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https://github.com/BenLangmead/bsmooth-align

Software statistics and alignment pipeline that performs the alignment of bisulfite sequence reads and tabulates read-level methylation measurements.

Proper citation: BSmooth-align (RRID:SCR_000013) Copy   

•   Source: SciCrunch Registry

http://srf.sourceforge.net/

A generic format for DNA sequence data. The primary motivation for creating SRF has been to enable a single format capable of storing data generated by any DNA sequencing technology.

Proper citation: Sequence Read Format (RRID:SCR_000132) Copy   

•   Source: SciCrunch Registry

http://www.epilepsygenetics.eu/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 16,2023. Group of clinical care and epilepsy research centers who are committed to improving the lives of people with epilepsy through an understanding of the genetics of epilepsy. The consoritum was in an effort to speed discovery to epilepsy genetics by pooling the resources of several research centres., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: EPIGEN (RRID:SCR_000093) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/meshmetric3d/

Software visualization tool based on the VTK library. Its main feature is to measure and display surface-to-surface distance between two triangle meshes using user-specified uniform sampling. Offers all the basic tools to visualize meshes such as color, opacity, smoothing, down sampling or type of representation.

Proper citation: 3DMeshMetric (RRID:SCR_000043) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/gmato/files/?source=navbar

A software tool used for simple sequence repeats (SSR) or microsatellite characterization. It also facilitates SSR marker design on a genomic scale, microsatellite mining at any length, and comprehensive statistical analysis for DNA sequences in any genome at any size. Analysis parameters are customizable.

Proper citation: GMATo (RRID:SCR_000165) Copy   

•   Source: SciCrunch Registry

https://trialweb.dcri.duke.edu/tads/index.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 16,2023. Multi-site clinical research study examining the short- and long-term effectiveness of an antidepressant medication and psychotherapy alone and in combination for treating depression in adolescents ages 12 to 17. For teens treated in TADS, the trial is designed to provide best-practice practical care for depression.

Proper citation: TADS - Treatment for Adolescents with Depression Study (RRID:SCR_000037) Copy   

•   Source: SciCrunch Registry

http://sw-tools.pdb.org/index.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Information Portal to Biological Macromolecular Structures provides variety of software tools made available through the RCSB. These tools include: data extraction and deposition preparation tools, data format conversion and validation tools, data parsing tools, dictionary and data management tools, visualization tools that support PDBx/mmCIF, and other PDBx/mmCIF software library tools.

Proper citation: RCSB PDB Software Tools (RRID:SCR_000035) Copy   

•   Source: SciCrunch Registry

http://bioconductor.org/packages/release/bioc/html/DESeq.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 30,2023. Software for differential gene expression analysis based on the negative binomial distribution. It estimates variance-mean dependence in count data from high-throughput sequencing assays and tests for differential expression.

Proper citation: DESeq (RRID:SCR_000154) 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://code.google.com/p/gasv/

Software tool for identifying structural variants (SVs) from paired-end sequencing data.GASV distribution includes three components that are typically run in succession: the BAM file of unique paired-read mappings is processed; structural variants are identified by clustering discordant fragments; and a probabilistic algorithm improves the specificity of GASV predictions.

Proper citation: GASV (RRID:SCR_000061) Copy   

•   Source: SciCrunch Registry

http://www.cdisc.org/

A global, open, multidisciplinary, non-profit organization that has established standards to support the acquisition, exchange, submission and archive of clinical research data and metadata. Its mission is to develop and support global, platform-independent data standards that enable information system interoperability to improve medical research and related areas of healthcare. CDISC standards are vendor-neutral, platform-independent and freely available via the CDISC website.

Proper citation: Clinical Data Interchange Standards Consortium (RRID:SCR_000219) Copy   

•   Source: SciCrunch Registry

http://knightadrc.wustl.edu/

The Charles F. and Joanne Knight Alzheimer Disease Research Center (Knight ADRC) supports researchers and our surrounding community in their pursuit of answers that will lead to improved diagnosis and care for persons with Alzheimer disease (AD). The Center is committed to the long-term goal of finding a way to effectively treat and prevent AD. The Knight ADRC facilitates advanced research on the clinical, genetic, neuropathological, neuroanatomical, biomedical, psychosocial, and neuropsychological aspects of Alzheimer disease, as well as other related brain disorders.

Proper citation: Washington University School of Medicine Knight Alzheimers Disease Research Center (RRID:SCR_000210) Copy   

•   Source: SciCrunch Registry

http://www.wavemetrics.com/products/igorpro/igorpro.htm

Software used for visualizing and graphing data, image processing, and programming. It is designed for use by scientists and engineers and supports large data sets, evenly spaced data, and various data import formats. The software includes a suite of image processing operations for image filtering, manipulation, and quantification and is completely programmable.

Proper citation: IGOR Pro (RRID:SCR_000325) Copy   

•   Source: SciCrunch Registry

https://resource.loni.usc.edu/resources/atlases/

Probabilistic reference system for human brain, including tools to establish this reference system for structural and functional anatomy on both macroscopic (in vivo) and microscopic (post mortem) levels. Project has expanded neuroinformatics tools for data sharing and created Conforming Site System that allows laboratories worldwide to contribute data to evolving atlas. Through implementation of ICBM data sharing policy space, they are fostering data exchange while still providing for scientific credit assignment and subject confidentiality.ICBM atlas collection consists of ICBM Template, tool developed to provide reference that includes both set of coordinates and associated anatomical labels; the ICBM 452 T1 atlas, average of T1-weighted MRIs of normal young adult brains, ICBM probabilistic atlases, and Cytoarchitectonic Atlas. ICBM Subject Database is web-based database infrastructure that simplifies image dataset collection, organization and dissemination. Authorized users may view representations of data and form collections of datasets that can be downloaded or fed directly into Pipeline environment for distributed processing and analysis.

Proper citation: International Consortium for Brain Mapping (RRID:SCR_000445) Copy   

•   Source: SciCrunch Registry

http://www.talairach.org/

Software automated coordinate based system to retrieve brain labels from the 1988 Talairach Atlas. Talairach Daemon database contains anatomical names for brain areas using x-y-z coordinates defined by the 1988 Talairach Atlas.

Proper citation: Talairach Daemon (RRID:SCR_000448) Copy   

•   Source: SciCrunch Registry

http://highwire.stanford.edu/

A division of the Stanford University Libraries, which produces the online versions of journals and other scholarly content.

Proper citation: HighWire Press (RRID:SCR_000761) Copy   

•   Source: SciCrunch Registry

http://cbrain.mcgill.ca/loris

A modular and extensible web-based data management system that integrates all aspects of a multi-center study, from heterogeneous data acquisition to storage, processing and ultimately dissemination, within a streamlined platform. Through a standard web browser, users are able to perform a wide variety of tasks, such as data entry, 3D image visualization and data querying. LORIS also stores data independently from any image processing pipeline, such that data can be processed by external image analysis software tools. LORIS provides a secure web-based and database-driven infrastructure to automate the flow of clinical data for complex multi-site neuroimaging trials and studies providing researchers with the ability to easily store, link, and access significant quantities of both scalar (clinical, psychological, genomic) and multi-dimensional (imaging) data. LORIS can collect behavioral, neurological, and imaging data, including anatomical and functional 3D/4D MRI models, atlases and maps. LORIS also functions as a project monitoring and auditing platform to oversee data acquisition across multiple study sites. Confidentiality during multi-site data sharing is provided by the Subject Profile Management System, which can perform automatic removal of confidential personal information and multiple real-time quality control checks. Additionally, web interactions with the LORIS portal take place over an encrypted channel via SSL, ensuring data security. Additional features such as Double Data Entry and Statistics and Data Query GUI are included.

Proper citation: LORIS - Longitudinal Online Research and Imaging System (RRID:SCR_000590) Copy   

•   Source: SciCrunch Registry

http://athina.biol.uoa.gr/CAST/

A novel algorithm for low-complexity region detection and selective masking. The algorithm is based on multiple-pass Smith-Waterman comparison of the query sequence against twenty homopolymers with infinite gap penalties. The output of the algorithm is both the masked query sequence for further analysis, e.g. database searches, as well as the regions of low complexity.

Proper citation: CAST (RRID:SCR_000628) Copy   

•   Source: SciCrunch Registry

http://fcp-indi.github.io

A configurable, open-source, Nipype-based, automated processing pipeline for resting state functional MRI (R-fMRI) data, for use by both novice and expert users. C-PAC was designed to bring the power, flexibility and elegance of the Nipype platform to users in a plug and play fashion?without requiring the ability to program. Using an easy to read, text-editable configuration file, C-PAC can rapidly orchestrate automated R-fMRI processing procedures, including: - quality assurance measurements - image preprocessing based upon user specified preferences - generation of functional connectivity maps (e.g., correlation analyses) - customizable extraction of time-series data - generation of local R-fMRI metrics (e.g., regional homogeneity, voxel-matched homotopic connectivity, fALFF/ALFF) C-PAC makes it possible to use a single configuration file to launch a factorial number of pipelines differing with respect to specific processing steps.

Proper citation: C-PAC (RRID:SCR_000862) Copy   

•   Source: SciCrunch Registry

http://genboree.org

A software application and database viewing system for genomic research, more specifically formulti-genome comparison and pattern discovery via genome self-comparison. Data are available for a range of species including Human Chr3, Human Chr12, Sea Urchin, Tribolium, and cow. The Genboree Discovery System is the largest software system developed at the bioinformatics laboratory at Baylor in close collaboration with the Human Genome Sequencing Center. Genboree is a turnkey software system for genomic research. Genboree is hosted on the Internet and, as of early 2007, the number of registered users exceeds 600. While it can be configured to support almost any genome-centric discovery process, a number of configurations already exist for specific applications. Current focus is on enabling studies of genome variation, including array CGH studies, PCR-based resequencing, genome resequencing using comparative sequence assembly, genome remapping using paired-end tags and sequences, genome analysis and annotation, multi-genome comparison and pattern discovery via genome self-comparison. Genboree database and visualization settings, tools, and user roles are configurable to fit the needs of specific discovery processes. Private permanent project-specific databases can be accessed in a controlled way by collaborators via the Internet. Project-specific data is integrated with relevant data from public sources such as genome browsers and genomic databases. Data processing tools are integrated using a plug-in model. Genboree is extensible via flexible data-exchange formats to accommodate project specific tools and processing steps. Our Positional Hashing method, implemented in the Pash program, enables extremely fast and accurate sequence comparison and pattern discovery by employing low-level parallelism. Pash enables fast and sensitive detection of orthologous regions across mammalian genomes, and fast anchoring of hundreds of millions of short sequences produced by next-generation sequencing technologies. We are further developing the Pash program and employing it in the context of various discovery pipelines. Our laboratory participates in the pilot stage of the TCGA (The Cancer Genome Atlas) project. We aim to develop comprehensive, rapid, and economical methods for detecting recurrent chromosomal aberrations in cancer using next-generation sequencing technologies. The methods will allow detection of recurrent chromosomal aberrations in hundreds of small (

Proper citation: Genboree Discovery System (RRID:SCR_000747) Copy   

•   Source: SciCrunch Registry