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 27 results

    asSeq

Cite this (asSeq, RRID:SCR_001625)

URL: http://bios.unc.edu/~weisun/software/asSeq.htm

Resource Type: Resource, software resource, software application, data analysis software, data processing software, source code

Software that establishes a statistical framework for future developments of eQTL (expression quantitative trait locus) mapping methods using RNA-seq data (e.g., linkage-based eQTL mapping), and the joint study of multiple genetic markers and/or multiple genes. This R package has been submitted to R/bioconductor. It will be available on bioconductor soon. It is recommended to install this R package from bioconductor. You can also install this R package from the source code by yourself. Since the R package contains C code, a C complier is required for installation. With both R and appropriate c complier installed, this R package can be installed using the following command (in Mac Terminal window or Windows command window) R CMD INSTALL asSeq

  • From Current Category

    Avadis

Cite this (Avadis, RRID:SCR_000644)

URL: http://www.avadis-ngs.com

Resource Type: Resource, data analysis software, data processing software, software library, software application, data management software, data visualization software, software resource, software toolkit, commercial organization

An integrated platform that provides analysis, management and visualization tools for next-generation sequencing data. It supports workflows for RNA-Seq, DNA-Seq, ChIP-Seq and small RNA-Seq experiments. Avadis has a built-in Gene Ontology browser to view ontology hierarchies. There are common ontology paths for multiple genes. Genes can be clustered based on ontology terms to identify functional signatures in gene expression clusters. AVADIS platform has a rich collection of data / text mining algorithms, data visualization libraries, workflow/application automation layers, and enterprise data organization functions. These functions are available as libraries that allow developers to rapidly build software prototypes, applications and off-the-shelf products. The collection of algorithms and visualizations in AVADIS grows as new applications using the platform are developed. Currently, the algorithms that AVADIS platform contains range from general purpose statistical mining and modelling algorithms, to text mining algorithms, to very application-specific algorithms for microarray / NGS data analysis, QSAR modelling and biological networks analysis. AVADIS has a collection of powerful mining algorithms like PCA, ANOVA, T-test, clustering, classification and regression methods. The range of visualizations includes most statistical and data modelling related graphing views, and very application-specific visualizations. Some of the statistical views include 2D/3D scatter plots, profile plots, heat maps, histograms and matrix plot; data modelling relevant views include dendrograms, cluster profiles, similarity images and SOM U-matrices. Application-specific views in AVADIS include pathway network views, genome browsers, chemical structure views and pipe-line views. Platform: Windows compatible, Mac OS X compatible, Linux compatible,

  • From Current Category

Cite this (categoryCompare, RRID:SCR_001223)

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

Resource Type: Resource, software resource, software application, data analysis software, data processing software

A software package for meta-analysis of high-throughput experiments using feature annotations. It calculates significant annotations (categories) in each of two (or more) feature (i.e. gene) lists, determines the overlap between the annotations, and returns graphical and tabular data about the significant annotations and which combinations of feature lists the annotations were found to be significant. Interactive exploration is facilitated through the use of RCytoscape (heavily suggested).

  • From Current Category

Cite this (DataAssist, RRID:SCR_014969)

URL: https://www.thermofisher.com/us/en/home/technical-resources/software-downloads/dataassist-software.html

Resource Type: Resource, software resource, software application, data analysis software, data processing software, data visualization software

Data analysis tool that utilizes the Comparative CT (ddCT) method to rapidly and accurately quantitate relative gene expression across a large number of genes and samples. Raw input from plates or arrays can be analyzed according to user-determined settings.

  • From Current Category

    DESeq

Cite this (DESeq, RRID:SCR_000154)

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

Resource Type: Resource, software resource, software application, data analysis software, data processing software

A 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.

  • From Current Category

    EasyqpcR

Cite this (EasyqpcR, RRID:SCR_003406)

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

Resource Type: Resource, software resource, software application, data analysis software, data processing software

Software package for low-throughput real-time quantitative PCR data analysis. The package allows you to import easily qPCR data files. Thereafter, you can calculate amplification efficiencies, relative quantities and their standard errors, normalization factors based on the best reference genes choosen (using the SLqPCR package), and then the normalized relative quantities, the NRQs scaled to your control and their standard errors.

  • From Current Category

    ErmineJ

Cite this (ErmineJ, RRID:SCR_006450)

URL: http://bioinformatics.ubc.ca/ermineJ/

Resource Type: Resource, software resource, software application, data analysis software, data processing software

Data analysis software for gene sets in expression microarray data or other genome-wide data that results in rankings of genes. A typical goal is to determine whether particular biological pathways are doing something interesting in the data. The software is designed to be used by biologists with little or no informatics background. A command-line interface is available for users who wish to script the use of ermineJ. Major features include: * Implementation of multiple methods for gene set analysis: ** Over-representation analysis ** A resampling-based method that uses gene scores ** A rank-based method that uses gene scores ** A resampling-based method that uses correlation between gene expression profiles (a type of cluster-enrichment analysis). * Gene sets receive statistical scores (p-values), and multiple test correction is supported. * Support of the Gene Ontology terminology; users can choose which aspects to analyze. * User files use simple text formats. * Users can modify gene sets or create new ones. * The results can be visualized within the software. * It is simple to compare multiple analyses of the same data set with different settings. * User-definable hyperlinks are provided to external sites to allow more efficient browsing of the results. * For programmers, there is a command line interface as well as a simple application programming interface that can be used to plug ermineJ functionality into your own code Platform: Online tool, Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible

  • From Current Category

Cite this (Fluidigm Singular Analysis Toolset, RRID:SCR_015685)

URL: https://www.fluidigm.com/software

Resource Type: Resource, data analysis software, data processing software, software application, sequence analysis software, data visualization software, software resource

Software toolkit for analyzing and visualizing data of single cell qPCR/RNA-seq. It offers methods for identifying gene expression and mutation patterns at the single-cell level and is designed for use with Biomark and C1 systems.

  • From Current Category

Cite this (FunCluster, RRID:SCR_005774)

URL: http://corneliu.henegar.info/FunCluster.htm

Resource Type: Resource, software resource, software application, data analysis software, data processing software

FunCluster is a genomic data analysis algorithm which performs functional analysis of gene expression data obtained from cDNA microarray experiments. Besides automated functional annotation of gene expression data, FunCluster functional analysis aims to detect co-regulated biological processes through a specially designed clustering procedure involving biological annotations and gene expression data. FunCluster''''s functional analysis relies on Gene Ontology and KEGG annotations and is currently available for three organisms: Homo Sapiens, Mus Musculus and Saccharomyces Cerevisiae. FunCluster is provided as a standalone R package, which can be run on any operating system for which an R environment implementation is available (Windows, Mac OS, various flavors of Linux and Unix). Download it from the FunCluster website, or from the worldwide mirrors of CRAN. FunCluster is provided freely under the GNU General Public License 2.0. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible

  • From Current Category

Cite this (GeneChip Operating Software, RRID:SCR_003408)

URL: http://www.scripps.edu/researchservices/dna_array/pages/Data_Analysis_GCOS.htm

Resource Type: Resource, data analysis software, data processing software, software application, sequence analysis software, core facility, service resource, access service resource, software resource

Affymetrix has recently released a new software for the acquisition, management, and analysis of gene expression data. The new GeneChip Operating Software (GCOS) platform enables researchers to perform gene expression, SNP mapping and resequencing analysis with integrated data management and scalable client server configurations. * Compatible with additional Affymetrix analysis software such as Data Mining Tool (DMT) and GeneChip DNA Analysis Software (GDAS) * Supports Gene Expression, Resequencing and Genotyping Applications * Baseline Comparison Analysis Input: Affymetrix .DAT file Output: Affymetrix files (.CEL, .CHP, .RPT, .EXP, .TXT) Availability: The Core Facility has a copy of GCOS, as well as an older version of the Affymetrix software, Microarray Suite (MAS), available for use upon request.

  • From Current Category

Cite this (GenePattern, RRID:SCR_003201)

URL: http://www.broadinstitute.org/cancer/software/genepattern

Resource Type: Resource, software resource, software application, data analysis software, data processing software

A powerful genomic analysis platform that provides access to hundreds of tools for gene expression analysis, proteomics, SNP analysis, flow cytometry, RNA-seq analysis, and common data processing tasks. A web-based interface provides easy access to these tools and allows the creation of multi-step analysis pipelines that enable reproducible in silico research.

  • From Current Category

    Genesis

Cite this (Genesis, RRID:SCR_015775)

URL: https://genome.tugraz.at/genesisclient/genesisclient_description.shtml

Resource Type: Resource, software resource, software application, data analysis software, data processing software, data visualization software

Software for cluster analysis of microarray data. Genesis is a platform independent Java package of tools to simultaneously visualize and analyze a whole set of gene expression experiments.

  • From Current Category

    GOdist

Cite this (GOdist, RRID:SCR_005770)

URL: http://basalganglia.huji.ac.il/links.htm

Resource Type: Resource, software resource, software application, data analysis software, data processing software

GOdist is a Matlab program that analyzes Affymetrix microarray expression data implementing Kolmogorov-Smirnov (KS) continuous statistics approach. It also implements the discrete approach using Fisher exact test employing a two-tailed hypergeometric distribution. GOdist enables detection of both kinds of changes within specific GO terms represented on the array in relation to different populations: the global array population, the direct parents of the analyzed GO term and the global parent of it (e.g. biological process, molecular function or cellular component). Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible

  • From Current Category

    Hipposeq

Cite this (Hipposeq, RRID:SCR_015730)

URL: http://hipposeq.janelia.org/

Resource Type: Resource, data analysis software, data processing software, database, software application, sequence analysis software, web application, software resource, data or information resource

Database of RNA-seq gene expression in hippocampal principal neurons. Hipposeq can analyze and visualize RNA-seq data for all excitatory cell populations in the hippocampus at multiple levels of granularity.

  • From Current Category

Cite this (L2L Microarray Analysis Tool, RRID:SCR_013440)

URL: https://omictools.com/l2l-tool

Resource Type: Resource, data analysis service, data analysis software, data processing software, production service resource, analysis service resource, software application, database, service resource, storage service resource, software resource, data repository, data or information resource

NO LONGER IN SERVICE. Documented on August 26, 2019.

Database of published microarray gene expression data, and a software tool for comparing that published data to a user''''s own microarray results. It is very simple to use - all you need is a web browser and a list of the probes that went up or down in your experiment. If you find L2L useful please consider contributing your published data to the L2L Microarray Database in the form of list files. L2L finds true biological patterns in gene expression data by systematically comparing your own list of genes to lists of genes that have been experimentally determined to be co-expressed in response to a particular stimulus - in other words, published lists of microarray results. The patterns it finds can point to the underlying disease process or affected molecular function that actually generated the observed changed in gene expression. Its insights are far more systematic than critical gene analyses, and more biologically relevant than pure Gene Ontology-based analyses. The publications included in the L2L MDB initially reflected topics thought to be related to Cockayne syndrome: aging, cancer, and DNA damage. Since then, the scope of the publications included has expanded considerably, to include chromatin structure, immune and inflammatory mediators, the hypoxic response, adipogenesis, growth factors, hormones, cell cycle regulators, and others. Despite the parochial origins of the database, the wide range of topics covered will make L2L of general interest to any investigator using microarrays to study human biology. In addition to the L2L Microarray Database, L2L contains three sets of lists derived from Gene Ontology categories: Biological Process, Cellular Component, and Molecular Function. As with the L2L MDB, each GO sub-category is represented by a text file that contains annotation information and a list of the HUGO symbols of the genes assigned to that sub-category or any of its descendants. You don''''t need to download L2L to use it to analyze your microarray data. There is an easy-to-use web-based analysis tool, and you have the option of downloading your results so you can view them at any time on your own computer, using any web browser. However, if you prefer, the entire L2L project, and all of its components, can be downloaded from the download page. Platform: Online tool, Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible

  • From Current Category

Cite this (larvalign, RRID:SCR_015815)

URL: https://github.com/larvalign/larvalign

Resource Type: Resource, data analysis software, data processing software, software application, sequence analysis software, data set, software resource, software toolkit, data or information resource

Software package including computational methods for aligning gene expression patterns from the larval brain of Drosophila melanogaster. Its method includes evaluation of the registration framework involved in template generation and mapping.

  • From Current Category

Cite this (MAPPFinder, RRID:SCR_005791)

URL: http://www.genmapp.org/help_v2/UsingMAPPFinder.htm

Resource Type: Resource, software resource, software application, data analysis software, data processing software

MAPPFinder is an accessory program for GenMAPP. This program allows users to query any existing GenMAPP Expression Dataset Criterion against GO gene associations and GenMAPP MAPPs (microarray pathway profiles). The resulting analysis provides the user with results that can be viewed directly upon the Gene Ontology hierarchy and within GenMAPP, by selecting terms or MAPPs of interest. Platform: Windows compatible

  • From Current Category

    metahdep

Cite this (metahdep, RRID:SCR_001225)

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

Resource Type: Resource, software resource, software application, data analysis software, data processing software

Software tools for meta-analysis in the presence of hierarchical (and/or sampling) dependence, including with gene expression studies.

  • From Current Category

Cite this (Microarray Literature-based Annotation, RRID:SCR_008206)

URL: http://bioinformatics.ekmd.huji.ac.il/milano/

Resource Type: Resource, software resource, software application, data analysis software, data processing software

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. MILANO provides a useful tool for the automatic custom annotation of microarray results which is based on all the available literature. It has two major advances over similar tools: the ability to expand gene names to include all their informative synonyms while removing synonyms that are not informative and access to the GeneRIF database which provides short summaries of curated articles relevant to known genes. MILANO allows annotation of lists of genes derived from microarray results by user defined terms. The annotation strategy is based on counting the number of literature co-occurrences of each gene on the list with a user defined term. This strategy allows the customization of the annotation procedure and thus overcomes one of the major limitations of the functional annotations usually provided with microarray results. MILANO expands the gene names to include all their informative synonyms while filtering out gene symbols that are likely to be less informative as literature searching terms. It supports searching two literature databases: GeneRIF and Medline (through PubMed), allowing retrieval of both quick and comprehensive results. MILANO''s ability can improve microarray analysis by analyzing a list of 150 genes that were affected by p53 overproduction. This analysis reveals that it enables immediate identification of known p53 target genes on this list and assists in sorting the list into genes known to be involved in p53 related pathways, apoptosis and cell cycle arrest. This program performs automatic searches in PubMed or the GeneRIF collection for articles containing co-occurrences of search terms with a list of genes (e.g. from a microarray experiment). The program is used by pasting the list of Gene ID''s or symbols in the Primary Search Term field, and the list of cross-reference search terms in the Secondary Search Term field. The output is a table containing the number of hits for each pair of search terms. Sample input is provided in the fields, so you can just click submit and see what happens. If you want to run data of your own, delete the sample input first.

  • From Current Category

    oligo

Cite this (oligo, RRID:SCR_015729)

URL: https://bioconductor.org/packages/release/bioc/html/oligo.html

Resource Type: Resource, software resource, source code, data analysis software, data processing software, software application

Software package to analyze oligonucleotide arrays (expression/SNP/tiling/exon) at probe-level. It currently supports Affymetrix (CEL files) and NimbleGen arrays (XYS files).

  • From Current Category

  1. RRID 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