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https://github.com/PacificBiosciences/stsPlots

Software to plot primary analysis quality control metrics to assess potential SMRTcell loading problems.

Proper citation: stsPlots (RRID:SCR_000449) Copy   

•   Source: SciCrunch Registry

http://neuralensemble.org/neo/

A Python package for representing electrophysiology data, together with support for reading a wide range of neurophysiology file formats, including Spike2, NeuroExplorer, AlphaOmega, Axon, Blackrock, Plexon, Tdt, and support for writing to a subset of these formats plus non-proprietary formats including HDF5. The goal of Neo is to improve interoperability between Python tools for analyzing, visualizing and generating electrophysiology data (such as OpenElectrophy, NeuroTools, G-node, Helmholtz, PyNN) by providing a common, shared object model. In order to be as lightweight a dependency as possible, Neo is deliberately limited to represention of data, with no functions for data analysis or visualization. Neo implements a hierarchical data model well adapted to intracellular and extracellular electrophysiology and EEG data with support for multi-electrodes (for example tetrodes). Neo's data objects build on the quantities package, which in turn builds on NumPy by adding support for physical dimensions. Thus Neo objects behave just like normal NumPy arrays, but with additional metadata, checks for dimensional consistency and automatic unit conversion.

Proper citation: Neo (RRID:SCR_000634) Copy   

•   Source: SciCrunch Registry

http://www.broadinstitute.org/cancer/cga/contest

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 8,2025. A software tool (and method) for estimating the amount of cross-sample contamination in next generation sequencing data.

Proper citation: ContEst (RRID:SCR_000595) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://gowiki.tamu.edu/wiki/

A wiki where users of the Gene Ontology can contribute and view notes about how specific GO terms are used. GONUTS can also be used as a GO term browser, or to search for GO annotations of specific genes from included organisms. The rationale for this wiki is based on helping new users of the gene ontology understand and use it. The GONUTS wiki is not an official product of the the Gene Ontology consortium. The GO consortium has a public wiki at their website, http://wiki.geneontology.org/. Maintaining the ontology involves many decisions to carefully choose terms and relationships. These decisions are currently made at GO meetings and via online discussion using the GO mailing lists and the Sourceforge curator request tracker. However, it is difficult for someone starting to use GO to understand these decisions. Some insight can be obtained by mining the tracker, the listservs and the minutes of GO meetings, but this is difficult, as these discussions are often dispersed and sometimes don't contain the GO accessions in the relevant messages. Wikis provide a way to create collaboratively written documentation for each GO term to explain how it should be used, how to satisfy the true path requirement, and whether an annotation should be placed at a different level. In addition, the wiki pages provide a discussion space, where users can post questions and discuss possible changes to the ontology. GONUTS is currently set up so anyone can view or search, but only registered users can edit or add pages. Currently registered users can create new users, and we are working to add at least one registered user for each participating database (So far we have registered users at EcoliHub, EcoCyc, GOA, BeeBase, SGD, dictyBase, FlyBase, WormBase, TAIR, Rat Genome Database, ZFIN, MGI, UCL and AgBase...

Proper citation: GONUTS (RRID:SCR_000653) Copy   

•   Source: SciCrunch Registry

https://www.wool.com/

Company focused on animal welfare and pest prevention in the wool industry.

Proper citation: Australian Wool Innovation Limited (RRID:SCR_000775) Copy   

•   Source: SciCrunch Registry

Discontinued

https://github.com/PacificBiosciences/blasr

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. C++ long-read aligner for PacBio reads., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: BLASR (RRID:SCR_000764) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://www.amprogress.org/

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://pharmtox.vcu.edu/

A graduate program for pharmacology and toxicology that is a component of the Virginia Commonwealth University. This organization also performs studies on medical disorders, and new pharmacology agents and their effects on human health.

Proper citation: Virginia Commonwealth University, Department of Pharmacology (RRID:SCR_000666) Copy   

•   Source: SciCrunch Registry