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/holab-hku/Vulture
Software scalable cloud based pipeline that performs microbial calling for single cell RNA sequencing data, enabling meta analysis of the single cell host microbial studies from AWS Open Data and other public domain.
Proper citation: Vulture (RRID:SCR_024720) Copy
https://github.com/liufan-creat/bulkGAN
Software tool for scRNA and spatial transcriptomics.Used to generate RNA data close to real bulk RNA-seq with constraints of scRNA-seq data, based on keras and tensflow framework.
Proper citation: bulkGAN (RRID:SCR_024798) Copy
Software finite element analysis package. Used to solve field problems.
Proper citation: CalculiX (RRID:SCR_024771) Copy
https://github.com/mcelotto/Feature_Info_Transfer
Software application as MATLAB scripts to compute measures of Feature-specific Information Transfer (FIT) and conditional FIT (cFIT). FIT quantifies direction and magnitude of information flow about specific feature S (such as feature of sensory stimulus) between simultaneously recorded brain regions X and Y. cFIT quantifies amount of directed feature information transmitted between regions X and Y that cannot be potentially routed through region Z.
Proper citation: Feature-specific Information Transfer scripts (RRID:SCR_024772) Copy
https://github.com/mcelotto/LemkeCelottoEtAl_codes_repo
Software code package associated to the paper: Lemke et al. Information flow between motor cortex and striatum reverses during skill learning. 2023. Quantifies information theoretic quantities used in the associated study.
Proper citation: LemkeCelottoEtAl_codes_repo (RRID:SCR_024773) Copy
https://github.com/STOmics/SGAE
Software graph neural network based tool for spatial domain deciphering. Used for deciphering spatial domains from spatially resolved transcriptomics.
Proper citation: SGAE (RRID:SCR_024803) Copy
https://github.com/google-deepmind/deepmind-research/tree/master/enformer
Software package provides implementation of the Enformer model and examples on running the model.
Proper citation: Enformer (RRID:SCR_024805) Copy
https://github.com/kundajelab/tfmodisco
Software application as algorithm for identifying motifs from basepair-level importance scores computed on genomic sequence data.
Proper citation: TF-Modisco (RRID:SCR_024811) Copy
https://www.tidyverse.org/blog/2018/11/parsnip-0-0-1/
Software R package to create and manipulate functions commonly used during modeling e.g. fitting the model, making predictions, etc.
Proper citation: Parsnip (RRID:SCR_024744) Copy
Python package for calculation of extracellular potentials from multicompartment neuron models. LFPy can be used to set up a model, run simulations, and calculate the extracellular potentials arising from activity in the given model neuron. It relies on the Python interface provided by the NEURON simulator.
Proper citation: LFPy (RRID:SCR_014805) Copy
http://www.msg.chem.iastate.edu/gamess/
Software program for ab initio molecular quantum chemistry. GAMESS can compute SCF wavefunctions ranging from RHF, ROHF, UHF, GVB, and MCSCF. Capabilities include using nuclear gradients for automatic geometry optimization, modeling of solvent effects, computation of the energy hessian for prediction of vibrational frequencies, as well as computation of nuclear wavefunctions. The program can also compute variety of molecular properties, ranging from simple dipole moments to frequency dependent hyperpolarizabilities.
Proper citation: Gamess (RRID:SCR_014896) Copy
An interchange format to represent, store and exchange data and annotations in a standardized manner.
Proper citation: BioC Java Library (RRID:SCR_014777) Copy
Software program for semiempirical quantum chemistry for handling of biomolecules.
Proper citation: MOPAC (RRID:SCR_014898) Copy
http://web.cmb.usc.edu/people/alber/Software/tomominer/
Software platform for large-scale cryo electron subtomogram classification, alignment, and averaging.
Proper citation: TomoMiner (RRID:SCR_015045) Copy
https://cran.r-project.org/web/packages/madsim/index.html
A function which allows users to generate two biological conditions synthetic microarray datasets. The user provides a subset of parameters, but default parameter settings can be modified.
Proper citation: madsim (RRID:SCR_014765) Copy
http://www.nitrc.org/projects/papaya
A pure JavaScript medical research image viewer, compatible across a range of popular web browsers. The orthogonal viewer supports NIFTI and DICOM files, overlays and atlas labels. It requires Firefox (7+), Chrome (7+), Safari (6+), MobileSafari (iOS 6+), or IE (10+).
Proper citation: Papaya (RRID:SCR_014188) Copy
http://www.nitrc.org/projects/efficient_pt
A Matlab implementation for efficient permutation testing by using matrix completion.
Proper citation: Efficient Permutation Testing (RRID:SCR_014104) Copy
http://www.lji.org/faculty-research/scientific-cores/dlac/#overview
The department of laboratory animal care at the La Jolla Institute for Allergy and Immunology.
Proper citation: La Jolla Institute for Allergy and Immunology Department of Laboratory Animal Care (RRID:SCR_014834) Copy
http://dx.doi.org/10.5281/zenodo.21157
A graphical source code file used for an automated motion detection and reward system for animal training (see comment for full paper title). It was designed on the LabVIEW programming system. Running the program requires the appropriate LabVIEW runtime software from National Instruments Corporation.
Proper citation: Monkey Motion (RRID:SCR_014285) 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
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 RRID Resources search. From here you can search through a compilation of resources used by RRID and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that RRID 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 RRID then you can log in from here to get additional features in RRID 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 RRID 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 RRID 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.
