Searching the RRID Resource Information Network
Are you sure you want to leave this community? Leaving the community will revoke any permissions you have been granted in this community.
SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
http://www.agcol.arizona.edu/software/tcw/
Software package for assembling, annotating, querying, and comparing transcript and expression level data that consists of two parts: * singleTCW (sTCW): Single transcript sets or assemblies; annotation; differential expression (EdgeR, DEGSeq, DESeq, GoSeq) * multiTCW (mTCW): Comparison of multiple transcript sets; ortholog grouping (e.g., OrthoMCL) It has been tested on Linux and uses Java, mySQL and optionally R.
Proper citation: TCW (RRID:SCR_001875) Copy
https://www.bioinformatics.babraham.ac.uk/projects/seqmonk/
Software tool to visualize and analyse high throughput mapped sequence data.
Proper citation: SeqMonk (RRID:SCR_001913) Copy
http://victorian-bioinformatics-consortium.github.io/degust/
An interactive web tool for visualizing differential gene expression data.
Proper citation: Degust (RRID:SCR_001878) Copy
http://www.bioconductor.org/packages/release/bioc/html/flowUtils.html
Software that provides utilities for flow cytometry data.
Proper citation: flowUtils (RRID:SCR_001879) Copy
https://github.com/hms-dbmi/spp
R analysis and processing package for Illumina platform Chip-Seq data.
Proper citation: SPP (RRID:SCR_001790) Copy
https://github.com/JialiUMassWengLab/TEMP
Software package for detecting transposable elements (TEs) insertions and excisions from pooled high-throughput sequencing data.
Proper citation: TEMP (RRID:SCR_001788) Copy
https://github.com/uci-cbcl/EXTREME
A motif discovery algorithm designed to find DNA-binding motifs in ChIP-Seq and DNase-Seq data.
Proper citation: EXTREME (RRID:SCR_001821) Copy
http://www.megabionet.org/atpid/webfile/
Centralized platform to depict and integrate the information pertaining to protein-protein interaction networks, domain architecture, ortholog information and GO annotation in the Arabidopsis thaliana proteome. The Protein-protein interaction pairs are predicted by integrating several methods with the Naive Baysian Classifier. All other related information curated is manually extracted from published literature and other resources from some expert biologists. You are welcomed to upload your PPI or subcellular localization information or report data errors. Arabidopsis proteins is annotated with information (e.g. functional annotation, subcellular localization, tissue-specific expression, phosphorylation information, SNP phenotype and mutant phenotype, etc.) and interaction qualifications (e.g. transcriptional regulation, complex assembly, functional collaboration, etc.) via further literature text mining and integration of other resources. Meanwhile, the related information is vividly displayed to users through a comprehensive and newly developed display and analytical tools. The system allows the construction of tissue-specific interaction networks with display of canonical pathways.
Proper citation: Arabidopsis thaliana Protein Interactome Database (RRID:SCR_001896) Copy
http://sourceforge.net/projects/openadam/
A web-based database management system for the large amount of genotype data generated from the Affymetrix GeneChip Mapping Array and Genome-Wide Human SNP Array platforms.
Proper citation: openADAM (RRID:SCR_002018) Copy
http://www.bioconductor.org/packages/release/bioc/html/flowTrans.html
Software for profile maximum likelihood estimation of parameters for flow cytometry data transformations.
Proper citation: flowTrans (RRID:SCR_002093) Copy
http://www.broadinstitute.org/mpg/snap/
A computer program and web-based service for the rapid retrieval of linkage disequilibrium proxy single nucleotide polymorphism (SNP) results given input of one or more query SNPs and based on empirical observations from the International HapMap Project and the 1000 Genomes Project. A series of filters allow users to optionally retrieve results that are limited to specific combinations of genotyping platforms, above specified pairwise r2 thresholds, or up to a maximum distance between query and proxy SNPs. SNAP can also generate linkage disequilibrium plots
Proper citation: SNAP - SNP Annotation and Proxy Search (RRID:SCR_002127) Copy
https://github.com/nicolazzie/AffyPipe
An open-source software pipeline for Affymetrix Axiom genotyping workflow.
Proper citation: AffyPipe (RRID:SCR_002032) Copy
https://github.com/adrlar/CanSNPer
Software that is a hierarchical genotype classifier of clonal pathogens.
Proper citation: CanSNPer (RRID:SCR_001980) Copy
http://sourceforge.net/projects/dmetanalyzer/
Software tool for the automatic association analysis among the variation of the patient genomes and the clinical conditions of patients, i.e. the different response to drugs. The system allows: (i) to automatize the workflow of analysis of DMET (drug metabolism enzymes and transporters)-SNP (Single Nucleotide Polymorphism) data avoiding the use of multiple tools; (ii) the automatic annotation of DMET-SNP data and the search in existing databases of SNPs (e.g. dbSNP), (iii) the association of SNP with pathway through the search in PharmaKGB, a major knowledge base for pharmacogenomic studies. It has a simple graphical user interface that allows users (doctors/biologists) to upload and analyze DMET files produced by Affymetrix DMET-Console in an interactive way.
Proper citation: DMET-Analyzer (RRID:SCR_002030) Copy
Statistical software tool for calling common and rare variants in analysis of pool or individual next-generation sequencing data. This software is optimized for analysis of whole-exome sequencing data and whole-genome sequencing data.
Proper citation: SNVer (RRID:SCR_002061) Copy
http://cmb.gis.a-star.edu.sg/ChIPSeq/paperChIPSeq.htm
THIS RESOURCE IS NO LONGER IN SERVICE, documented on April 12, 2017. A software tool to find peaks from ChIPSeq data generated from the Solexa/Illumina platform., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: ChIPSeq Peak Finder (RRID:SCR_002081) Copy
https://github.com/homopolymer/PyroTools/
A software program to call short indels and SNPs for Ion Torrent and 454 data.
Proper citation: PyroHMMvar (RRID:SCR_002073) Copy
An agency responsible for the evaluation and supervision of medicines developed by pharmaceutical companies for use in the European Union. Its main responsibility is the protection and promotion of public and animal health through the evaluation and supervision of medicines for human and veterinary use. The Agency also plays a role in stimulating innovation and research in the pharmaceutical sector. The Agency gives scientific advice and other assistance to companies for the development of new medicines. It publishes guidelines on quality-, safety- and efficacy-testing requirements. A dedicated SME Office provides special assistance to small and medium-sized enterprises.
Proper citation: European Medicines Agency (RRID:SCR_011215) Copy
http://www.cisd.ethz.ch/software/openBIS
Software for an open, distributed system for managing biological information that supports biological research data workflows from the source (i.e. the measurement instruments) to facilitate the process of answering biological questions by means of cross-domain queries against raw data, processed data, knowledge resources and its corresponding metadata. The openBIS software framework can be easily extended and has been customized for the following technologies: * High Content Screening * Proteomics * Deep Sequencing * Metabolomics
Proper citation: openBIS (RRID:SCR_011815) Copy
http://www.ebi.ac.uk/Tools/msa/kalign/
A fast and accurate multiple sequence alignment algorithm.
Proper citation: Kalign (RRID:SCR_011810) Copy
Can't find your Tool?
We recommend that you click next to the search bar to check some helpful tips on searches and refine your search firstly. Alternatively, please register your tool with the SciCrunch Registry by adding a little information to a web form, logging in will enable users to create a provisional RRID, but it not required to submit.
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.
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.
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.
Here is the search term that is being executed, you can type in anything you want to search for. Some tips to help searching:
You can save any searches you perform for quick access to later from here.
We recognized your search term and included synonyms and inferred terms along side your term to help get the data you are looking for.
If you are logged into RRID you can add data records to your collections to create custom spreadsheets across multiple sources of data.
Here are the sources that were queried against in your search that you can investigate further.
Here are the categories present within RRID that you can filter your data on
Here are the subcategories present within this category that you can filter your data on
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.
