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://bioinf.shenwei.me/seqkit/
Software tool as cross platform and ultrafast toolkit for FASTA/Q file manipulation.
Proper citation: SeqKit (RRID:SCR_018926) Copy
https://pypi.org/project/jupyter-client/5.2.3/
Jupyter protocol implementation and client libraries. Part of Project Jupyter which exists to develop open-source software, open-standards, and services for interactive computing across dozens of programming languages. Jupyter-client contains reference implementation of Jupyter protocol and provides client and kernel management APIs for working with kernels.
Proper citation: Jupyter-client (RRID:SCR_018413) Copy
https://CRAN.R-project.org/package=mHG
Software R package to run minimum hypergeometric test.
Proper citation: Minimum-Hypergeometric Test (RRID:SCR_018776) Copy
https://github.com/HMPNK/CSA2.6
Software pipeline for high-throughput chromosome level vertebrate genome assembly. Pipeline, which after contig assembly performs post assembly improvements by ordering assembly and closing gaps, as well as splitting of low supported regions.
Proper citation: Chromosome Scale Assembler (RRID:SCR_017960) Copy
https://github.com/smithlabcode/riborex
Software R package for identification of differential translation from Ribo-seq data. Computational tool for mapping genome wide differences in translation efficiency.
Proper citation: riborex (RRID:SCR_019104) Copy
https://github.com/jupyter/jupyter_console
Terminal based console frontend for Jupyter kernels. This code is based on single process IPython terminal.
Proper citation: Jupyter-console (RRID:SCR_018414) Copy
https://github.com/anuprulez/galaxy_tool_recommendation
Software developed by analyzing workflows composed by researchers on European Galaxy server, using deep learning approach. Used to recommend tools in Galaxy. Gated recurrent units neural network.
Proper citation: Tool recommender system in Galaxy (RRID:SCR_018491) Copy
https://github.com/DReichLab/AdmixTools
Software package that supports formal tests of whether admixture occurred, and makes it possible to infer admixture proportions and dates.
Proper citation: ADMIXTOOLS (RRID:SCR_018495) Copy
https://CRAN.R-project.org/package=openxlsx
Software R package to simplify creation of .xlsx files by providing high level interface to writing, styling and editing worksheets.
Proper citation: openxlsx (RRID:SCR_019185) Copy
https://github.com/dorianps/LESYMAP
Software R package to conduct lesion-to-symptom mapping from human MRI data.Takes lesion maps and cognitive performance scores from patients with stroke, and maps brain areas responsible for cognitive deficit.
Proper citation: LESYMAP (RRID:SCR_017967) Copy
https://nose.readthedocs.io/en/latest/
Software tool to extend unittest to make testing easier. Python unit test framework. Note, Nose has been in maintenance mode for the past several years and will likely cease without a new person/team to take over maintainership. New projects should consider using Nose2, py.test, or just plain unittest/unittest2.
Proper citation: Python Nose (RRID:SCR_018418) Copy
https://hoohm.github.io/CITE-seq-Count/
Software python package that allows to count antibody TAGS from CITE-seq and/or cell hashing experiment. Software tool that allows to get UMI counts from single cell protein assay. Used to count (UMI counts) antibody-derived-tags (ADTs) or Cell Hashing tags (HTOs) in raw sequencing reads and build count matrix.
Proper citation: CITE-seq-Count (RRID:SCR_019239) Copy
https://github.com/dorianps/LINDA
Software R package for automated segmentation of chronic stroke lesions. Automated segmentation algorithm capable of learning relationship between existing manual segmentations and single T1-weighted MRI.
Proper citation: LINDA (RRID:SCR_017971) Copy
https://bioconductor.org/packages/release/bioc/html/MetaVolcanoR.html
Software R package to combine differential gene expression results. Differential expression meta analysis tool. Gene expression meta analysis visualization tool. Used to identify genes whose expression is consistently perturbed across several studies., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: MetaVolcanoR (RRID:SCR_018549) Copy
Software Python package for Bayesian statistical modeling and probabilistic machine learning which focuses on advanced Markov chain Monte Carlo and variational fitting algorithms. Allows model specification directly in Python code.
Proper citation: PyMC3 (RRID:SCR_018547) Copy
https://www.flidea.tech/flic-support
Software tool as user interface for running Fly Liquid Food Interaction Counter experiments.
Proper citation: FLIC Monitor (RRID:SCR_018387) Copy
https://w3.psychology.su.se/sleipner/
Software package as collection of modules implementing methods of analysis that form self-contained and empirically grounded toolbox for handling longitudinal data within person oriented paradigm.
Proper citation: sleipner (RRID:SCR_018143) Copy
Software Python package enabling Biological Expression Language to act as semantic integration layer for multi modal and multi scale data sets in life sciences. Used for integrating biological databases and structured data sources in BEL. Has ability to support curation of pathway mappings, integration of pathway databases, and machine learning applications.
Proper citation: Bio2BEL (RRID:SCR_017659) Copy
http://bioconductor.org/packages/org.Rn.eg.db/
Software R tool for genome wide annotation for Rat, primarily based on mapping using Entrez Gene identifiers.
Proper citation: org.Rn.eg.db (RRID:SCR_018358) Copy
https://woldlab.caltech.edu/wiki/Condor
Condor project maintains, distributes, and supports variety of computing systems that are deployed by commercial and academic interests world wide. Explores social and technical problems of cooperative computing on scales ranging from desktop to world wide computational Grid.
Proper citation: Condor (RRID:SCR_017664) 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.
