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University in Victoria, Australia that provides undergraduate and graduate degree programs.
Proper citation: University of Melbourne; Victoria; Australia (RRID:SCR_000999) Copy
http://www.dystonia-parkinsons.org
A nonprofit organization whose goal is to find better treatments and cures for the movement disorders dystonia and Parkinson's disease. Funding opportunities are available through the collaborative research program between BSDPF and the Michael J. Fox Foundation.
Proper citation: BSDPF (RRID:SCR_001162) Copy
Software for discriminative motif optimization based on perceptron training. It takes a seed motif along with a positive and a negative database and improves the motif based on a discriminative strategy. They use the area under receiver-operating characteristic curve (AUC) as a measure of discriminating power of motifs and a strategy based on perceptron training that maximizes AUC rapidly in a discriminative manner.
Proper citation: DiMO (RRID:SCR_001168) Copy
http://www.loni.usc.edu/Software/Pipeline
A free workflow application primarily aimed at neuroimaging researchers that allows users to easily describe their executables in a graphical user interface (ie. create a module) and connect them together to create complex analyses all without having to code a single line in a scripting language. The Pipeline Client runs on your PC/Mac/Linux computer upon which you can create sophisticated processing workflows using a variety of commonly available executable tools (e.g. FSL, AIR, FreeSurfer, AFNI, Diffusion Toolkit, etc). The Distributed Pipeline Server can be installed on your Linux cluster and you can submit processing jobs directly to your own compute systems. Once you����??ve created a module for use in the LONI Pipeline, you can save it into your personal library and reuse it in other workflows you create by simply dragging and dropping it in. Because the LONI Pipeline is written in Java, you can work in whatever operating system suits you best. If there are tools that you need that can only work on another operating system, you can install a Pipeline server on that computer and connect from your client to do processing and analysis remotely.
Proper citation: LONI Pipeline Processing Environment (RRID:SCR_001161) Copy
http://www.bioconductor.org/packages/release/bioc/html/exomePeak.html
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 18,2025. Software package developed for the analysis of affinity-based epitranscriptome shortgun sequencing data from MeRIP-seq (maA-seq). It was built on the basis of the exomePeak MATLAB package with new functions for differential analysis of two experimental conditions to unveil the dynamics in post-transcriptional regulation of the RNA methylome. The exomePeak R-package accepts and statistically supports multiple biological replicates, internally removes PCR artifacts and multi-mapping reads, outputs exome-based binding sites (RNA methylation sites) and detects differential post-transcriptional RNA modification sites between two experimental conditions in term of percentage rather the absolute amount.
Proper citation: ExomePeak (RRID:SCR_001076) Copy
Center dedicated to providing statistical information to guide policies to improve the health of the American people. An affiliate of the Center for Disease Control and Prevention.
Proper citation: National Center for Health Statistics (RRID:SCR_001078) Copy
Collection of high resolution images and databases of brains from many genetically characterized strains of mice with aim to systematically map and characterize genes that modulate architecture of mammalian CNS. Includes detailed information on genomes of many strains of mice. Consists of images from approximately 800 brains and numerical data from just over 8000 mice. You can search MBL by strain, age, sex, body or brain weight. Images of slide collection are available at series of resolutions. Apple's QuickTime Plugin is required to view available MBL Movies.
Proper citation: Mouse Brain Library (RRID:SCR_001112) Copy
A software tool for comparative visualization of genomes. It is based in the GBrowse frameworks and integrates with the annotation features.
Proper citation: SynView (RRID:SCR_001106) Copy
https://bitbucket.org/mckinsel/shortfuse
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. A software package with tools for identifying fusion transcripts from RNA-Seq data. It is written in C++, and has dependencies on packages from Python 2.
Proper citation: ShortFuse (RRID:SCR_001107) Copy
http://www.riken.jp/engn/index.html
An independent administrative institution dedicated to comprehensive research in science and technology and the dissemination of scientific research and technological developments to the public. RIKEN works in a range of fields, including physics, chemistry, medical science, biology, and engineering, covering the entire range from basic research to practical application.
Proper citation: RIKEN (RRID:SCR_001065) Copy
http://sourceforge.net/projects/sparseassembler/
Software for memory-efficient genome assembly. It utilizes sparse k-mer.
Proper citation: SparseAssembler (RRID:SCR_001100) Copy
A public co-educational university in Lexington, Kentucky that offers undergraduate, graduate and postgraduate degree programs in a variety of fields such as nursing, the arts, law and medicine.
Proper citation: University of Kentucky; Kentucky; USA (RRID:SCR_001062) Copy
A commercial biomaterial supply resource for laboratory reagent assays. IBL-American provides resources to further research and clinical testing in various areas including autoimmunity, endocrinology, infectious disease, oncology and neuroscience among others.
Proper citation: IBL-America (RRID:SCR_001131) Copy
https://cloud.google.com/products/compute-engine
An infrastructure as a service that lets you run your large-scale computing workloads on Linux virtual machines hosted on Google's infrastructure.
Proper citation: Google Compute Engine (RRID:SCR_001011) Copy
Commercial supplier and developer of mitochondrial antibodies and mitochondrial assays. The company focuses on supporting critical research areas in cancer, neurodegeneration and metabolic disorders.
Proper citation: MitoScience (RRID:SCR_001130) Copy
An antibody supplier that specializes in high-affinity custom chicken antibody production, providing clients with chicken IgY and other immunoreagents for biomedical research and antibody manufacturing.
Proper citation: Aves Labs (RRID:SCR_001136) Copy
http://sourceforge.net/projects/cuda-ec/
A fast parallel error correction tool for short reads.
Proper citation: CUDA-EC (RRID:SCR_001090) Copy
An application designed for compression of data files containing reads from DNA sequencing in FASTQ format. Its main features include multithreaded compression of FASTQ output, python and C++ libraries, and support for lossy IDs compression.
Proper citation: DSRC (RRID:SCR_001005) Copy
A national research university in Canberra, Australia. It offers undergraduate and graduate degrees in fields such as law, medicine, business, arts and the social sciences.
Proper citation: Australian National University; Acton; Australia (RRID:SCR_001086) Copy
A high-performance visualization tool for interactive exploration of large, integrated genomic datasets written primarily in JavaScript. It supports a wide variety of data types, including array-based and next-generation sequence data, and genomic annotations.
Proper citation: JBrowse (RRID:SCR_001004) Copy
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