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http://www.c2b2.columbia.edu/danapeerlab/html/jistic.html

Software tool for analyzing datasets of genome-wide copy number variation to identify driver aberrations in cancer.

Proper citation: JISTIC (RRID:SCR_003482) Copy   

•   Source: SciCrunch Registry

http://www.brainfacts.org/

A web portal that aggregates information and educational materials about the brain and brain diseases. Resources such as videos, key brain concepts, and hands-on activities may be used and shared with the public.

Proper citation: brainfacts.org (RRID:SCR_003514) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/

Software repository for comparing structural (MRI) and functional neuroimaging (fMRI, PET, EEG, MEG) software tools and resources. NITRC collects and points to standardized information about structural or functional neuroimaging tool or resource.

Proper citation: NeuroImaging Tools and Resources Collaboratory (NITRC) (RRID:SCR_003430) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/genomation/

Software R package for simplfiying common tasks in genomic feature analysis. Toolkit to summarize, annotate and visualize genomic intervals. Provides functions for reading BED and GFF files as GRanges objects, summarizing genomic features over predefined windows so users can make average enrichment of features over defined regions or produce heatmaps. Can annotate given regions with other genomic features such as exons,introns and promoters.

Proper citation: genomation (RRID:SCR_003435) Copy   

•   Source: SciCrunch Registry

http://genomicsandhealth.org/

An international coalition formed to enable the sharing of genomic and clinical data to help unlock potential advancements in medicine and science. Bringing together more than 145 leading institutions working in healthcare, research, disease advocacy, life science, and information technology, the Global Alliance is working together to create and promulgate harmonized approaches to enable the responsible, voluntary, and secure sharing of genomic and clinical data.

Proper citation: Global Alliance for Genomics and Health (RRID:SCR_003555) Copy   

•   Source: SciCrunch Registry

http://www.genabel.org/packages/MetABEL

Software for meta-analysis of genome-wide SNP association results.

Proper citation: MetABEL (RRID:SCR_003429) Copy   

•   Source: SciCrunch Registry

http://www.eurodiagnostica.com/

Antibody supplier.

Proper citation: Euro-Diagnostica (RRID:SCR_003421) Copy   

•   Source: SciCrunch Registry

http://mods.rna.albany.edu

The RNA modification database provides a comprehensive listing of posttranscriptionally modified nucleosides from RNA. Information provided for each nucleoside includes: the type of RNA in which it occurs and phylogenetic distribution; common chemical name and symbol; Chemical Abstracts registry number and index name; chemical structure; initial literature citations for structural characterization or occurrence, and for chemical synthesis. Both the structural diversity and extent of posttranscriptional modification in RNA is remarkable, with 107 different nucleosides presently known in all types of RNA. The discovery of new modified nucleosides as well as increasing knowledge of the array of functional roles of modification, based largely on extensive studies of tRNA, mandates a need for a comprehensive database of RNA nucleosides. The RNA Modification Database is maintained as an extension of the initial version published in mid-1994. The database consists of all RNA-derived ribonucleosides of known structure, including those from established sequence positions, as well as those detected or characterized from hydrolysates of RNA. The information provided permits access to the modified nucleoside literature through provision of both computer-searchable Chemical Abstracts registry numbers and key literature citations. This database also provides an historical record of the initial reports of occurrence, characterization and chemical synthesis of modified nucleosides from RNA. It is our judgement that the total number of RNA nucleosides listed, and the chemical structures reported, are very accurate. However, the distributions listed are in some cases a matter of concern, due primarily to the possibility of inhomogeneity of the RNA isolate and the use of methods of nucleoside identification that are not sufficiently rigorous. Reinvestigation of some of the unusual or single-report source distributions is warranted, and will likely lead to future refinements in the listings. The authors invite comments concerning new entries, errors or omissions and on the format presently used for electronic access to the database.

Proper citation: RNA Modification Database (RRID:SCR_003535) Copy   

•   Source: SciCrunch Registry

https://github.com/dbitton/LaSSO

An R script that creates a FASTA database containing all possible lariat signatures from a given set of introns.

Proper citation: LaSSO (RRID:SCR_003418) Copy   

•   Source: SciCrunch Registry

http://www.metafor-project.org/doku.php

A free and open-source add-on for conducting meta-analyses with the statistical software environment R.

Proper citation: metaphor (RRID:SCR_003450) Copy   

•   Source: SciCrunch Registry

http://prosite.expasy.org/

Database of protein families and domains that is based on the observation that, while there is a huge number of different proteins, most of them can be grouped, on the basis of similarities in their sequences, into a limited number of families. Proteins or protein domains belonging to a particular family generally share functional attributes and are derived from a common ancestor. It is complemented by ProRule, a collection of rules based on profiles and patterns, which increases the discriminatory power of profiles and patterns by providing additional information about functionally and/or structurally critical amino acids. ScanProsite finds matches of your protein sequences to PROSITE signatures. PROSITE currently contains patterns and profiles specific for more than a thousand protein families or domains. Each of these signatures comes with documentation providing background information on the structure and function of these proteins. The database is available via FTP.

Proper citation: PROSITE (RRID:SCR_003457) Copy   

•   Source: SciCrunch Registry

http://everestbiotech.com/

An Antibody supplier

Proper citation: Everest Biotech (RRID:SCR_003456) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/2.12/bioc/html/minfi.html

Software that improves the results from the Illumina infinium HumanMethylation450 BeadChips by reducing technical variation within and between arrays. SWAN is available in the minfi Bioconductor package.

Proper citation: SWAN (RRID:SCR_003455) Copy   

•   Source: SciCrunch Registry

https://code.google.com/p/bmiq/

Software using a beta-mixture quantile normalization method for correcting probe design bias in Illumina Infinium 450 k DNA methylation data.

Proper citation: BMIQ (RRID:SCR_003446) Copy   

•   Source: SciCrunch Registry

http://gepat.sourceforge.net/

A web-based software tool offering an integrated analysis of transcriptome data under genomic, proteomic and metabolic context.

Proper citation: GEPAT (RRID:SCR_003597) Copy   

•   Source: SciCrunch Registry

http://www.topogen.com/

An Antibody supplier

Proper citation: TopoGEN (RRID:SCR_003630) Copy   

•   Source: SciCrunch Registry

http://btcure.eu/

Consortium bringing together academic and industry researchers to advance the understanding of disease causing factors and disease progression in Rheumatoid Arthritis (RA), with a focus on accelerating the development of new drugs. The efforts under this consortium aim to develop: (1) animal models; (2) human biobanks, databases and technologies; (3) research network to address critical biologic and clinical questions; (4) community to network patients and companies. The focus will be the development of new diagnostic methods to discover the early forms of RA as well as tools to separate the different forms of RA, where different molecular mechanisms are involved and where different therapies may be required. The ultimate goal for therapeutic development is to identify the disease-causing molecular events early in the disease and then influence immunity and inflammation so that functional deterioration is halted, immunity is re-regulated and the disease is cured. Samples from biobanks will be analysed in vitro and models will be aligned with different variants of human arthritis. In addition, new models will be established using similar molecular pathways as the relevant human arthritis subsets, leading to the understanding of the etiology and early pathology of the disease for a program aimed at early and curative treatment of RA and RA-like diseases. A major focus of these efforts will be to understand and subsequently alter the adaptive immune reactions in patients from a disease-inducing mode into either a protective mode against the disease or become asymptomatic.

Proper citation: Be The Cure (RRID:SCR_003746) Copy   

•   Source: SciCrunch Registry

http://osprey.ucalgary.ca/

Oligonucleotide design software that calculates optimal oligonucleotides for a range of tasks: sequence assembly, differential expression, and microarrays (cDNA and spotted oligos)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Osprey (RRID:SCR_003627) Copy   

•   Source: SciCrunch Registry

https://github.com/nornir/

A set of Python software packages that takes large sets of overlapping images in 2D and 3D and produces registered (aligned) 3D volumes at any size and scale. These tools were originally designed to construct 3D connectomics volumes from terabytes of image data for the Marc lab at the University of Utah Moran Eye Center.

Proper citation: Nornir (RRID:SCR_003585) Copy   

•   Source: SciCrunch Registry

https://github.com/jamesra/nornir-buildmanager/wiki

Software package that constructs 2D and 3D datasets from 2D image mosaics using the nornir tools. This produces a set of images and transforms on disk which can be accessed via Viking, HTTP, or written as a stack of images.

Proper citation: nornir-buildmanager (RRID:SCR_003584) Copy   

•   Source: SciCrunch Registry