephi (RRID:SCR_004293) Copy   

•   Source: SciCrunch Registry

http://bioinformatics.biol.rug.nl/standalone/fiva/

Functional Information Viewer and Analyzer (FIVA) aids researchers in the prokaryotic community to quickly identify relevant biological processes following transcriptome analysis. Our software is able to assist in functional profiling of large sets of genes and generates a comprehensive overview of affected biological processes. Currently, seven different modules containing functional information have been implemented: (i) gene regulatory interactions, (ii) cluster of orthologous groups (COG) of proteins, (iii) gene ontologies (GO), (iv) metabolic pathways (v) Swiss Prot keywords, (vi) InterPro domains - and (vii) generic functional categories. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible

Proper citation: FIVA - Functional Information Viewer and Analyzer (RRID:SCR_005776) Copy   

•   Source: SciCrunch Registry

http://ftp://ftp.geneontology.org/pub/go/www/GO.tools_by_type.term_enrichment.shtml#gobean

GoBean is a Java application for gene ontology enrichment analysis. It utilizes the NetBeans platform framework. Features * Graphical comparison of multiple enrichment analysis results * Versatile filter facility for focused analysis of enrichment results * Effective exploitation of the graphical/hierarchical structure of GO * Evidence code based association filtering * Supports local data files such as the ontology obo file and gene association files * Supports late enrichment methods and multiple testing corrections * Built-in ID conversion for common species using Ensembl biomart service Platform: Windows compatible, Mac OS X compatible, Linux compatible

Proper citation: GoBean - a Java application for Gene Ontology enrichment analysis (RRID:SCR_005808) Copy   

•   Source: SciCrunch Registry

http://www.seqexpress.com/

A comprehensive analysis and visualization software package for gene expression experiments that provides: a number of clustering and analysis techniques; integrated gene expression and analysis result visualizations, integration with the Gene Expression Omnibus; and an optional data sharing architecture. GO is used to assign functional enrichment scores to clusters, using a combination of specially developed techniques and general statistical methods. These results can be explored using the in built ontology browsing tool or through the generated web pages. SeqExpress also supports numerous data transformation, projection, visualization, file export/import, searching, integration (with R), and clustering options.

Proper citation: SeqExpress (RRID:SCR_007075) Copy   

•   Source: SciCrunch Registry

http://www.nih.gov/science/brain/

Project aimed at revolutionizing understanding of human brain, to show how individual cells and complex neural circuits interact, enable rapid progress in development of new technologies and data analysis tools to treat and prevent brain disorders. BRAIN Initiative encourages collaborations between neurobiologists and scientists from disciplines such as statistics, physics, mathematics, engineering, and computer and information sciences. Institutes and centers contributing to NIH BRAIN Initiative support those research efforts.

Proper citation: BRAIN Initiative (RRID:SCR_006770) Copy   

•   Source: SciCrunch Registry

http://amp.pharm.mssm.edu/l2n/upload/register.php

A web-based software system that allows users to upload lists of mammalian genes/proteins onto a server-based program for integrated analysis. The system includes web-based tools to manipulate lists with different set operations, to expand lists using existing mammalian networks of protein-protein interactions, co-expression correlation, or background knowledge co-annotation correlation, as well as to apply gene-list enrichment analyses against many gene-list libraries of prior biological knowledge such as pathways, gene ontology terms, kinase-substrate, microRNA-mRAN, and protein-protein interactions, metabolites, and protein domains. Such analyses can be applied to several lists at once against many prior knowledge libraries of gene-lists associated with specific annotations. The system also contains features that allow users to export networks and share lists with other users of the system.

Proper citation: Lists2Networks (RRID:SCR_006323) Copy   

•   Source: SciCrunch Registry

http://cbl-gorilla.cs.technion.ac.il/

A tool for identifying and visualizing enriched GO terms in ranked lists of genes. It can be run in one of two modes: * Searching for enriched GO terms that appear densely at the top of a ranked list of genes or * Searching for enriched GO terms in a target list of genes compared to a background list of genes.

Proper citation: GOrilla: Gene Ontology Enrichment Analysis and Visualization Tool (RRID:SCR_006848) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://nipy.org/nitime/

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   

•   Source: SciCrunch Registry

Issue

https://github.com/spm

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://www.chemservice.com

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   

•   Source: SciCrunch Registry