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://bioinformatics.mdanderson.org/main/PRADA:Overview
A pipeline to analyze paired end RNA-Seq data to generate gene expression values (RPKM) and gene-fusion candidates.
Proper citation: PRADA (RRID:SCR_011906) Copy
https://mcdonaldlab.biology.gatech.edu/r-sap/
An automated bioinformatics pipeline that analyzes and quantitates high-throughput RNA-Seq datasets.
Proper citation: R-SAP (RRID:SCR_011907) Copy
http://mapman.gabipd.org/web/guest/robin
Software package for RNA-Seq-based transcriptomics. Used to analyse Illumina/Solexa-based RNA-Seq data, Affymetrix data and generic tabular two color or single channel array data. Offers variety of quality control methods that can be used to gain overview of experimental data technical quality and structure.
Proper citation: RobiNA (RRID:SCR_011908) Copy
https://code.google.com/p/rseqflow/
An RNA-Seq analysis pipeline which offers an express implementation of analysis steps for RNA sequencing datasets.
Proper citation: RseqFlow (RRID:SCR_011909) Copy
https://code.google.com/p/seqpipe/
A command line-based pipeline framework for bioinformatics research.
Proper citation: SeqPipe (RRID:SCR_011862) Copy
http://1001genomes.org/software/shore.html
A mapping and analysis pipeline for short read data produced on the Illumina platform.
Proper citation: SHORE (RRID:SCR_011863) Copy
A question and answer site for professional and enthusiast programmers.
Proper citation: Stack Overflow (RRID:SCR_011984) Copy
Open Access Bioinformatics resource portal.
Proper citation: Bioinformaticsweb (RRID:SCR_011988) Copy
http://wwwdev.ebi.ac.uk/fg/hts_mappers/
Data set providing an up-to-date compendium of HTS mappers initially provided in the article Tools for mapping high-throughput sequencing data. Please let fill out the provided form if you are a developer and your mapper is not listed or you want to update the data for your mapper.
Proper citation: HTS Mappers (RRID:SCR_011991) Copy
http://en.wikibooks.org/wiki/Next_Generation_Sequencing
The Need for an Up-To-Date Synthesis of Next Generation Sequencing Know-How.
Proper citation: Next Generation Sequencing WikiBook (RRID:SCR_011993) Copy
http://topaz.gatech.edu/GeneTack/cgi/print_page.cgi?fn=db_home.html&title=Frameshift%20Database
Tools for frameshift prediction and a frameshift database.
Proper citation: GeneTack (RRID:SCR_011953) Copy
Web based instant protein network modeler for newly sequenced species. Web server designed to instantly construct genome scale protein networks using protein sequence data. Provides network visualization, analysis pages and solution for instant network modeling of newly sequenced species.
Proper citation: JiffyNet (RRID:SCR_011954) Copy
http://www.optimaldesign.com/ArrayMiner/ArrayMiner.htm
A set of analysis tools using advanced algorithms to reveal the true structure of your gene expression data.
Proper citation: ArrayMiner (RRID:SCR_011955) Copy
http://tagcleaner.sourceforge.net/
A software tool which can automatically detect and efficiently remove tag sequences from genomic and metagenomic datasets.
Proper citation: TagCleaner (RRID:SCR_011846) Copy
International collaboration of the International Nucleotide Sequence Databases (INSD), DDBJ, ENA, and GenBank, maintained for over 18 years. Individuals submitting data to the international sequence databases should be aware of INSDC policy.
Proper citation: INSDC (RRID:SCR_011967) Copy
http://sourceforge.net/projects/mirplant/
A user-friendly plant miRNA prediction tool.
Proper citation: miRPlant (RRID:SCR_012105) Copy
http://pypedal.sourceforge.net/
A pedigree analysis software package that provides tools for error checking, mathematical analysis, report generation, pedigree simulation, and data visualization.
Proper citation: PyPedal (RRID:SCR_012104) Copy
http://sourceforge.net/projects/simulatepcr/
Software that can be run from the command line for high throughput applications which can calculate all products from large lists of primers and probes compared to a large sequence database such as nt.
Proper citation: Simulate PCR (RRID:SCR_012106) Copy
https://code.google.com/p/condr/
Software that implements a HMM Model to detect copy number variants in exome sequence data.
Proper citation: CONDEX (RRID:SCR_012109) Copy
http://sourceforge.net/projects/sat-assembler/
A targeted gene assembly software program which aims to recover gene families of particular interest to biologists.
Proper citation: SAT-Assembler (RRID:SCR_012108) 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 NIF Resources search. From here you can search through a compilation of resources used by NIF and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that NIF 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 NIF then you can log in from here to get additional features in NIF 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 NIF 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 NIF 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.
Welcome to the Neuroscience Information Framework Project, designed to serve the biomedical research community. NIF maintains the largest searchable collection of neuroscience data, the largest catalog of biomedical resources, and the largest ontology for neuroscience on the web. We welcome all feedback and suggestions and are actively looking for resource providers to make their resources accessible through NIF. Learn about the tools available to help you share your data and discover a dynamic inventory of Web-based neuroscience resources.
