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http://www.helsinki.fi/bsg/software/BEBaC/
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software for Bayesian estimation of bacterial communities.
Proper citation: BEBaC (RRID:SCR_000621) Copy
http://bioconductor.org/packages/release/bioc/html/flipflop.html
Software that discovers which isoforms of a gene are expressed in a given sample together with their abundances, based on RNA-Seq read data.
Proper citation: FlipFlop (RRID:SCR_000625) Copy
Company focused on animal welfare and pest prevention in the wool industry.
Proper citation: Australian Wool Innovation Limited (RRID:SCR_000775) Copy
http://sourceforge.net/projects/gmcloser/
Software that fills and closes the gaps present in scaffold assemblies, especially those generated by the de novo assembly of whole genomes with next-generation sequencing (NGS) reads. Unlike other gap-closing tools that use only NGS reads, GMcloser uses preassembled contig sets or long read sets as the sequences to close gaps and uses paired-end (PE) reads and a likelihood-based algorithm to improve the accuracy and efficiency of gap closure. The efficiency of gap closure can be increased by successive treatments with different contig sets.
Proper citation: GMcloser (RRID:SCR_000646) Copy
http://sourceforge.net/projects/detecttd/
Software tool to detect tandem duplications in sequencing reads. It is written in Python and requires NCBI Blast standalone.
Proper citation: detecttd (RRID:SCR_000681) Copy
http://sourceforge.net/projects/fastuniq/
A software tool for removal of de novo duplicates in paired short DNA sequences.
Proper citation: FastUniq (RRID:SCR_000682) Copy
https://www.thermofisher.com/order/catalog/product/4474950
A software that gives the user the ability to basecall, trim, display, edit, and print data for the entire line of capillary DNA sequencing instruments for data analysis and quality control. This software benefits from being able to obtain longer read lengths, greater accuracy on the 5' end, and the ability to filter out low-quality sequence ends.
Proper citation: Sequencing Analysis Software (RRID:SCR_000718) Copy
http://psychiatry.stanford.edu/
A Stanford-affiliated organization which is primarily concerned with the study and treatment of sleep disorders, the treatment of psychological illnesses, and the training of medical students, residents and research fellows in psychiatry and sleep medicine.
Proper citation: Stanford University Psychiatry and Behavioral Sciences (RRID:SCR_000719) Copy
http://www.scrippscollege.edu/academics/department/neuroscience/index.php
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 14,2025. A neuroscience program that prepares the student for graduate work in biology, psychology, neuroscience, or preparation for medical school or a career in the health services.
Proper citation: Scripps Women's College, Neuroscience Department (RRID:SCR_000717) Copy
https://github.com/shinout/clipcrop
Software tool for detecting structural variations with single-base resolution using soft-clipping information from SAM files.
Proper citation: clipcrop (RRID:SCR_000678) Copy
A non-profit charity dedicated to providing education about animal research for the purpose of protecting medical and scientific progress. The organization seeks to provide accurate and incisive information to foster a balanced public debate on animal research issues. They work to do outreach by distributing timely and relevant news, information and analysis about animal rights extremism to the research community.
Proper citation: Americans for Medical Progress (RRID:SCR_000711) Copy
http://sourceforge.net/projects/triagetools/
A collection of tools for partitioning raw data (fastq reads) from high-throughput sequencing projects. The tools are designed for basic data management as well for prioritizing analysis of certain subsets.
Proper citation: TriageTools (RRID:SCR_000675) Copy
http://pharmacy.oregonstate.edu/
The college of pharmacy at Oregon State University that offers professional education in pharmacy. The foundational goals are to provide professional education, foster research to contribute to public health initiatives and promote safe and affordable medication access.
Proper citation: Oregon State University College of Pharmacy (RRID:SCR_000715) Copy
http://software.markdpreston.com/varb
A variation browsing and analysis tool for variants derived from next-generation sequencing data.
Proper citation: VarB (RRID:SCR_000671) Copy
http://www.bccancer.bc.ca/default.htm
A portal that provides a province-wide, population-based cancer control program for the residents of British Columbia and the Yukon. The BC Cancer Agency''s mandate covers the spectrum of cancer care, from prevention and screening, to diagnosis, treatment, and through to rehabilitation. The BC Cancer Agency''s mandate is driven by a three-fold mission: 1. To reduce the incidence of cancer; 2. To reduce the mortality rate of people with cancer; 3. To improve the quality of life of people living with cancer. This mission drives everything we do, including providing screening, diagnosis and care, setting treatment standards, and conducting research into causes of, and cures for, cancer. The BC Cancer Agency operates five regional cancer centers, providing assessment and diagnostic services, chemotherapy, radiation therapy, and supportive care. Each of the BC Cancer Agency''s centers delivers cancer treatment based on provincial standards and guidelines established by the Agency. We work in partnership with communities to provide a network of chemotherapy clinics so patients can receive care closer to home. Research is an essential part of the BC Cancer Agency''s mission to not only find the causes of cancer, but to find better treatments for prolonged life and better quality of life. With direct links between the BC Cancer Agency''s physicians and researchers at our five centers, the Deeley Research Centre (located in Victoria) and the BC Cancer Agency''s Research Centre (located in Vancouver), we can quickly translate new discoveries into clinical applications. The BC Cancer Agency''s Research Centre includes eight specialty laboratories including the Genome Sciences Centre, and the Terry Fox Laboratory. The BC Cancer Foundation raises funds for cancer research and enhancements to care at the BC Cancer Agency.
Proper citation: BC Cancer Agency (RRID:SCR_004201) Copy
An Antibody supplier
Proper citation: Echelon Biosciences (RRID:SCR_004169) Copy
The OBO Relation Ontology is an ontology of core relations for use by OBO Foundry ontologies. To enhance the treatment of relations in biomedical ontologies we advance a methodology for providing consistent and unambiguous formal definitions of the relational expressions used in such ontologies in a way designed to assist developers and users in avoiding errors in coding and annotation. The resulting Relation Ontology can promote interoperability of ontologies and support new types of automated reasoning about the spatial and temporal dimensions of biological and medical phenomena. The OBO Relation ontology is undergoing substantial changes: * Core domain-independent relations will live in BFO * Biology specific relations (defined in terms of core relations) will live in RO
Proper citation: OBO Relation Ontology (RRID:SCR_004285) Copy
http://genomics.princeton.edu/AndolfattoLab/MSG.html
A pipeline of scripts to assign ancestry to genomic segments using next-gen sequence data. This method can identify recombination breakpoints in a large number of individuals simultaneously at a resolution sufficient for most mapping purposes, such as quantitative trait locus (QTL) mapping and mapping of induced mutations.
Proper citation: MSG (RRID:SCR_004161) Copy
A provider for commercial products for analyzing neuronal morphology, stereology, etc.
Proper citation: MicroBrightfield, Inc. (RRID:SCR_004314) Copy
University of Pennsylvania is private Ivy League research university located in University City neighborhood of Philadelphia, Pennsylvania. Established in 1740, UPenn has 4 undergraduate schools and 12 graduate schools.
Proper citation: University of Pennsylvania; Philadelphia; USA (RRID:SCR_004275) Copy
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