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://github.com/satijalab/sctransform
Software R package for normalization and variance stabilization of single-cell RNA-seq data using regularized negative binomial regression.
Proper citation: sctransform (RRID:SCR_022146) Copy
https://gitlab.com/maaly7/emerald_metagenomics_annotations
Software metagenomics annotations pipeline that regularly enrich up-to-date ENA and MGnify metagenomics studies with metadata extracted from research articles in EuropePMC.
Proper citation: EMERALD METAGENOMICS ANNOTATIONS PIPELINE (RRID:SCR_022541) Copy
https://github.com/jkimlab/PLR-GEN
Software package for generation of pseudo long reads by using short reads of metagenomic sample and microbial reference genome sequences as input.
Proper citation: PLR-GEN (RRID:SCR_022264) Copy
http://membres-timc.imag.fr/Olivier.Francois/LEA/index.htm
Software R package for landscape and ecological associations studies.Dedicated to genomewide association tests in general, with emphasis on association with ecological gradients. Runs analyses of population structure and scans for genomic signatures of local adaptation.
Proper citation: LEA (RRID:SCR_022020) Copy
https://github.com/PacificBiosciences/pb-assembly
Software tool as PacBio assembly tool suite.
Proper citation: pb assembly (RRID:SCR_021967) Copy
Issue
https://cran.r-project.org/package=pcadapt
Software R package for fast Principal Component Analysis for outlier detection.Used to detect genetic markers involved in biological adaptation. Performs genome scans for selection based on principal component analysis.
Proper citation: pcadapt (RRID:SCR_022019) Copy
https://github.com/SydneyBioX/SurvBenchmark_package
Software package for comprehensive benchmarking study of survival analysis methods using both omics data and clinical data. Evaluates diverse collection of survival models for both clinical and omics datasets.
Proper citation: SurvBenchmark (RRID:SCR_022503) Copy
Open source software package for creating and controlling visual environments.Software package for Bonsai which allows for control of 2D and 3D environments.
Proper citation: BonVision (RRID:SCR_021534) Copy
https://github.com/VisionandCognition/Tracker-MRI
Software package for experimental control from Vision and Cognition Lab at Netherlands Institute for Neuroscience. Matlab based software for fMRI, Psychophysical experimentation and NHP training, with eye control using Measurement and Computing IO card. Interfaces with ISCAN eye tracker and communicates with the MRI console using trigger pulses. Uses Psychtoolbox3 graphics and control engine.
Proper citation: Tracker MRI (RRID:SCR_021816) Copy
https://github.com/h2oai/h2o4gpu
Interface to H2O4GPU, collection of GPU solvers for machine learning algorithms.
Proper citation: h2o4gpu (RRID:SCR_022520) Copy
https://github.com/ModelOriented/randomForestExplainer
Software R package to help explain which variables are most important in random forests. Various variable importance measures are calculated and visualized in different settings in order to get idea on how their importance changes classification or regression model accuracy.
Proper citation: randomForestExplainer (RRID:SCR_021823) Copy
https://bioconductor.org/packages/karyoploteR/
Software R package used to karyoplots. Bioconductor package to plot customizable genomes displaying arbitrary data.
Proper citation: karyoploteR (RRID:SCR_021824) Copy
https://github.com/NollmannLab/qudi-HiM
Software package for control of optical microscope setups with different hardware components optimized to perform multiplexed imaging experiments. Modular laboratory experiment management suite.
Proper citation: qudi-HiM (RRID:SCR_022114) Copy
https://github.com/sqjin/CellChat
Software R toolkit for inference, visualization and analysis of cell-cell communication from single cell data.Quantitatively infers and analyzes intercellular communication networks from single-cell RNA-sequencing data. Predicts major signaling inputs and outputs for cells and how those cells and signals coordinate for functions using network analysis and pattern recognition approaches. Classifies signaling pathways and delineates conserved and context specific pathways across different datasets.
Proper citation: CellChat (RRID:SCR_021946) Copy
https://bids-matlab.readthedocs.io/en/latest/
Software MATLAB/Octave tools to interact with datasets conforming to Brain Imaging Data Structure format.
Proper citation: BIDS-Matlab (RRID:SCR_022292) Copy
https://CRAN.R-project.org/package=ggforce
Software R package providing missing functionality to ggplot2 through extension system introduced with ggplot2 v2.0.0.
Proper citation: ggforce (RRID:SCR_022575) Copy
http://cns.hkbu.edu.hk/RIDE.htm
Software Matlab based toolbox for temporal decomposition of EEG signal. Used for decomposition, reconstruction, and single trial analysis of event related potentials.
Proper citation: Residue Iteration Decomposition (RRID:SCR_022174) Copy
https://github.com/alexcwsmith/PiRATeMC
Software data management pipeline for camera synchronization and combined data directories.
Proper citation: Pi-based Remote Acquisition Technology for Motion Capture (RRID:SCR_022327) Copy
https://github.com/sdorkenw/MeshParty
Software package for working with neuronal meshes, skeletons, and annotations from electron microscopy data. Used to work with meshes, designed around use cases for analyzing neuronal morphology.
Proper citation: MeshParty (RRID:SCR_021873) Copy
https://github.com/leylabmpi/endoR/
Software R package to interpret fitted tree ensemble model.Used to extract and visualize how predictive variables contribute to tree ensemble model accuracy.
Proper citation: endoR (RRID:SCR_021916) 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
