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://zhanglab.ccmb.med.umich.edu/TM-align/
Software tool for protein structure alignment based on TM-score.Used to identify structural alignment between protein pairs that combines the TM-score rotation matrix and Dynamic Programming. Used for sequence independent protein structure comparisons.
Proper citation: TM-align (RRID:SCR_024390) Copy
https://github.com/BD2KGenomics/toil
Software pipeline management system, written in Python. Enables reproducible, open source, big biomedical data analyses.
Proper citation: toil (RRID:SCR_024391) Copy
https://gitlab.com/andreas.andrusch/paipline
Software Python program to search for pathogen nucleic acid sequences in NGS datasets.Used for pathogen identification in metagenomic and clinical next generation sequencing samples.
Proper citation: PAIPline (RRID:SCR_024151) Copy
https://sourceforge.net/projects/pipasic/
Software tool for similarity and expression correction for strain level identification and quantification in metaproteomics. Peptide intensity weighted proteome abundance similarity correction tool to correct identification and spectral counting based quantification results. Pipasic has distinct advantages over approaches only regarding unique peptides or aggregating results to the lowest common ancestor.
Proper citation: pipasic (RRID:SCR_024165) Copy
https://github.com/BU-ISCIII/plasmidID
Software mapping based, assembly assisted plasmid identification tool that analyzes and gives graphic solution for plasmid identification. Computational pipeline implemented in BASH that maps Illumina reads over plasmid database sequences.
Proper citation: PlasmidID (RRID:SCR_024166) Copy
https://github.com/PacificBiosciences/kineticsTools
Software tools for detecting DNA modifications from single molecule, real-time sequencing data. This tool implements the P_ModificationDetection module in SMRT� Portal, used by the RS_Modification_Detection and RS_Modifications_and_Motif_Detection protocol.
Proper citation: kineticsTools (RRID:SCR_024049) Copy
http://www.biolchem.ucla.edu/labs/ernst/ChromImpute/
Software tool for large scale systematic epigenome imputation. ChromImpute takes existing compendium of epigenomic data and uses it to predict signal tracks for mark-sample combinations not experimentally mapped or to generate a potentially more robust version of data sets that have been mapped experimentally.
Proper citation: ChromImpute (RRID:SCR_023990) Copy
Open source, software cross-platform library that provides suite of software tools for image analysis.ITK builds on proven, spatially-oriented architecture for processing, segmentation, and registration of scientific images in two, three, or more dimensions.
Proper citation: Insight Toolkit (RRID:SCR_024040) Copy
https://github.com/HadrienG/InSilicoSeq
Software tool as sequencing simulator producing realistic Illumina reads. Primarily intended for simulating metagenomic samples, it can also be used to produce sequencing data from a single genome.
Proper citation: InSilicoSeq (RRID:SCR_024041) Copy
https://bitbucket.org/genomicepidemiology/resfinder
Software tool identifies acquired antimicrobial resistance genes in total or partial sequenced isolates of bacteria. Used for identification of acquired antimicrobial resistance genes in whole-genome data.
Proper citation: resfinder (RRID:SCR_024314) Copy
https://github.com/reedacartwright/ngila
Software alignment program that can align pairs of sequences using logarithmic and affine gap penalties.
Proper citation: Ngila (RRID:SCR_024133) Copy
https://github.com/medvedevgroup/varmatch
Software tool for variant matching problem.Used for robust matching of small variant datasets using flexible scoring schemes
Proper citation: VarMatch (RRID:SCR_024375) Copy
https://github.com/Nextomics/nextsv
Software tool for automated structrual variation detection from long-read sequencing using state-of-the-art tools. NextSV3 uses Minimap2 to do read mapping and uses two state-of-the-art SV callers (Sniffles and cuteSV) to do SV calling.
Proper citation: NextSV (RRID:SCR_024134) Copy
https://github.com/nextflow-io/nextflow
Software workflow manager that enables development of portable and reproducible workflows.Supports deploying workflows on variety of execution platforms including local, HPC schedulers, AWS Batch, Google Cloud Life Sciences, and Kubernetes. Provides support to manage workflow dependencies through built-in support for Conda, Spack, Docker, Podman, Singularity, Modules, and more.
Proper citation: Nextflow (RRID:SCR_024135) Copy
https://github.com/nawrockie/vadr
Software suite of tools for classifying and analyzing sequences homologous to set of reference models of viral genomes or gene families.
Proper citation: VADR (RRID:SCR_024377) Copy
http://labs.bio.unc.edu/Vision/FISH/
Software tool for identifying regions of common ancestry between genome maps. Used for identification and statistical evaluation of segmental homologies in comparative maps.
Proper citation: FISH (RRID:SCR_024378) Copy
https://github.com/fccoelho/epigrass
Software Python library aimed at making the simulation of metapopulation models. Software tool to study disease spread in complex networks.Used to help designing and simulating network-epidemic models with any kind of node behavior.
Proper citation: Epigrass (RRID:SCR_024016) Copy
https://github.com/jnktsj/DNApi/
Software de novo adapter prediction algorithm for small RNA sequencing data.
Proper citation: DNApi (RRID:SCR_024009) Copy
http://www.danielwilson.me.uk/omegaMap.html
Software tool for detecting natural selection and recombination in DNA or RNA sequences.
Proper citation: omegaMap (RRID:SCR_024143) Copy
Open source software for electronic health records and medical practice management solution.
Proper citation: OpenEMR (RRID:SCR_024144) 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
