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http://bioinformatics.med.yale.edu/group/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 10th,2023. An R code for Bayesian modeling of paired RNA-seq experiments.

Proper citation: pairedBayes (RRID:SCR_001738) Copy   

•   Source: SciCrunch Registry

http://www.yahrparkinson.org/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on March 28, 2017. Foundation that helps junior physicians and neuroscientists continue their research on Parkinson's Disease and related disorders, with financial support for professional and intellectual development. It promotes an international community of researchers, focusing on the young enthusiastic investigators and clinicians who might otherwise be forced to abandon their ideas and efforts.

Proper citation: Melvin Yahr International Parkinson's Disease Foundation (RRID:SCR_001652) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/dnaclust/

Software program for clustering large number of short similar DNA sequences. It was originally designed for clustering targeted 16S rRNA pyrosequencing reads.

Proper citation: DNACLUST (RRID:SCR_001771) Copy   

•   Source: SciCrunch Registry

http://intermine.org/

An open source data warehouse system built for the integration and analysis of complex biological data that enables the creation of biological databases accessed by sophisticated web query tools. Parsers are provided for integrating data from many common biological data sources and formats, and there is a framework for adding data. InterMine includes a user-friendly web interface that works "out of the box" and can be easily customized for specific needs, as well as a powerful, scriptable web-service API to allow programmatic access to data.

Proper citation: InterMine (RRID:SCR_001772) Copy   

•   Source: SciCrunch Registry

http://www.atcc.org/

Global nonprofit biological resource center (BRC) and research organization that provides biological products, technical services and educational programs to private industry, government and academic organizations. Its mission is to acquire, authenticate, preserve, develop and distribute biological materials, information, technology, intellectual property and standards for the advancement and application of scientific knowledge. The primary purpose of ATCC is to use its resources and experience as a BRC to become the world leader in standard biological reference materials management, intellectual property resource management and translational research as applied to biomaterial development, standardization and certification. ATCC characterizes cell lines, bacteria, viruses, fungi and protozoa, as well as develops and evaluates assays and techniques for validating research resources and preserving and distributing biological materials to the public and private sector research communities.

Proper citation: ATCC (RRID:SCR_001672) Copy   

•   Source: SciCrunch Registry

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

Software package that implements the unified Wilcoxon-Mann-Whitney Test for qPCR data. This modified test allows for testing differential expression in qPCR data.

Proper citation: unifiedWMWqPCR (RRID:SCR_001706) Copy   

•   Source: SciCrunch Registry

https://github.com/sbotond/rlsim

Software package for simulating RNA-seq library preparation with parameter estimation.

Proper citation: rlsim (RRID:SCR_001703) Copy   

•   Source: SciCrunch Registry

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

A software package for the simulation of deletions, insertions, inversions, tandem duplications and translocations of various sizes in any genome available as FASTA-file or data package in R. SV breakpoints can be placed uniformly accross the whole genome, with a bias towards repeat regions and regions of high homology (for hg19) or at user-supplied coordinates.

Proper citation: RSVSim (RRID:SCR_001777) Copy   

•   Source: SciCrunch Registry

http://www.annualreviews.org/

Annual Reviews offers comprehensive, timely collections of critical reviews written by leading scientists. It publishes authoritative, analytic reviews in 37 focused disciplines within the Biomedical, Life, Physical, and Social Sciences. The mission of Annual Reviews is to provide systematic, periodic examinations of scholarly advances in a number of fields of science through critical authoritative reviews. The comprehensive critical review not only summarizes a topic but also roots out errors of fact or concept and provokes discussion that will lead to new research activity. The critical review is an essential part of the scientific method. Sponsors: Annual Reviews is a non-profit organization created and managed by scientists to serve science by publishing reviews in 40 different scientific fields.

Proper citation: Annual Reviews: A Nonprofit Scientific Publisher (RRID:SCR_001655) Copy   

•   Source: SciCrunch Registry

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

An R package that provides a series of functions for differential expression analysis from RNA-seq count data using robust normalization strategy (called DEGES). The basic idea of DEGES is that potential differentially expressed genes or transcripts (DEGs) among compared samples should be removed before data normalization to obtain a well-ranked gene list where true DEGs are top-ranked and non-DEGs are bottom ranked. This can be done by performing a multi-step normalization strategy (called DEGES for DEG elimination strategy). A major characteristic of TCC is to provide the robust normalization methods for several kinds of count data (two-group with or without replicates, multi-group/multi-factor, and so on) by virtue of the use of combinations of functions in other sophisticated packages (especially edgeR, DESeq, and baySeq).

Proper citation: TCC (RRID:SCR_001779) Copy   

•   Source: SciCrunch Registry

http://cmb.gis.a-star.edu.sg/ChIPSeq/paperCCAT.htm

THIS RESOURCE IS OUT OF SERVICE, documented on April 5, 2017, A software package for the analysis of ChIP-seq data with negative control., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: CCAT (RRID:SCR_001843) Copy   

•   Source: SciCrunch Registry

http://compbio.iupui.edu/group/6/pages/alteventfinder

Software tool for deriving data-driven alternative splicing (AS) events from RNA-seq data. It analyses the transcripts built by Cufflinks or Scripture and outputs AS event annotations which is compatible with MISO. It can be used for annotating novel AS events from a well-annotated species such as human. It can also be used for species of which known AS event annotation is not available. The current release (v0.1) supports skipped exon events only.

Proper citation: Alt Event Finder (RRID:SCR_001846) Copy   

•   Source: SciCrunch Registry

http://blog.expressionplot.com/

Software package consisting of a default back end, which prepares raw sequencing or Affymetrix microarray data, and a web-based front end, which offers a biologically centered interface to browse, visualize, and compare different data sets.

Proper citation: ExpressionPlot (RRID:SCR_001904) Copy   

•   Source: SciCrunch Registry

https://urgi.versailles.inra.fr/Tools/S-Mart

Software toolbox that manages your RNA-Seq and ChIP-Seq data and also produces many different plots to visualize your data. It performs several tasks that are usually required during the analysis of mapped RNA-Seq and ChIP-Seq reads, including data selection and data visualization. It includes the selection (or the exclusion) of the data that overlaps with a reference set, clustering and comparative analysis. It also provides many ways to visualize data: size of the reads, density on the genome, distance with respect to a reference set, and the correlation of two data sets (with cloud plots). A computer science background is not required to run it through a graphical interface and it can be run on any personal computer, yielding results within an hour for most queries.

Proper citation: S-MART (RRID:SCR_001908) Copy   

•   Source: SciCrunch Registry

http://www.kaist.edu/html/en/index.html

Institute dedicated to research in science and technology in South Korea modeled after a research university.

Proper citation: Korea Advanced Institute of Science and Technology; Daejeon; South Korea (RRID:SCR_001902) Copy   

•   Source: SciCrunch Registry

https://github.com/raphael-group/THetA

An algorithm that estimates the tumor purity and clonal / subclonal copy number aberrations directly from high-throughput DNA sequencing data.

Proper citation: THetA (RRID:SCR_001860) Copy   

•   Source: SciCrunch Registry

http://www.ualberta.ca/

Public research university in Edmonton, Alberta, Canada that offers degree programs in a variety of fields including business, arts, education, engineering, nursing, and medicine.

Proper citation: University of Alberta; Alberta; Canada (RRID:SCR_001853) Copy   

•   Source: SciCrunch Registry

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

Software that identifies cell population in flow cytometry data. It demonstrates significant advantages in proper identification of populations with non-elliptical shapes, low density populations close to dense ones, minor subpopulations of a major population and rare populations. It samples large data such that spectral clustering is possible while preserving density information in edge weights. More specifically, given a matrix of coordinates as input, SamSPECTRAL first builds the communities to sample the data points. Then, it builds a graph and after weighting the edges by conductance computation, the graph is passed to a classic spectral clustering algorithm to find the spectral clusters. The last stage of SamSPECTRAL is to combine the spectral clusters. The resulting connected components estimate biological cell populations in the data sample.

Proper citation: SamSPECTRAL (RRID:SCR_001858) Copy   

•   Source: SciCrunch Registry

http://www.sdsc.edu/

Founded in 1985, the San Diego Supercomputer Center (SDSC) enables international science and engineering discoveries through advances in computational science and data-intensive, high-performance computing. SDSC is considered a leader in data-intensive computing, providing resources, services and expertise to the national research community including industry and academia. The mission of SDSC is to extend the reach of scientific accomplishments by providing tools such as high-performance hardware technologies, integrative software technologies, and deep interdisciplinary expertise to these communities. From 1997 to 2004, SDSC extended its leadership in computational science and engineering to form the National Partnership for Advanced Computational Infrastructure (NPACI), teaming with approximately 40 university partners around the country. Today, SDSC is an Organized Research Unit of the University of California, San Diego with a staff of talented scientists, software developers, and support personnel. A broad community of scientists, engineers, students, commercial partners, museums, and other facilities work with SDSC to develop cyberinfrastructure-enabled applications to help manage their extreme data needs. Projects run the gamut from creating astrophysics visualization for the American Museum of Natural History, to supporting more than 20,000 users per day to the Protein Data Bank, to performing large-scale, award-winning simulations of the origin of the universe or how a major earthquake would affect densely populated areas such as southern California. Along with these data cyberinfrastructure tools, SDSC also offers users full-time support including code optimization, training, 24-hour help desk services, portal development and a variety of other services. As one of the NSF's first national supercomputer centers, SDSC served as the data-intensive site lead in the agency's TeraGrid program, a multiyear effort to build and deploy the world's first large-scale infrastructure for open scientific research. SDSC currently provides advanced user support and expertise for XSEDE (Extreme Science and Engineering Discovery Environment) the five-year NSF-funded program that succeeded TeraGrid in mid-2011.

Proper citation: San Diego Supercomputer Center (RRID:SCR_001856) Copy   

•   Source: SciCrunch Registry

http://www.nsgc.org/

Professional society of genetic counselors that promotes networking, continuing education opportunities, advocacy, and discussion of relevant issues in the field of genetics.

Proper citation: National Society of Genetic Counselors (RRID:SCR_001803) Copy   

•   Source: SciCrunch Registry