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://tophat.cbcb.umd.edu/fusion_index.html
An algorithm for Discovery of Novel Fusion Transcripts with the ability to align reads across fusion points, which results from the breakage and re-joining of two different chromosomes, or from rearrangements within a chromosome.
Proper citation: TopHat-Fusion (RRID:SCR_011899) Copy
http://genome.ucsc.edu/cgi-bin/hgBlat?command=start
Software designed to quickly find sequences of 95% and greater similarity of length 25 bases or more.
Proper citation: BLAT (RRID:SCR_011919) Copy
http://www.bios.unc.edu/research/genomic_software/BBSeq/
A Powerful and Flexible Approach to the Analysis of RNA Sequence Count Data.
Proper citation: BBSeq (RRID:SCR_011877) Copy
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://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://sourceforge.net/projects/mirplant/
A user-friendly plant miRNA prediction tool.
Proper citation: miRPlant (RRID:SCR_012105) Copy
https://code.google.com/p/slidesort-bpr/
Software using a reference-free method for detecting clusters of breakpoints from the chromosomal rearrangements.
Proper citation: SlideSort-BPR (RRID:SCR_012079) Copy
http://www.bioinf.jku.at/software/fabia/fabia.html
A model-based technique for biclustering that is clustering rows and columns simultaneously.
Proper citation: FABIA (RRID:SCR_012002) Copy
Software that allows fast and user-friendly verification of Mascot result files, as well as data quantification using isotopic labeling methods (SILAC/ICAT) or label free approaches (spectral counting, MS signal comparison).
Proper citation: MFPaQ (RRID:SCR_012049) Copy
http://sourceforge.net/projects/multiplierz/
An open-source Python-based environment that provides a scriptable framework for efficient access to manufacturers'' proprietary data files via mzAPI.
Proper citation: multiplierz (RRID:SCR_012058) Copy
http://www.computationalbioenergy.org/meta-storms.html
Optimized GPU-based software to efficiently measure the quantitative phylogenetic similarity among massive amount of microbial community samples.
Proper citation: GPU-Meta-Storms (RRID:SCR_012029) Copy
http://opencobra.sourceforge.net/openCOBRA/Welcome.html
Software Python package that provides support for basic COnstraint-Based Reconstruction and Analysis (COBRA) methods.
Proper citation: COBRApy (RRID:SCR_012096) Copy
https://code.google.com/p/netcoffee/
A fast and accurate algorithm which allows to find a global alignment of multiple protein-protein interaction networks.
Proper citation: NetCoffee (RRID:SCR_012095) Copy
Database on transcriptional regulation in Escherichia coli K-12 containing knowledge manually curated from original scientific publications, complemented with high throughput datasets and comprehensive computational predictions. Graphic and text-integrated environment with friendly navigation where regulatory information is always at hand. They provide integrated views to understand as well as organized knowledge in computable form. Users may submit data to make it publicly available.
Proper citation: RegulonDB (RRID:SCR_003499) Copy
http://compbio.cs.toronto.edu/CNVer/
A method for CNV detection that supplements the depth-of-coverage with paired-end mapping information, where matepairs mapping discordantly to the reference serve to indicate the presence of variation.
Proper citation: CNVer (RRID:SCR_010820) Copy
http://www.popgen.dk/software/index.php/Relate
Software providing a method that estimates the probability of sharing alleles identity by descent (IBD) across the genome and can also be used for mapping disease loci using distantly related individuals.
Proper citation: Relate (RRID:SCR_010794) Copy
http://compbio.cs.toronto.edu/modil/
Software for a novel method for finding medium sized indels from high throughput sequencing datasets.
Proper citation: MoDIL (RRID:SCR_010764) Copy
http://pgrc.ipk-gatersleben.de/misa/
Software tool that allows the identification and localization of perfect microsatellites as well as compound microsatellites which are interrupted by a certain number of bases.
Proper citation: MISA (RRID:SCR_010765) Copy
http://www.phenosystems.com/www/index.php/products/gensearchngs
An integrated software solution for the analysis of DNA-Seq data from commonly used NGS equipments such as Roche/454, Illumina and Ion Torrent.
Proper citation: GensearchNGS (RRID:SCR_010802) 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.
