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http://cran.r-project.org/src/contrib/Archive/iFad/

An R software package implementing a bayesian sparse factor model for the joint analysis of paired datasets, the gene expression and drug sensitivity profiles, measured across the same panel of samples, e.g. cell lines.

Proper citation: iFad (RRID:SCR_000271) Copy   

•   Source: SciCrunch Registry

http://www.stat.purdue.edu/~doerge/software/TSPM.R

Software using a statistical approach, based on a two-stage Poisson model, for modeling RNA sequencing data and testing for biologically important changes in gene expression.

Proper citation: TSPM.R (RRID:SCR_012021) Copy   

•   Source: SciCrunch Registry

https://www.idtdna.com/site/order/designtool/index/CRISPR_CUSTOM

Company offers range of products and services for next generation sequencing, CRISPR genome editing, qPCR, gene expression, and other molecular biology applications.

Proper citation: Integrated DNA Technologies (RRID:SCR_025813) Copy   

•   Source: SciCrunch Registry

https://ssbd.riken.jp/azebex/

Collection of in situ hybridization data of gene expression in the brain of adult fish. Data can be viewed and downloaded.

Proper citation: Adult Zebrafish Brain Gene Expression Database (RRID:SCR_025122) Copy   

•   Source: SciCrunch Registry

https://ocimumbio.com/

Comprehensive Integrated Life Science Informatics solutions provider with service offerings that span Sample and Data Management (LIMS, Biologics Data Management), Genomics Data Analysis Services such as Gene Expression, Genotyping, and Next Gen Sequencing, Bioinformatics and Genomics Databases (BioExpress, ToxExpress) and Bio-IT consulting services.

Proper citation: Ocimum Biosolutions (RRID:SCR_012307) Copy   

•   Source: SciCrunch Registry

http://www.dnastar.com/t-genvision.aspx

A genomic visualization application to support easy generation of publication quality graphics and maps. It produces high quality images of annotated genomes but it can also be customized to accentuate specific areas of interest, such as comparing gene functionality, illustrating gene expression levels, and visualizing the coverage in an assembled contig.

Proper citation: GenVision (RRID:SCR_001166) Copy   

•   Source: SciCrunch Registry

http://titan.biotec.uiuc.edu/bee/honeybee_project.htm

A database integrating data from the bee brain EST sequencing project with data from sequencing and gene research projects from other organisms, primarily the fruit fly Drosophila melanogaster. The goal of Bee-ESTdb is to provide updated information on the genes of the honey bee, currently using annotation primarily from flies to suggest cellular roles, biological functions, and evolutionary relationships. The site allows searches by sequence ID, EST annotations, Gene Ontology terms, Contig ID and using BLAST. Very nice resource for those interested in comparative genomics of brain. A normalized unidirectional cDNA library was made in the laboratory of Prof. Bento Soares, University of Iowa. The library was subsequently subtracted. Over 20,000 cDNA clones were partially sequenced from the normalized and subtracted libraries at the Keck Center, resulting in 15,311 vector-trimmed, high-quality, sequences with an average read length of 494 bp. and average base-quality of 41. These sequences were assembled into 8966 putatively unique sequences, which were tested for similarity to sequences in the public databases with a variety of BLAST searches. The Clemson University Genomics Institute is the distributor of these public domain cDNA clones. For information on how to purchase an individual clone or the entire collection, please contact www.genome.clemson.edu/orders/ or generobi (at) life.uiuc.edu.

Proper citation: Honey Bee Brain EST Project (RRID:SCR_002389) Copy   

•   Source: SciCrunch Registry

https://www.signalingpathways.org/ominer/query.jsf

THIS RESOURCE IS NO LONGER IN SERVICE.Documented on February 25, 2022.Software tool as knowledge environment resource that accrues, develops, and communicates information that advances understanding of structure, function, and role in disease of nuclear receptors (NRs) and coregulators. It specifically seeks to elucidate roles played by NRs and coregulators in metabolism and development of metabolic disorders. Includes large validated data sets, access to reagents, new findings, library of annotated prior publications in field, and journal covering reviews and techniques.As of March 20, 2020, NURSA is succeeded by the Signaling Pathways Project (SPP).

Proper citation: Nuclear Receptor Signaling Atlas (RRID:SCR_003287) Copy   

•   Source: SciCrunch Registry

http://www.sanger.ac.uk/mouseportal/

Database of mouse research resources at Sanger: BACs, targeting vectors, targeted ES cells, mutant mouse lines, and phenotypic data generated from the Institute''''s primary screen. The Wellcome Trust Sanger Institute generates, characterizes, and uses a variety of reagents for mouse genetics research. It also aims to facilitate the distribution of these resources to the external scientific community. Here, you will find unified access to the different resources available from the Institute or its collaborators. The resources include: 129S7 and C57BL6/J bacterial artificial chromosomes (BACs), MICER gene targeting vectors, knock-out first conditional-ready gene targeting vectors, embryonic stem (ES) cells with gene targeted mutations or with retroviral gene trap insertions, mutant mouse lines, and phenotypic data generated from the Institute''''s primary screen.

Proper citation: Sanger Mouse Resources Portal (RRID:SCR_006239) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/p/fbbtdv/wiki/Home/

A structured controlled vocabulary of the anatomy of Drosophila melanogaster. These ontologies are query-able reference sources for information on Drosophila anatomy and developmental stages. They also provide controlled vocabularies for use in annotation and classification of data related to Drosophila anatomy, such as gene expression, phenotype and images. They were originally developed by FlyBase, who continue to maintain them and have used them for over 200,000 annotations of phenotypes and expression. Extensive use of synonyms means that, given a suitably sophisticated autocomplete, users can find relevant content by searching with almost any anatomical term they find in the literature. These ontologies are developed in the web ontology language OWL2. Their extensive formalization in OWL can be used to drive sophisticated query systems.

Proper citation: Drosophila anatomy and development ontologies (RRID:SCR_001607) Copy   

•   Source: SciCrunch Registry

http://globin.cse.psu.edu/

Data and tools for studying the function of DNA sequences, with an emphasis on those involved in the production of hemoglobin. It includes information about naturally-occurring human hemoglobin mutations and their effects, experimental data related to the regulation of the beta-like globin gene cluster, and software tools for comparing sequences with one another to discover regions that are likely to play significant roles.

Proper citation: Globin Gene Server (RRID:SCR_001480) Copy   

•   Source: SciCrunch Registry

http://www.stjudebgem.org/web/mainPage/mainPage.php

This database contains gene expression patterns assembled from mouse nervous tissues at 4 time points throughout brain development including embryonic (e) day 11.5, e15.5, postnatal (p) day 7 and adult p42. Using a high throughput in situ hybridization approach we are assembling expression patterns from selected genes and presenting them in a searchable database. The database includes darkfield images obtained using radioactive probes, reference cresyl violet stained sections, the complete nucleotide sequence of the probes used to generate the data and all the information required to allow users to repeat and extend the analyses. The database is directly linked to Pubmed, LocusLink, Unigene and Gene Ontology Consortium housed at the National Center for Biotechnology Information (NCBI) in the National Library of Medicine. These data are provided freely to promote communication and cooperation among research groups throughout the world.

Proper citation: Brain Gene Expression Map (RRID:SCR_001517) Copy   

•   Source: SciCrunch Registry

http://www.gudmap.org

Project aggregates and provides experimental gene expression data from genito-urinary system. International consortium providing molecular atlas of gene expression for developing organs of GenitoUrinary (GU) tract. Mouse strains to facilitate developmental and functional studies within GU system. Experimental protocols and standard specifications. Tutorials describing GU organogenesis and primary data via database. Data are from large-scale in situ hybridization screens (wholemount and section) and microarray gene expression data of microdissected, laser-captured and FACS-sorted components of developing mouse genitourinary (GU) system.

Proper citation: GenitoUrinary Development Molecular Anatomy Project (RRID:SCR_001554) Copy   

•   Source: SciCrunch Registry

http://talasso.cnb.csic.es/

Tool for quantification of human miRNA-mRNA Interactions. TaLasso is also available as Matlab or R code.

Proper citation: TaLasso (RRID:SCR_001726) Copy   

•   Source: SciCrunch Registry

http://fulxie.0fees.us/?type=reference&ckattempt=1

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 1,2023. Web-based tool for evaluating and screening reference genes from extensive experimental datasets. It integrates major computational programs (geNorm, Normfinder, BestKeeper, and the comparative delta-Ct method) to compare and rank the tested candidate reference genes. Based on the rankings from each program, it assigns an appropriate weight to an individual gene and calculated the geometric mean of their weights for the overall final ranking.

Proper citation: RefFinder (RRID:SCR_000472) Copy   

•   Source: SciCrunch Registry

http://bioconductor.org/packages/release/bioc/html/DESeq.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 30,2023. Software for differential gene expression analysis based on the negative binomial distribution. It estimates variance-mean dependence in count data from high-throughput sequencing assays and tests for differential expression.

Proper citation: DESeq (RRID:SCR_000154) Copy   

•   Source: SciCrunch Registry

http://www.betacell.org/

THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone., documented on August 1, 2015. Consortium that aims to facilitate interdisciplinary collaborations to advance the understanding of pancreatic islet development and function, with the goal of developing innovative therapies to correct the loss of beta cell mass in diabetes, including cell reprogramming, regeneration and replacement. They are responsible for collaboratively generating the necessary reagents, mouse strains, antibodies, assays, protocols, technologies and validation assays that are beyond the scope of any single research effort. The scientific goals for the BCBC are to: * Use cues from pancreatic development to directly differentiate pancreatic beta cells and islets from stem / progenitor cells for use in cell-replacement therapies for diabetes, * Determine how to stimulate beta cell regeneration in the adult pancreas as a basis for improving beta cell mass in diabetic patients, * Determine how to reprogram progenitor / adult cells into pancreatic beta-cells both in-vitro and in-vivo as a mean for developing cell-replacement therapies for diabetes, and * Investigate the progression of human type-1 diabetes using patient-derived cells and tissues transplanted in humanized mouse models. Many of the BCBC investigator-initiated projects involve reagent-generating activities that will benefit the larger scientific community. The combination of programs and activities should accelerate the pace of major new discoveries and progress within the field of beta cell biology.

Proper citation: Beta Cell Biology Consortium (RRID:SCR_005136) Copy   

•   Source: SciCrunch Registry

http://www.ebi.ac.uk/biomodels-main/

Repository of mathematical models of biological and biomedical systems. Hosts selection of existing literature based physiologically and pharmaceutically relevant mechanistic models in standard formats. Features programmatic access via Web Services. Each model is curated to verify that it corresponds to reference publication and gives proper numerical results. Curators also annotate components of models with terms from controlled vocabularies and links to other relevant data resources allowing users to search accurately for models they need. Models can be retrieved in SBML format and import/export facilities are being developed to extend spectrum of formats supported by resource.

Proper citation: BioModels (RRID:SCR_001993) Copy   

•   Source: SciCrunch Registry

http://www.sanbi.ac.za/resources/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23, 2022. The South African National Bioinformatics Institute delivers biomedical discovery appropriate to both international and African context. Researchers at SANBI perform the highest level of research and provide excellence in education. Research at SANBI has set well recognized milestones in the field of computational biology. The tools and techniques used have not only been developed but also implemented across heterogeneous domains of advanced research. Local and international efforts have driven our discoveries. Until recently, the core of SANBIs research has focused upon gene expression biology. Methods developed and applied at SANBI revolve around a greater understanding of the underlying causes of diseases. SANBI approaches the problem by comparison of genes, genomes and transcriptomes. It uses computational gene expression biology to create novel biological insights and to provide biomarkers for experimental validation. It also performs analysis of human genome variation, transcriptional diversity on both the expression and splicing level and the unravelling of transcriptional regulatory networks. Resources - Hinv, STACKdb, Malaria resources and Trypanosome databases are available for on-line seaching. - SANBI offers WCD, STACKdb, stackPACK and eVOC and the eVOKE viewer as tools that can be downloaded. Sponsors: SANBI receives funding and support from a range of organisations in South Africa and Internationally. Organisations currently supporting SANBI include: South Africa * South African Medical Research Council * South African AIDS Vaccine Initiative * National Bioinformatics Network * National Research Foundation * Claude Leon Foundation * International Business Machines Inc. Europe * European Unions 6th Framework Programme * World Health Organization USA * US National Institutes of Health * Fogarty International Centre * Ludwig Institute for Cancer Research

Proper citation: South African National Bioinformatics Institute: Resources (RRID:SCR_001867) Copy   

•   Source: SciCrunch Registry

http://www.dkfz.de/en/mol_embryology/axeldb.html

THIS RESOURCE IS NO LONGER IN SERVICE, documented on June 21, 2011. Database focusing on gene expression in the frog Xenopus laevis, it is the web companion to the research papers describing a large-scale in situ hybridization screening in Xenopus embryos. The goals of this large-scale in situ screen project are to identify genes by the characterization of their expression pattern, to partially sequence the corresponding cDNAs and to maintain a database collecting the results.

Proper citation: Axel Database (RRID:SCR_001890) Copy   

•   Source: SciCrunch Registry