Searching across hundreds of databases

Our searching services are busy right now. Your search will reload in five seconds.

  • Register
X
Forgot Password

If you have forgotten your password you can enter your email here and get a temporary password sent to your email.

X

Leaving Community

Are you sure you want to leave this community? Leaving the community will revoke any permissions you have been granted in this community.

No
Yes
X
Forgot Password

If you have forgotten your password you can enter your email here and get a temporary password sent to your email.

Search

Type in a keyword to search

on page 1 showing 20 out of 338 results

    ACME

Cite this (ACME, RRID:SCR_001464)

URL: http://www.bioconductor.org/packages/release/bioc/html/ACME.html

Resource Type: Resource, software resource

A set of tools for analysing tiling array ChIP/chip, DNAse hypersensitivity, or other experiments that result in regions of the genome showing enrichment. It does not rely on a specific array technology (although the array should be a tiling array), is very general (can be applied in experiments resulting in regions of enrichment), and is very insensitive to array noise or normalization methods. It is also very fast and can be applied on whole-genome tiling array experiments quite easily with enough memory.

  • From Current Category

    ADaCGH2

Cite this (ADaCGH2, RRID:SCR_001981)

URL: http://www.bioconductor.org/packages/release/bioc/html/ADaCGH2.html

Resource Type: Resource, software resource

Software for analysis and plotting of array comparative genomic hybridization (CGH) data. It allows usage of Circular Binary Segementation, wavelet-based smoothing (both as in Liu et al., and HaarSeg as in Ben-Yaacov and Eldar), HMM, BioHMM, GLAD, CGHseg. Most computations are parallelized (either via forking or with clusters, including MPI and sockets clusters) and use ff for storing data.

  • From Current Category

    ADGO

Cite this (ADGO, RRID:SCR_006343)

URL: http://www.btool.org/ADGO2

Resource Type: Resource, analysis service resource, data analysis service, service resource, production service resource

A web-based tool that provides composite interpretations for microarray data comparing two sample groups as well as lists of genes from diverse sources of biological information. It provides multiple gene set analysis methods for microarray inputs as well as enrichment analyses for lists of genes. It screens redundant composite annotations when generating and prioritizing them. It also incorporates union and subtracted sets as well as intersection sets. Users can upload their gene sets (e.g. predicted miRNA targets) to generate and analyze new composite sets.

  • From Current Category

Cite this (AffyExpress, RRID:SCR_001321)

URL: http://www.bioconductor.org/packages/release/bioc/html/AffyExpress.html

Resource Type: Resource, software resource

Software package for quality assessment and to identify differentially expressed genes in the Affymetrix gene expression data.

  • From Current Category

Cite this (affylmGUI, RRID:SCR_001320)

URL: http://bioinf.wehi.edu.au/affylmGUI/

Resource Type: Resource, software resource

R software package providing a Graphical User Interface for analysis of Affymetrix microarray data, using the limma package (Linear Models for MicroArray data). While not as powerful as limma to the expert user, it offers a simple point-and-click interface to many of the commonly-used limma and affy functions. You need to have R 1.9.0 or later, Tcl/Tk 8.3 or later (ActiveTcl for Windows, Tcl/Tk Source for Linux/Unix, or X11 Tcl/Tk for MacOSX) and the limma, affylmGUI, and tkrplot R packages. It has been succesfully tested on Windows 2000, Windows XP, RedHat/Fedora Linux, and on Mac OSX with X11.

  • From Current Category

    affyPLM

Cite this (affyPLM, RRID:SCR_001319)

URL: http://www.bioconductor.org/packages/release/bioc/html/affyPLM.html

Resource Type: Resource, software resource

Software for fitting probe-level models and tools using these models. Probe-level models (PLM) based quality assessment tools.

  • From Current Category

Cite this (affyQCReport, RRID:SCR_001318)

URL: http://www.bioconductor.org/packages/release/bioc/html/affyQCReport.html

Resource Type: Resource, software resource

Software package to create a QC report for an AffyBatch object. The report is intended to allow the user to quickly assess the quality of a set of arrays in an AffyBatch object.

  • From Current Category

Cite this (AffyRNADegradation, RRID:SCR_000118)

URL: http://www.bioconductor.org/packages/release/bioc/html/AffyRNADegradation.html

Resource Type: Resource, software resource

Software package that helps with the assessment and correction of RNA degradation effects in Affymetrix 3' expression arrays. The parameter d gives a robust and accurate measure of RNA integrity. The correction removes the probe positional bias, and thus improves comparability of samples that are affected by RNA degradation.

  • From Current Category

Cite this (Aged Rodent Tissue Arrays, RRID:SCR_007332)

URL: http://www.nia.nih.gov/research/dab/aged-rodent-tissue-bank-handbook/tissue-arrays

Resource Type: Resource, biomaterial analysis service, analysis service resource, service resource, production service resource, material analysis service

Offer high-throughput analysis of tissue histology and protein expression for the biogerontology research community. Each array is a 4 micron section that includes tissue cores from multiple tissues at multiple ages on one slide. The arrays are made from ethanol-fixed tissue and can be used for all techniques for which conventional tissue sections can be used. Ages are chosen to span the life from young adult to very old age. (available ages: 4, 12, 18, 24 and 28 months of age) Images of H&E stained punches are available for Liver, Cardiac Muscle, and Brain. The NIA aged rodent tissue arrays were developed with assistance from the National Cancer Institute (NCI) Tissue Array Research Program (TARP), led by Dr. Stephen Hewitt, Director. NCI TARP contains more information on tissue array construction, protocols for using arrays, and references. Preparation and Product Description Tissue arrays are prepared in parallel from different sets of animals so that experiments can be conducted in duplicate, with each array using unique animals with a unique product number. The product descriptions page describes each array, including: * Strain * Gender * Ages * Tissues * Animal Identification Numbers

  • From Current Category

    AlleleID

Cite this (AlleleID, RRID:SCR_014790)

URL: http://www.premierbiosoft.com/bacterial-identification/index.html

Resource Type: Resource, software resource, software application

Desktop software application for bacterial identification, pathogen detection, or species identification. It can be used for cross-species identification for microarrays and real time PCR primers. It uses ClustalW to align sequences then analyzes conserved and species specific regions within those sequences.

  • From Current Category

Cite this (Allen Brain Atlas API, RRID:SCR_005984)

URL: http://www.brain-map.org/api/index.html

Resource Type: Resource, software resource, software application, source code

API and demo application for accessing the Allen Brain Atlas Mouse Brain data. Data available via the API includes download high resolution images, expression data from a 3D volume, 3D coordinates of the Allen Reference Atlas, and searching genes with similar gene expression profiles using NeuroBlast. Data made available includes: * High resolution images for gene expression, connectivity, and histology experiments, as well as annotated atlas images * 3-D expression summaries registered to a reference space for the Mouse Brain and Developing Mouse Brain * Primary microarray results for the Human Brain and Non-Human Primate * RNA sequencing results for the Developing Human Brain * MRI and DTI files for Human Brain The API consists of the following resources: * RESTful model access * Image download service * 3-D expression summary download service * Differential expression search services * NeuroBlast correlative searches * Image-to-image synchronization service * Structure graph download service

  • From Current Category

Cite this (Allen Human Brain Atlas, RRID:SCR_007416)

URL: http://human.brain-map.org/

Resource Type: Resource, data processing software, database, software application, data visualization software, software resource, atlas, data or information resource

A multi-modal atlas of the human brain that integrates anatomic and genomic information, coupled with a suite of visualization and mining tools to create an open public resource for brain researchers and other scientists across a wide range of specialties. Data modalities incorporated into this resource include magnetic resonance imaging (MRI), diffusion tensor imaging (DTI), histology and gene expression data derived from both microarray and in situ hybridization (ISH) approaches. Brain Explorer 2 is a desktop software application for viewing the human brain anatomy and gene expression data in 3D. It is available for download. After installing Brain Explorer 2, you can view gene expression data by performing a gene search from the Microarray page or from within Brain Explorer 2''s main window.

  • From Current Category

Cite this (Allen Institute for Brain Science Sleep Study, RRID:SCR_002983)

URL: http://sleep.alleninstitute.org

Resource Type: Resource, data set, atlas, data or information resource

A comprehensive collection of gene expression data in the mouse brain for five different conditions of sleep and wakefulness. Generated in collaboration with SRI International, this unique dataset is intended to help sleep researchers advance understanding of sleep deprivation and the dynamic changes underlying sleep/wake cycles. A high-throughput colorimetric in situ hybridization platform has been used to generate cellular resolution expression data for over 200 genes. In addition, microarray data for seven brain regions from the same five experimental conditions are downloadable from the web site; and difference grids are available for viewing differences between conditions in 3-D using Brain Explorer. Sleep deprivation leads to a repertoire of cognitive, attentional and emotional deficits that are seriously detrimental in occupations requiring alertness. These deficits may be associated with changes in gene expression in specific regions of the brain. The Allen Institute is in the process of generating a collection of cellular resolution data for gene expression in the mouse brain in response to sleep deprivation and sleep state. Using the Allen Institute high throughput in situ hybridization platform, gene expression has been examined under five experimental conditions in mice in collaboration with SRI International, and the images are presented online as a resource for sleep researchers. Sleep conditions include: Sleep-deprived for 6 hours; Time of day control for sleep-deprivation; Recovery sleep (4 hours) following 6 hours of sleep deprivation; Time of day control for recovery sleep; and waking. Project data is available in the following formats: Colorimetric ISH and Nissl images for 224 genes across 5 conditions, some with replicates Microarray data for 7 brain regions across 5 conditions Difference grids for viewing differences between conditions in 3-D using Brain Explorer Microarray data is available for seven brain regions collected from five experimental conditions: sleep deprivation, recovery sleep, and three time-of-day controls. The brain regions include four regions associated with sleep-wake regulation or circadian rhythm: suprachiasmatic nucleus, locus coeruleus, tuberomammillary nucleus and lateral hypothalamus in the vicinity of the hypocretin neurons. In order to assess the effect of sleep deprivation on gene expression in regions potentially involved in mood, memory, or executive function, an additional three brain regions were analyzed by microarray: orbital cortex, cortical amygdala (posteromedial), and dorsal entorhinal cortex. 140 microarray files are available for download in text, Codelink, and Rosetta Resolver file formats. Difference Grids allow the user to navigate changes in gene expression for a given gene across two experimental conditions, such as sleep deprivation compared to its time of day control. Difference grids are available for genes which have been assayed in replicate by ISH.

  • From Current Category

Cite this (AltAnalyze - Alternative Splicing Analysis Tool, RRID:SCR_002951)

URL: http://www.altanalyze.org/

Resource Type: Resource, software resource, software application

Software application for microarry, RNA-Seq and metabolomics analysis. For splicing sensitive platforms (RNA-Seq or Affymetrix Exon, Gene and Junction arrays), it will assess alternative exon (known and novel) expression along protein isoforms, domain composition and microRNA targeting. In addition to splicing-sensitive platforms, it provides comprehensive methods for the analysis of other data (RMA summarization, batch-effect removal, QC, statistics, annotation, clustering, network creation, lineage characterization, alternative exon visualization, gene-set enrichement and more). AltAnalyze can be run through an intuitive graphical user interface or command-line and requires no advanced knowledge of bioinformatics programs or scripting. Alternative regulated exons can be subsequently visualized in the context of proteins, domains and microRNA binding sites with the Cytoscape Plugin DomainGraph.

  • From Current Category

Cite this (AltSplice Database of Alternative Spliced Events, RRID:SCR_008162)

URL: http://www.ebi.ac.uk/asd/altsplice/index.html

Resource Type: Resource, data or information resource, database

AltSplice is a computer generated high quality data set of human transcript-confirmed splice patterns, alternative splice events, and the associated annotations. This data is being integrated with other data that is generated by other members of the ASD consortium. The ASD project will provide the following in its three year duration: -human curated database of alternative spliced genes and their properties -a computer generated database of alternatively spliced genes and their properties -the integration of the above and newly found knowledge in a user-friendly interface and research workbench for both bioinformaticists and biologists -DNA chips that are based on the data in the above databases -the DNA chips will be used to test against predisposition for and diagnoses of human diseases ASD aims to analyse this mechanism on a genome-wide scale by creating a database that contains all alternatively spliced exons from human, and other model species. Disease causing mutations seem to induce aberrations in the process of splicing and its regulation. The ASD consortium will develop a DNA microarray (chip) that contains cDNAs of all the splicing regulatory proteins and their isoforms, as well as a chip that contains a number of disease relevant genes. We will concentrate on three models of disease (breast cancer, FTDP-17, male infertility) in which a connection between mis-splicing and a pathological state has been observed. Finally, these chips will be developed as demonstrative kits to detect predisposition for and diagnosis of such diseases. Categories: Nucleotide Sequences: Gene Structure, Introns and Exons, & Splice Sites Databases

  • From Current Category

Cite this (AmaZonia: Explore the Jungle of Microarrays Results, RRID:SCR_008405)

URL: http://amazonia.montp.inserm.fr/

Resource Type: Resource, data or information resource, database

A web interface and associated tools for easy query of public human transcriptome data by keyword, through thematic pages with list annotations. Amazonia provides a thematic entry to public transcriptomes: users may for instance query a gene on a Stem Cells page, where they will see the expression of their favorite gene across selected microarray experiments related to stem cell biology. This selection of samples can be customized at will among the 6331 samples currently present in the database. Every transcriptome study results in the identification of lists of genes relevant to a given biological condition. In order to include this valuable information in any new query in the Amazonia database, they indicate for each gene in which lists it is included. This is a straightforward and efficient way to synthesize hundreds of microarray publications.

  • From Current Category

    AnnTools

Cite this (AnnTools, RRID:SCR_005170)

URL: http://anntools.sourceforge.net/

Resource Type: Resource, software resource

Software tool for annotating single nucleotide substitutions (SNP/SNV), small insertions/deletions (indels), and copy number variations (CNV) calls generated from sequencing and microarray data. Only human genome build 37/hg19 can be annotated at this time.

  • From Current Category

Cite this (ApiDB ToxoDB, RRID:SCR_013453)

URL: http://toxodb.org/toxo/

Resource Type: Resource, data or information resource, database

A genome and functional genomic database for the protozoan parasite Toxoplasma gondii. It incorporates the sequence and annotation of the T. gondii ME49 strain, as well as genome sequences for the GT1, VEG and RH (Chr Ia, Chr Ib) strains. Sequence information is integrated with various other genomic-scale data, including community annotation, ESTs, gene expression and proteomics data. Organisms * Toxoplasma gondii (ME49, RH, GT1, Veg strains) * Neospora caninum * environmental isolate sequences from numerous species Tools * BLAST: Identify Sequence Similarities * Sequence Retrieval: Retrieve Specific Sequences using IDs and coordinates * PubMed and Entrez: View the Latest Toxoplasma, Neospora Pubmed and Entrez Results * Genome Browser: View Sequences and Features in the genome browser * Ancillary Genome Browse: Access Additional info like Probeset data and Toxoplasma Array info

  • From Current Category

Cite this (Arabidopsis Hormone Database, RRID:SCR_001792)

URL: http://ahd.cbi.pku.edu.cn

Resource Type: Resource, data repository, ontology, database, service resource, storage service resource, controlled vocabulary, data or information resource

Database providing a systematic and comprehensive view of morphological phenotypes regulated by plant hormones, as well as regulatory genes participating in numerous plant hormone responses. By integrating the data from mutant studies, transgenic analysis and gene ontology annotation, genes related to the stimulus of eight plant hormones were identified, including abscisic acid, auxin, brassinosteroid, cytokinin, ethylene, gibberellin, jasmonic acid and salicylic acid. Another pronounced characteristics of this database is that a phenotype ontology was developed to precisely describe all kinds of morphological processes regulated by plant hormones with standardized vocabularies. To increase the coverage of phytohormone related genes, the database has been updated from AHD to AHD2.0 adding and integrating several pronounced features: (1) added 291 newly published Arabidopsis hormone related genes as well as corrected information (e.g. the arguable ABA receptors) based on the recent 2-year literature; (2) integrated orthologues of sequenced plants in OrthoMCLDB into each gene in the database; (3) integrated predicted miRNA splicing site in each gene in the database; (4) provided genetic relationship of these phytohormone related genes mining from literature, which represents the first effort to construct a relatively comprehensive and complex network of hormone related genes as shown in the home page of our database; (5) In convenience to in-time bioinformatics analysis, they also provided links to a powerful online analysis platform Weblab that they have recently developed, which will allow users to readily perform various sequence analysis with these phytohormone related genes retrieved from AHD2.0; (6) provided links to other protein databases as well as more expression profiling information that would facilitate users for a more systematic analysis related to phytohormone research. Please help to improve the database with your contributions.

  • From Current Category

    ARACNE

Cite this (ARACNE, RRID:SCR_002180)

URL: http://wiki.c2b2.columbia.edu/califanolab/index.php/Software/ARACNE

Resource Type: Resource, software resource, software application

An algorithm, using microarray expression profiles, to scale up to the complexity of regulatory networks in mammalian cells, yet general enough to address a wider range of network deconvolution problems. This method uses an information theoretic approach to eliminate the vast majority of indirect interactions typically inferred by pairwise analysis.

  • From Current Category

  1. Resource Identification Portal Resources

    Welcome to the RRID Resources search. From here you can search through a compilation of resources used by RRID and see how data is organized within our community.

  2. Navigation

    You are currently on the Community Resources tab looking through categories and sources that RRID has compiled. You can navigate through those categories from here or change to a different tab to execute your search through. Each tab gives a different perspective on data.

  3. Logging in and Registering

    If you have an account on RRID then you can log in from here to get additional features in RRID such as Collections, Saved Searches, and managing Resources.

  4. Searching

    Here is the search term that is being executed, you can type in anything you want to search for. Some tips to help searching:

    1. Use quotes around phrases you want to match exactly
    2. You can manually AND and OR terms to change how we search between words
    3. You can add "-" to terms to make sure no results return with that term in them (ex. Cerebellum -CA1)
    4. You can add "+" to terms to require they be in the data
    5. Using autocomplete specifies which branch of our semantics you with to search and can help refine your search
  5. Save Your Search

    You can save any searches you perform for quick access to later from here.

  6. Query Expansion

    We recognized your search term and included synonyms and inferred terms along side your term to help get the data you are looking for.

  7. Collections

    If you are logged into RRID you can add data records to your collections to create custom spreadsheets across multiple sources of data.

  8. Sources

    Here are the sources that were queried against in your search that you can investigate further.

  9. Categories

    Here are the categories present within RRID that you can filter your data on

  10. Subcategories

    Here are the subcategories present within this category that you can filter your data on

  11. Further Questions

    If you have any further questions please check out our FAQs Page to ask questions and see our tutorials. Click this button to view this tutorial again.

X