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.
https://web.archive.org/web/20180316202959/http://zombie.cb.k.u-tokyo.ac.jp/sprai/
Software tool to correct sequencing errors in single pass reads for de novo assembly.
Proper citation: sprai (RRID:SCR_024353) Copy
https://github.com/streamlit/streamlit
Software tool to turn data scripts into shareable web apps in minutes. Faster way to build and share data apps.
Proper citation: streamlit (RRID:SCR_024354) Copy
https://cme.h-its.org/exelixis/web/software/sweed/
Software tool for likelihood based detection of selective sweeps in thousands of genomes. Software parallel and checkpointable tool that implements composite likelihood ratio test for detecting selective sweeps.
Proper citation: sweed (RRID:SCR_024357) Copy
https://metacpan.org/dist/Bio-Tools-Run-Alignment-TCoffee
Software object for calculation of multiple sequence alignment from set of unaligned sequences or alignments using the TCoffee program.
Proper citation: Bio-Tools-Run-Alignment-TCoffee (RRID:SCR_024070) Copy
https://github.com/magnusmanske/snpomatic
Short read mapping software. Read mapping tool offering variety of analytical output functions, with emphasis on genotyping,
Proper citation: snpomatic (RRID:SCR_024348) Copy
Software tool to assist in recovery and prevention of Repetitive Strain Injury. Monitors keyboard and mouse usage and using this information, it frequently alerts you to take microbreaks, rest breaks and restricts you to your daily computer usage.
Proper citation: Workrave (RRID:SCR_024364) Copy
http://xmedcon.sourceforge.net/
Open source software toolkit for medical image conversion.
Proper citation: XMedCon (RRID:SCR_024366) Copy
http://www.ks.uiuc.edu/Research/vmd/
Software tool as molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. VMD supports computers running MacOS X, Unix, or Windows, is distributed free of charge, and includes source code.
Proper citation: VMD (RRID:SCR_024368) Copy
https://github.com/miRTop/mirtop
Command lines tool to annotate miRNAs with standard mirna/isomir naming.
Proper citation: mirtop (RRID:SCR_024116) Copy
https://sourceforge.net/projects/mpsqed/
Software tool for the design of multiplex pyrosequencing assays.
Proper citation: mPSQed (RRID:SCR_024118) Copy
http://www-igm.univ-mlv.fr/~marsan/smile_english.html
Software tool that infers motifs in set of sequences to infer exceptionnal sites as binding sites in DNA sequences. 1.4 version allows to infer motifs written on any alphabet in any kind of sequences. Allows to deal with motifs associated by some distance constraints. Used to group under unique model different occurrences composed of several boxes separated by spacers of different lengths.
Proper citation: SMILE (RRID:SCR_024119) Copy
http://technelysium.com.au/?page_id=13
Software ideal for the most basic of sequencing projects, where assembly of multiple sequences is not required., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: Chromas (RRID:SCR_000598) Copy
http://decgpu.sourceforge.net/homepage.htm
Software tool as parallel and distributed error correction algorithm for high-throughput short reads using CUDA and MPI parallel programming models.
Proper citation: DecGPU (RRID:SCR_000585) Copy
http://www.microbesonline.org/fasttree/
Source code that infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. It uses the Jukes-Cantor or generalized time-reversible (GTR) models of nucleotide evolution and the JTT, WAG, or LG models of amino acid evolution.
Proper citation: FastTree (RRID:SCR_015501) Copy
https://cran.r-project.org/web/packages/phytools/index.html
Software R package for phylogenetic comparative biology. The package contains various functions for phylogenetic analysis of comparative data from species.
Proper citation: phytools (RRID:SCR_015502) Copy
https://cran.r-project.org/web/packages/lme4/index.html
Software R package. Fit linear and generalized linear mixed-effects models. The models and their components are represented using S4 classes and methods. The core computational algorithms are implemented using the 'Eigen' C++ library for numerical linear algebra and 'RcppEigen' "glue."
Proper citation: lme4 (RRID:SCR_015654) Copy
http://www.bioinformatics.org/go2msig/
THIS RESOURCE IS NO LONGER IN SERVICE, documented on April 24, 2020. Software tool as automated Gene Ontology based multi species gene set generator for gene set enrichment analysis. Used to generate gene sets required for Gene Set Enrichment Analysis for almost any organism for which GO term association data exists.
Gene set collections can be automatically created for wide variety of species.
Proper citation: GO2MSIG (RRID:SCR_018359) Copy
http://genome.sph.umich.edu/wiki/Minimac
Software application that is a low memory, computationally efficient implementation of the MaCH algorithm for genotype imputation. It is designed to work on phased genotypes and can handle very large reference panels with hundreds or thousands of haplotypes. The name has two parts. The first, mini, refers to the modest amount of computational resources it requires. The second, mac, is short hand for MaCH, our widely used algorithm for genotype imputation. (entry from Genetic Analysis Software)
Proper citation: MINIMAC (RRID:SCR_009292) Copy
http://research.nhgri.nih.gov/ROMPrev/
Software tool for testing for association between polymorphisms and quantitative traits, as well as estimating trait heritability and locus-specific heritability using family data. (entry from Genetic Analysis Software)
Proper citation: ROMPREV (RRID:SCR_009361) Copy
http://www.jurgott.org/linkage/simulate.html
Software program to simulate genotypes in family members for a map of linked markers unlinked to a given affection status locus. the output is ready for analysis with UNKNOWN, ISIM, LSIM, or MSIM of the SLINK package. (entry from Genetic Analysis Software)
Proper citation: SIMULATE (RRID:SCR_009391) 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 dkNET Resources search. From here you can search through a compilation of resources used by dkNET and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that dkNET 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 dkNET then you can log in from here to get additional features in dkNET 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 dkNET 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 dkNET 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.
The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
Email: info_at_ dknet.org
