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.bioconductor.org/packages/release/bioc/html/TDARACNE.html
Software package to infer gene regulatory networks from time-series measurements. The algorithm is expected to be useful in reconstruction of small biological directed networks from time course data.
Proper citation: TDARACNE (RRID:SCR_000498) Copy
Software package for noise-robust soft clustering of gene expression time-series data (including a graphical user interface)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: Mfuzz (RRID:SCR_000523) Copy
http://gmt.genome.wustl.edu/pindel/0.2.4/
Software to detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data. It uses a pattern growth approach to identify the breakpoints of these variants from paired-end short reads., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: Pindel (RRID:SCR_000560) Copy
http://www.broadinstitute.org/genome_bio/siphy/
Software that implements rigorous statistical tests to detect bases under selection from a multiple alignment data. It takes full advantage of deeply sequenced phylogenies to estimate both unlikely substitution patterns as well as slowdowns or accelerations in mutation rates. It can be applied as an Hidden Markov Model (HMM), in sliding windows, or to specific regions.
Proper citation: SiPhy (RRID:SCR_000564) Copy
http://edwards.sdsu.edu/scaffold_builder/
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 6,2023. Tool designed to generate scaffolds (super contigs of sequences joined by N-bases) using the homology provided by a closely related reference sequence. Scaffold_builder is an advanced wrapper for Nucmer, written in Python that resolves several situations that may arise when mapping contigs to the reference genome.
Proper citation: Scaffold builder (RRID:SCR_000556) Copy
http://lilab.stanford.edu/SNPiR/
Software for reliable Identification of Genomic Variants Using RNA-seq Data.
Proper citation: SNPiR (RRID:SCR_000557) Copy
http://paleogenomics.irmacs.sfu.ca/FPSAC/
Sogftware for fast Phylogenetic Scaffolding of Ancient Contigs.
Proper citation: FPSAC (RRID:SCR_000555) Copy
http://bbc.mdc-berlin.de/software
Multi-purpose SNV calling software enhanced by probabilistic integration of quality scores.
Proper citation: ACCUSA2 (RRID:SCR_000558) Copy
https://code.google.com/p/dysc/
Software for Greedy Clustering of 16S rRNA Reads which uses a dynamic seeding strategy.
Proper citation: DySC (RRID:SCR_000553) Copy
https://sourceforge.net/projects/popbam/
A tool to perform evolutionary or population-based analyses of next-generation sequencing data. POPBAM takes a BAM file as its input and can compute many widely used evolutionary genetics measures in sliding windows across a genome.
Proper citation: POPBAM (RRID:SCR_000464) Copy
http://drfast.sourceforge.net/
A software which maps di-base reads (SOLiD color space reads) to reference genome assemblies in a fast and memory-efficient manner.
Proper citation: drFAST (RRID:SCR_000586) Copy
http://genome.crg.es/software/gfftools/GFF2PS.html
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software program for visualizing annotations of genomic sequences. The program has features such as the ability to create comprehensive plots, customizable parameters, and flexibility in file format.
Proper citation: Genome BioInformatics Research Lab - gff2ps (RRID:SCR_000462) Copy
http://bioinfo2.ugr.es/NGSmethPipe/
A software tool which generates high-quality methylation maps.
Proper citation: NGSmethPipe (RRID:SCR_000583) Copy
https://cran.r-project.org/src/contrib/Archive/sybil/
A Systems Biology Library for R, implementing algorithms for constraint based analyses of metabolic networks (e.g. flux-balance analysis (FBA), minimization of metabolic adjustment (MOMA), regulatory on/off minimization (ROOM), robustness analysis and flux variability analysis). This is an implementation of COBRA toolbox in R language.
Proper citation: sybil - Efficient Constrained Based Modelling in R (RRID:SCR_000457) Copy
https://github.com/holtjma/msbwt
A software package for creating, merging, and querying multi-string BWTs.
Proper citation: msbwt (RRID:SCR_000458) Copy
http://bioconductor.org/packages/release/bioc/html/Rdisop.html
Software for identification of metabolites using high precision mass spectrometry. MS Peaks are used to derive a ranked list of sum formulae, alternatively for a given sum formula the theoretical isotope distribution can be calculated to search in MS peak lists.
Proper citation: Rdisop (RRID:SCR_000453) Copy
http://bsec.ornl.gov/AdaptiveCrawler.shtml
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 9,2022. A web crawler that can intelligently acquire social media content on the Internet to meet the specific online data source acquisition needs of cancer researchers.
Proper citation: AdaptiveCrawler (RRID:SCR_000573) Copy
https://github.com/PacificBiosciences/stsPlots
Software to plot primary analysis quality control metrics to assess potential SMRTcell loading problems.
Proper citation: stsPlots (RRID:SCR_000449) Copy
A division of the Stanford University Libraries, which produces the online versions of journals and other scholarly content.
Proper citation: HighWire Press (RRID:SCR_000761) Copy
http://www.helsinki.fi/bsg/software/BEBaC/
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software for Bayesian estimation of bacterial communities.
Proper citation: BEBaC (RRID:SCR_000621) 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
