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://sourceforge.net/projects/plek/
An alignment-free software tool which uses a computational pipeline based on an improved k-mer scheme and a support vector machine (SVM) algorithm to distinguish lncRNAs from messenger RNAs (mRNAs), in the absence of genomic sequences or annotations. It is especially suitable for PacBio or 454 sequencing data and large-scale transcriptome data.
Proper citation: PLEK (RRID:SCR_012132) Copy
http://sourceforge.net/projects/ldx/
A computational software tool for estimating linkage disequilibrium (LD) from pooled resequencing data.
Proper citation: LDx (RRID:SCR_012131) Copy
http://pprospector.sourceforge.net/
A pipeline of software programs to design and analyze PCR primers. It is built in Python using the open-source PyCogent toolkit.
Proper citation: PrimerProspector (RRID:SCR_012136) Copy
http://musite.sourceforge.net/
A Java-based standalone application for predicting both general and kinase-specific protein phosphorylation sites.
Proper citation: Musite (RRID:SCR_012141) Copy
http://sourceforge.net/projects/phosphosite/
A bioinformatical software tool for analyzing (quantitative) phosphoproteome datasets. The program retrieves kinase-substrate predictions from NetworKIN and contains various statistical modules for futher analysis.
Proper citation: PhosphoSiteAnalyzer (RRID:SCR_012142) Copy
http://sourceforge.net/projects/cnv/
Software for a web-enabled platform for analyzing genome variation such as copy number variation (CNV).
Proper citation: CNV Workshop (RRID:SCR_012635) Copy
http://sourceforge.net/p/krona/home/krona/
Software that allows hierarchical data to be explored with zoomable pie charts.
Proper citation: Krona (RRID:SCR_012785) Copy
http://sourceforge.net/projects/acaciaerrorcorr/?source=navbar
Accurate error-correction of amplicon pyrosequences.
Proper citation: Acacia (RRID:SCR_012896) Copy
http://sourceforge.net/projects/ibdld/
A C++ software program for multipoint IBD estimation based on high density SNP genotype data.
Proper citation: IBDLD (RRID:SCR_013043) Copy
http://sourceforge.net/projects/solsnp/
A Java-based DNA variant calling tool for Next-Generation Sequencing alignment data.
Proper citation: SolSNP (RRID:SCR_013045) Copy
http://sourceforge.net/projects/tumorhats/
A software tool that calls the amplified alleles, and thus amplified haplotype, in copy number aberration regions in next generation sequencing tumor data.
Proper citation: HATS (RRID:SCR_013044) Copy
http://sourceforge.net/projects/chipotle-perl/
A peak-finding algorithm used to analyze ChIP-chip microarray data.
Proper citation: ChIPOTle Peak Finder (RRID:SCR_012991) Copy
http://trinityrnaseq.sourceforge.net/
Software for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data.
Proper citation: Trinity (RRID:SCR_013048) Copy
http://sourceforge.net/projects/ngspeanalysis/
A pipeline using open-source tools which can implement a set of pair ended Next-generation sequencing analysis, include short reads alignment, high-quality variation genotype calling and variants annotation.
Proper citation: NGSpeAnalysis (RRID:SCR_013040) Copy
http://sourceforge.net/projects/lofreq/
A fast and sensitive variant-caller for inferring single-nucleotide variants (SNVs) from high-throughput sequencing data.
Proper citation: LoFreq (RRID:SCR_013054) Copy
http://sourceforge.net/projects/genecounter/
A computational pipeline for analyzing RNA-Sequencing (RNA-Seq) data for differential gene expression of eukaryotes, prokaryotes, as well as organisms with no available genome reference sequence.
Proper citation: GENE-counter (RRID:SCR_013056) Copy
http://sourceforge.net/projects/rnacompass/
A web-based GUI distributed computational pipeline, provides all-in-one functionality including human transcriptome quantification and the typical endogenous RNA-Sequencing analysis along with the investigation of exogenous sequences.
Proper citation: RNA CoMPASS (RRID:SCR_013058) Copy
http://sourceforge.net/projects/snptools/
A suite of software tools that enables integrative SNP analysis in next generation sequencing data with large cohorts.
Proper citation: SNPTools (RRID:SCR_013052) Copy
http://sourceforge.net/projects/swiftng/
An open source package for primary data analysis on next-gen sequence data from images to basecalls. Currently Swift is targeted toward Solexa/Illumina sequencing, but is designed to be platform agnostic.
Proper citation: Swift (RRID:SCR_013018) Copy
http://sourceforge.net/projects/cloudaligner/
A map/reduce based application for mapping short reads generated by the next-generation sequencing machines.
Proper citation: CloudAligner (RRID:SCR_012962) 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.
