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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

https://www.hgsc.bcm.edu/content/sea-urchin-genome-project

Provides informationa about Genome of California Purple Sea Urchin, one species (Strongylocentrotus purpuratus) of which has been sequenced and annotated by Sea Urchin Genome Sequencing Consortium led by HGSC. Reports sequence and analysis of genome of sea urchin Strongylocentrotus purpuratus, a model for developmental and systems biology.

Proper citation: Sea Urchin Genome Project (RRID:SCR_001735) 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.intute.ac.uk/

Intute is a free online service that helps you to find the best web resources for your studies and research. It was created in response to users' needs and the changing Internet information environment. With millions of resources available on the Internet, it can be difficult to find useful material. The Intute subject specialists review and evaluate thousands of resources to help you choose the key websites in your subject. Intute can also help you develop your Internet research skills through our Virtual Training Suite tutorials, written by lecturers and librarians from universities across the UK. The discipline focus of their service is delivered through four new subject groups: * Science, Engineering and Technology (including geography) * Arts and Humanities * Social Sciences * Health and Life Sciences Intute is created by a consortium of seven universities, working together with a whole host of partners. The Intute consortium includes: * University of Birmingham * University of Bristol * Heriot-Watt University * The University of Manchester * Manchester Metropolitan University * University of Nottingham * University of Oxford Sponsors: Intute is funded by the Joint Information Systems Committee (JISC).

Proper citation: Intute: The Best Web Resources For Education and Research (RRID:SCR_001764) Copy   

•   Source: SciCrunch Registry

http://protein.bio.unipd.it/pasta2/

Online interface that utilizes an algorithm to predict the most aggregation-prone portions and the corresponding beta-strand inter-molecular pairing for a given input sequence. Users can paste the sequence into the interface and output the appropriate sequence.

Proper citation: Prediction of Amyloid Structure Aggregation (RRID:SCR_001768) Copy   

•   Source: SciCrunch Registry

https://www.uniklinik-freiburg.de/mr-en/research-groups/diffperf/fibertools.html

Implemented under MATLAB, this DTI image processing toolbox provides import-filters for several MR file standards, a processing unit to calculate the diffusion tensors; several GUI based tools to calculate fiber tracks and to evaluate the DTI dataset. The results can be filed as images with 3D impression or can be logged in formatted ASCII files. Tools and features: * DTI Processing Unit: Calculates the diffusion tensors and their eigenvalues and eigenvectors. Different file formats are supported (like DICOM, Bruker, binary files, Matlab structures). The standard SIEMENS and GE diffusion encoding schemes are supported; other schemes have to be defined in a separate text, .m or .mat file. * FiberTracking: ** Fiber tracking is realized by using the FACT algorithm (Mori et al., Annal. Neurol 1999). ** Probabilistic tracking realized by using the PiCo (Parker et al., JMRI 2003) approach but with DTI data as basis. It is possible to extract pathways between two seeds by combining two maps (Kreher et al., NeuroImage 2008). ** Global Fiber Tracking on basis of HARDI or DTI data. The method is based on the approach reported in (Marco Reisert et al: Global fiber reconstruction becomes practical. NeuroImage 54(2):955-62) * FiberViewer: ** Visualization and Navigation through different data modalities like DTI maps, fiber tracks, diffusion main directions. ** Supports different kinds of DTI maps (e.g. FA, Trace, lambda images ) ** Creation and manipulation of mask based ROIs. ** Selection of streamline fibers ** Visualization of probabilistic fiber tracking results ** Documentation by logging statistics of ROIs and fiber tracks into text files. ** Import/Export from/to ANALYZE or Nifti * 3D Visualizer: Visualization of map slices, ROIs, and fiber tracks with 3D impression. * Batch Editor: Automatic processing of high amounts of data. Possibility to link processing with SPM8 easily.

Proper citation: DTI and Fibertools Software Package (RRID:SCR_001641) Copy   

•   Source: SciCrunch Registry

http://www.bioit.org.cn/ao/aobase

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 15, 2013. AOBase is a database for antisense oligonucleotides (AOs) selection and design. AOBase is a database developed to facilitate Antisense Oligonucleotides (ODNs) selection for gene expression modulation and to provide a free data source for computer aided ODNs design. Information about valid and invalid ODNs reported in literature are collected and stored in the database, including oligo sequences, target sequences, secondary structures of the target sites, oligo activity measured, and the assay type used for activity measurement. The details on target RNA molecules and reference literature can be explored through the hyperlinks linked to GenBank and PubMed respectively. Each record can be searched for via two web retrieval interfaces: 1) TargetSearch interface, which allows users to query ODNs by name, accession number, or only imprecise descriptions of its target RNA; 2) AOSearch interface, which allows users to search ODNs with several parameters combined, such as oligo activity measured, oligo concentration applied, and motifs involved in oligo sequences. With these two retrieval interfaces, AOBase can be used to select effective ODNs for gene function exploration without expensive in vitro screening experiments, and contribute to mining rules for rational ODNs design. A user friendly interface to encourage data submission is provided.

Proper citation: Database for Antisense Oligonucleotides Selection and Design (RRID:SCR_001753) Copy   

•   Source: SciCrunch Registry

Issue

http://www.nitrc.org/projects/plink

Open source whole genome association analysis toolset, designed to perform range of basic, large scale analyses in computationally efficient manner. Used for analysis of genotype/phenotype data. Through integration with gPLINK and Haploview, there is some support for subsequent visualization, annotation and storage of results. PLINK 1.9 is improved and second generation of the software.

Proper citation: PLINK (RRID:SCR_001757) 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/2.13/bioc/html/cqn.html

A normalization tool for RNA-Seq data, implementing the conditional quantile normalization method.

Proper citation: CQN (RRID:SCR_001786) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/src/contrib/Archive/PoissonSeq/

Software package that implements a method for normalization, testing, and false discovery rate estimation for RNA-sequencing data.

Proper citation: PoissonSeq (RRID:SCR_001784) Copy   

•   Source: SciCrunch Registry

http://meme-suite.org/

Suite of motif-based sequence analysis tools to discover motifs using MEME, DREME (DNA only) or GLAM2 on groups of related DNA or protein sequences; search sequence databases with motifs using MAST, FIMO, MCAST or GLAM2SCAN; compare a motif to all motifs in a database of motifs; associate motifs with Gene Ontology terms via their putative target genes, and analyze motif enrichment using SpaMo or CentriMo. Source code, binaries and a web server are freely available for noncommercial use.

Proper citation: MEME Suite - Motif-based sequence analysis tools (RRID:SCR_001783) 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://www.genabel.org/packages/GenABEL

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. R software library for genome-wide association analysis for quantitative, binary and time-till-event traits.

Proper citation: GenABEL (RRID:SCR_001842) Copy   

•   Source: SciCrunch Registry

http://surfer.nmr.mgh.harvard.edu/

Open source software suite for processing and analyzing human brain MRI images. Used for reconstruction of brain cortical surface from structural MRI data, and overlay of functional MRI data onto reconstructed surface. Contains automatic structural imaging stream for processing cross sectional and longitudinal data. Provides anatomical analysis tools, including: representation of cortical surface between white and gray matter, representation of the pial surface, segmentation of white matter from rest of brain, skull stripping, B1 bias field correction, nonlinear registration of cortical surface of individual with stereotaxic atlas, labeling of regions of cortical surface, statistical analysis of group morphometry differences, and labeling of subcortical brain structures.Operating System: Linux, macOS.

Proper citation: FreeSurfer (RRID:SCR_001847) Copy   

•   Source: SciCrunch Registry