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/wehr-lab/autopilot
Software tool as open source Python framework for behavioral neuroscience that distributes experiments over networked swarms of Raspberry Pis. Toolkit of flexible modules to design experiments without rigid programming and API limitations.
Proper citation: AutoPilot (RRID:SCR_021518) Copy
https://iopscience.iop.org/article/10.1088/0957-0233/20/10/104035
Software package for advanced time domain analysis of magnetic resonance spectroscopy (MRS) and spectroscopic imaging (MRSI) data.
Proper citation: jMRUI (RRID:SCR_021893) Copy
https://github.com/oushujun/EDTA
Software package to filter out false discoveries in raw TE candidates and generate high quality non redundant TE library for whole genome TE annotations.Produces filtered non redundant TE library for annotation of structurally intact and fragmented elements.
Proper citation: EDTA (RRID:SCR_022063) Copy
https://github.com/jgraving/DeepPoseKit
Software toolkit with high level API for 2D pose estimation of user defined keypoints using deep learning.Written in Python and built using Tensorflow and Keras.Method for pose estimation developed by behavioral scientists at the Max Planck Institute of Animal Behavior.
Proper citation: DeepPoseKit (RRID:SCR_021405) Copy
https://neurokit2.readthedocs.io/en/latest/
Software Python package for neurophysiological signal processing. Used to analyze physiological data.
Proper citation: Neurokit2 (RRID:SCR_021889) Copy
https://github.com/DrCoffey/DeepSqueak
Software MATLAB package for high throughput ultrasonic vocalizations detection, classification, and analysis.
Proper citation: DeepSqueak (RRID:SCR_021524) Copy
https://github.com/ggruenhagen3/coselens
Software R package to detect gene level differential selection between two groups of samples.Used for calculation of excess of non synonymous mutations between two groups.
Proper citation: Coselens (RRID:SCR_022578) Copy
https://github.com/jokergoo/EnrichedHeatmap
Software R package for comprehensive visualization of genomic signal associations. Visualizes enrichment of genomic signals on specific target regions. Used to visualize e.g. how histone marks are enriched to specific sites.
Proper citation: EnrichedHeatmap (RRID:SCR_023082) Copy
https://github.com/plaisier-lab/sygnal
Software pipeline to integrate correlative, causal and mechanistic inference approaches into unified framework that systematically infers causal flow of information from mutations to TFs and miRNAs to perturbed gene expression patterns across patients. Used to decipher transcriptional regulatory networks from multi-omic and clinical patient data. Applicable for integrating genomic and transcriptomic measurements from human cohorts.
Proper citation: SYGNAL (RRID:SCR_023080) Copy
https://cran.r-project.org/package=NMF
Software R package for nonnegative matrix factorization. Implements set of already published algorithms and seeding methods, and provides framework to test, develop and plug new/custom algorithms.
Proper citation: Algorithms and Framework for Nonnegative Matrix Factorization (RRID:SCR_023124) Copy
https://yeatmanlab.github.io/pyAFQ/
Software package focused on automated delineation of major fiber tracts in individual human brains, and quantification of tissue properties within the tracts.Software for automated processing and analysis of diffusion MRI data. Automates tractometry.
Proper citation: Automated Fiber Quantification in Python (RRID:SCR_023366) Copy
https://github.com/Vaa3D/vaa3d_tools/tree/master/hackathon/mBrainAligner
Software package provides cross modality image registration pipeline to support whole brain mapping projects. Contains three modules: (1) image preprocessing and global registration, (2) Coherent Landmark Mapping (CLM) based automatic registration, and (3) optional semi-automatic refinement.
Proper citation: mBrainAligner (RRID:SCR_022791) Copy
https://cran.r-project.org/web/packages/rms/
Software R package as collection of functions that assist with streamline modeling. Works with binary or ordinal regression models, Cox regression, accelerated failure time models, ordinary linear models, Buckley-James model, generalized least squares for serially or spatially correlated observations, generalized linear models, and quantile regression.
Proper citation: Regression Modeling Strategies (RRID:SCR_023242) Copy
https://bioconductor.org/packages/release/bioc/html/Maaslin2.html
SoftwareR package that identifies microbial taxa correlated with factors of interest using generalized linear models and mixed models.Used for efficiently determining multivariable association between clinical metadata and microbial meta'omic features.
Proper citation: MaAsLin2 (RRID:SCR_023241) Copy
https://github.com/plger/scDblFinder
Software package for detection and handling of doublets/multiplets in single cell sequencing data.
Proper citation: scDblFinder (RRID:SCR_022700) Copy
https://ndphillips.github.io/FFTrees/
Software package as decision algorithms for solving binary classification problems. Faster and more frugal because every node allows making decision. Apart from being faster and requiring less information, FFTs tend to be robust against overfitting, and are easy to interpret, use, and communicate.
Proper citation: FFTrees (RRID:SCR_023359) Copy
https://entap.readthedocs.io/en/latest/
Software package as eukaryotic non model annotation pipeline.Used for bringing functional annotation to non-model eukaryotic transcriptomes to improve the accuracy, speed, and flexibility of functional gene annotation for de novo assembled transcriptomes in non-model eukaryotes. Addresses fragmentation and related assembly issues that result in inflated transcript estimates and poor annotation rates of protein-coding transcripts.
Proper citation: EnTAP (RRID:SCR_023010) Copy
https://cran.r-project.org/web/packages/reshape2/index.html
Software R package to flexible rearrange, reshape and aggregate data. Reshape2 is reboot of reshape package.
Proper citation: reshape2 (RRID:SCR_022679) Copy
https://cran.r-project.org/web/packages/Peptides/index.html
Software R package to calculate indices and theoretical physicochemical properties of peptides and protein sequences.
Proper citation: Peptides (RRID:SCR_022675) Copy
https://www.cbcb.umd.edu/software/epiviz
Software package as interactive visualization tool for functional genomics data. Interactive visual analytics for functional genomics data.
Proper citation: Epiviz (RRID:SCR_022796) 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
