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http://www.bioconductor.org/packages/release/bioc/html/rBiopaxParser.html

A software package that provides a comprehensive set of functions for parsing, viewing and modifying BioPAX pathway data within R. At the moment BioPAX level 2 and level 3 are supported.

Proper citation: rBiopaxParser (RRID:SCR_002744) Copy   

•   Source: SciCrunch Registry

http://sncid.stanleyresearch.org/

A database of 1749 neuropathological markers measured in 12 different brain regions from 60 brains in the Consortium Collection from the Stanley Medical Research Institute combined with microarray data and statistical tools. Fifteen brains each are from patients diagnosed with schizophrenia, bipolar disorder, or major depression, and unaffected controls. The four groups are matched by age, sex, race, postmortem interval, pH, side of brain, and mRNA quality. A Repository of raw data is also included. Users must register for access.

Proper citation: Stanley Neuropathology Consortium Integrative Database (RRID:SCR_002749) Copy   

•   Source: SciCrunch Registry

http://www.cuni.cz/UKEN-1.html

Research university located in Prague, Czech Republic.

Proper citation: Charles University; Prague; Czech Republic (RRID:SCR_002931) Copy   

•   Source: SciCrunch Registry

http://www.genox.com

Biotechnological company that produces and supplies materials to oxidative stress and aging researchers.

Proper citation: Genox Corpooration (RRID:SCR_002930) Copy   

•   Source: SciCrunch Registry

http://biohealth.snu.ac.kr/software/TRAP/

A comprehensive software package integrating all necessary tasks such as mapping short reads, measuring gene expression levels, finding differentially expressed genes (DEGs), clustering and pathway analysis for time-series data in a single environment.

Proper citation: Time-series RNA-seq Analysis Package (RRID:SCR_002935) Copy   

•   Source: SciCrunch Registry

http://www.cisreg.ca/

This portal leads to the numerous Wasserman Lab online software tools available for use. The following are list of active Software tools available: - ConSite: Transcription factor binding site detection using phylogenetic footprinting - dbMTN: Multiple Tissue Northern Blot Comparison Tool - Gene Set Builder: A tool for collation, curation and distribution of sets of genes - The Gene Characterization Index: a bioinformatics method for scoring the extent to which a protein-encoding gene is functionally described - JASPAR: Transcription Factor Binding Profile Database - MSCAN: Algorithm that detects clusters of transcription factor binding sites in genomic sequences - NHRscan: A computational predictor of nuclear hormone receptor binding sites - oPOSSUM: Web-based analysis of over-represented transcription factor binding sites - ORCA: Transcription factor binding site detection using phylogenetic footprinting (alternative to ConSite) - OrthoSeq: Alignment of DNA sequences - PAZAR: An open-access system for the collection and dissemination of regulatory sequence annotation - Phylofoot: Tools for phylogenetic footprinting - RAVEN: Regulatory analysis of Variation in ENhancers - SAGE2Splice: A tool that uses unmapped SAGE tags to predict novel splice junctions in the genome - TFBS: Perl modules for transcription factor binding site detection and analysis - TFCat: TFCat is a catalog of mouse and human TFs based on a reliable core collection of annotations obtained by expert review of the scientific literature. - TFe: An online encyclopedic collection of well-studied transcription factor proteins in the human, mouse, and rat genomes - Ulysses: Protein Interactions Conserved Across Evolution

Proper citation: Wasserman Lab Online Software Tools (RRID:SCR_002892) Copy   

•   Source: SciCrunch Registry

http://www.genscript.com

Commercial organization which provides life science services and products to researchers. They specialize in gene synthesis, peptide, protein, antibody and preclinical drug development service.

Proper citation: GenScript (RRID:SCR_002891) Copy   

•   Source: SciCrunch Registry

http://pfind.ict.ac.cn/software/pBuild/index.html

A software tool that can compare several search engines' results and combine them together.

Proper citation: pBuild (RRID:SCR_002929) Copy   

•   Source: SciCrunch Registry

http://www.nationalpostdoc.org/

Representative organization for postdoctoral scholars in the United States. It is member-driven and non-profit.

Proper citation: National Postdoctoral Association (RRID:SCR_002928) Copy   

•   Source: SciCrunch Registry

http://cran.r-project.org/src/contrib/Archive/aCGH.Spline/

An R package for array comparative genomic hybridization (aCGH) dye bias normalization.

Proper citation: aCGH.Spline (RRID:SCR_002927) Copy   

•   Source: SciCrunch Registry

https://github.com/GiBacci/StreamingTrim/

A DNA reads trimming software, written in Java, with which researchers are able to analyse the quality of DNA sequences in fastq files and to search for low-quality zones in a very conservative way.

Proper citation: StreamingTrim (RRID:SCR_002922) Copy   

•   Source: SciCrunch Registry

http://www.mrn.org/

Non-profit organization focused on imaging technology that is dedicated to advancing the diagnosis and treatment of mental illness and brain injury. MRN consists of an interdisciplinary association of scientists located at universities, national laboratories and research centers around the world and is focused on imaging technology and its emergence as an integral element of neuroscience investigation. The MRNs initial plan called for the building of state-of-the-art magnetic resonance imaging (MRI) and magnetoencephalogram (MEG) neuroimaging systems to be applied to studies of mental illness. This important task was carried out by Minds initial collaborators: Massachusetts General Hospitals Martinos Biomedical Imaging Center (Harvard and MIT), the University of Minnesota, the University of New Mexico, and Los Alamos National Laboratory. Since both the Network and the mission have expanded beyond building neuroimaging tools, a comprehensive understanding of mental illness and more fundamental and systematic understanding of the brain, is possible. The MRN Mobile Imaging system is a custom designed one-of-a-kind facility.

Proper citation: Mind Research Network (RRID:SCR_002925) Copy   

•   Source: SciCrunch Registry

http://pfind.ict.ac.cn/software/pLabel/index.html

Mass spectral peak labeling software developed for proteomics research., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: pLabel (RRID:SCR_002923) Copy   

•   Source: SciCrunch Registry

https://github.com/itojal/hot_scan

A free software to detect genomic regions unusually rich in translocation breakpoints. More generally, it may be used to detect a region that is unusually rich in a given character of a binary sequence.

Proper citation: hot scan (RRID:SCR_002840) Copy   

•   Source: SciCrunch Registry

http://www.math.uh.edu/~mpapadak/centerline/

An application for the automatic segmentation and tracing of three-dimensional neuronal images.

Proper citation: centerline (RRID:SCR_002961) Copy   

•   Source: SciCrunch Registry

http://www.greenphyl.org/

A database designed for plant comparative and functional genomics based on complete genomes. It comprises complete proteome sequences from the major phylum of plant evolution. The clustering of these proteomes was performed to define a consistent and extensive set of homeomorphic plant families. Based on this, lists of gene families such as plant or species specific families and several tools are provided to facilitate comparative genomics within plant genomes. The analyses follow two main steps: gene family clustering and phylogenomic analysis of the generated families. Once a group of sequences (cluster) is validated, phylogenetic analyses are performed to predict homolog relationships such as orthologs and ultraparalogs.

Proper citation: GreenPhylDB (RRID:SCR_002834) Copy   

•   Source: SciCrunch Registry

http://www.celgene.com

An American global biotechnology company that manufactures drug therapies for cancer and inflammatory disorders. The company's major products are Thalomid (thalidomide), which is approved for the acute treatment of the cutaneous manifestations of moderate to severe erythema nodosum leprosum (ENL), as well as in combination with dexamethasone for patients with newly diagnosed multiple myeloma, and Revlimid (lenalidomide), for which the company has received FDA and EMA approval in combination with dexamethasone for the treatment of multiple myeloma patients who have received at least one prior therapy. Revlimid is also approved in the United States for the treatment of patients with transfusion-dependent anemia due to Low- or Intermediate-1-risk Myelodysplastic syndromes (MDS) associated with a deletion 5q cytogenetic abnormality with or without additional cytogenetic abnormalities. Both Thalomid and Revlimid are sold through proprietary risk-management distribution programs to ensure safe and appropriate use of these pharmaceuticals. Vidaza is approved for the treatment of patients with MDS. Celgene also receives royalties from Novartis Pharma AG on sales of the entire Ritalin family of drugs, which are widely used to treat Attention Deficit Hyperactivity Disorder (ADHD). (Adapted from Wikipedia) There are numerous clinical trials at major medical centers using compounds from Celgene. Investigational compounds are being studied for patients with incurable hematological and solid tumor cancers, including multiple myeloma, myelodysplastic syndromes, chronic lymphocyte leukemia (CLL), non-Hodgkin's lymphoma (NHL), glioblastoma, and ovarian, pancreatic and prostate cancer.

Proper citation: Celgene (RRID:SCR_002955) Copy   

•   Source: SciCrunch Registry

http://www.mmrrc.org/

National public repository system for mutant mice. Archives and distributes scientifically valuable spontaneous and induced mutant mouse strains and ES cell lines for use by biomedical research community. Includes breeding/distribution facilities and information coordinating center. Mice strains are cryopreserved, unless live colony must be established. Live mice are supplied from production colony, from colony recovered from cryopreservation, or via micro-injection of cell line into host blastocysts. MMRRC member facilities also develop technologies to improve handling of mutant mice, including advances in assisted reproductive techniques, cryobiology, genetic analysis, phenotyping and infectious disease diagnostics.

Proper citation: Mutant Mouse Resource and Research Center (RRID:SCR_002953) Copy   

•   Source: SciCrunch Registry

http://rdock.sourceforge.net/

A fast and versatile Open Source docking software program that can be used to dock small molecules against proteins and nucleic acids.

Proper citation: rDock (RRID:SCR_002838) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/Basic4Cseq.html

An R/Bioconductor package for basic filtering, analysis and subsequent near-cis visualization of 4C-seq data. Virtual fragment libraries can be created for any BSGenome package, and filter functions for both reads and fragments and basic quality controls are included. Fragment data in the vicinity of the experiment's viewpoint can be visualized as a coverage plot based on a running median approach and a multi-scale contact profile.

Proper citation: Basic4Cseq (RRID:SCR_002836) Copy   

•   Source: SciCrunch Registry