Tools   Select Another Resource Report Type

https://github.com/vcflib/tabixpp

Software C++ wrapper around tabix project which abstracts some of the details of opening and jumping in tabix-indexed files.Wrapper to tabix indexer

Proper citation: tabixpp (RRID:SCR_024107) Copy   

•   Source: SciCrunch Registry
  

https://gitlab.orc.gmu.edu/kbijari/zebrafish-analysis-protocol

Project for quantitative neuronal morphometry by supervised and unsupervised learning. Includes protocol to quantify and interpret morphological properties of individual neurons reconstructed from microscopic imaging.Includes information about installation of analysis tools and downloading datasets and custom codes.

Proper citation: neuronal reconstruction analysis project (RRID:SCR_021638) Copy   

•   Source: SciCrunch Registry
  

https://www.fredhutch.org/en/research/shared-resources.html

Through Shared Resources, investigators in Fred Hutch/University of Washington Cancer Consortium and external academic and industry organizations can access services tailored to their specific research goals, including novel assay development or early access to new technologies.

Proper citation: Fred Hutchinson Cancer Center Shared Resources (RRID:SCR_022607) Copy   

•   Source: SciCrunch Registry
  

https://github.com/brentp/cyvcf2

Software Python library and software package for fast parsing and querying of VCF and BCF files and illustrate its speed, simplicity and utility. Used for variant analysis.

Proper citation: cyvcf2 (RRID:SCR_024000) Copy   

•   Source: SciCrunch Registry
  

http://www.commontk.org/

Software to support biomedical image computing.

Proper citation: CTK (RRID:SCR_024002) Copy   

•   Source: SciCrunch Registry
  

https://github.com/wdecoster/nanolyse

Software package to remove reads mapping to the lambda phage genome from a fastq file.

Proper citation: NanoLyse (RRID:SCR_024125) Copy   

•   Source: SciCrunch Registry
  

http://lipiddroplet.org/

Interactive portal provides datasets, across variety of cell types, for LD biology, including transcriptional profiles of induced lipid storage, organellar proteomics, genome-wide screen phenotypes, and ties to human genetics. Provides comprehensive picture of genes and pathways affecting lipid droplet biology, including gene expression, proteomics, and LD morphology phenotypes, by integrating multiple relevant data types.

Proper citation: Lipid Droplet Knowledge Portal (RRID:SCR_021650) Copy   

•   Source: SciCrunch Registry
  

https://www.utsouthwestern.edu/labs/danuser/software/

Software package as quantitative image analysis software for measurement of microtubule dynamics. MATLAB software for tracking full dynamics of microtubules based on plusTIP marker live cell image sequences.

Proper citation: plusTipTracker (RRID:SCR_021890) Copy   

•   Source: SciCrunch Registry
  

https://ror.org/

Community led project to develop open, sustainable, usable, and unique identifier for every research organization in the world. Implementation of ROR IDs in scholarly infrastructure and metadata will enable more efficient discovery and tracking of research outputs across institutions and funding bodies.

Proper citation: Research Organization Registry (RRID:SCR_021891) Copy   

•   Source: SciCrunch Registry
  

https://github.com/muriloHoracio/TERL

Software tool for classification of transposable elements by convolutional neural networks. Preprocesses and transforms one dimensional sequences into two dimensional space data, image like data of sequences, and apply it to deep convolutional neural networks.

Proper citation: TERL (RRID:SCR_022064) Copy   

•   Source: SciCrunch Registry
  

https://neurobridges.org/

Platform for data discovery to enhance the reuse of clinical neuroscience and neuroimaging data. Provides NeuroBridge ontology, and combines machine learning with ontology based search of both neuroimaging repositories like XNAT databases and open access full text journals such as PubMed Central. Connects researchers with potential neuroimaging data, by searching text of papers describing neuroimaging studies that contain information on neuroimaging data.

Proper citation: NeuroBridge (RRID:SCR_023703) Copy   

•   Source: SciCrunch Registry
  

https://azphewas.com/

Repository of gene phenotype associations for phenotypes derived from electronic health records, questionnaire data, and continuous traits computed on exomes released by UK Biobank. Repository was made available by AstraZeneca for public research.

Proper citation: AstraZeneca PheWAS Portal (RRID:SCR_021643) Copy   

•   Source: SciCrunch Registry
  

http://fair.dei.unipd.it/software/

Software platform for integration of imaging data and Allen Human Brain Atlas mRNA data. MENGA investigates correlation patterns between various imaging modalities and gene expression profiles based on the Allen Brain Atlas in order to create comprehensive, integrated data platform.

Proper citation: Multimodal Environment for Neuroimaging and Genomic Analysis (RRID:SCR_023822) Copy   

•   Source: SciCrunch Registry
  

https://www.cs.bham.ac.uk/~ibs/imzMLConverter/

Software tool for generating imzML. Allows conversion to imzML mass spectrometry imaging standard utilising mzML mass spectrometry standard as intermediary format.

Proper citation: imzMLConverter (RRID:SCR_021642) Copy   

•   Source: SciCrunch Registry
  

https://github.com/toddy15/medicalterms

Software package to create specialized dictionaries for medical terms used in various languages.German medical dictionary words.

Proper citation: medicalterms (RRID:SCR_024117) Copy   

•   Source: SciCrunch Registry
  

https://cran.r-project.org/package=psychometric

Software R package for measurement theory, meta-analysis, reliability, item analysis, inter-rater reliability, classical utility, and correlation

Proper citation: psychometric (RRID:SCR_024295) Copy   

•   Source: SciCrunch Registry
  

http://www.rnasoft.ca/sstrand

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A scientific community-crowdsourced database containing the RNA secondary structures of known types and organisms. It is meant to provide a simple and powerful way to analyze, search and update a shared repository of information.

Proper citation: RNA STRAND-The RNA secondary STRucture and statistical ANalysis Database (RRID:SCR_000086) Copy   

•   Source: SciCrunch Registry
  

https://www.bioinformatics.org/~tryphon/populations/

Population genetic software for individuals or populations distances based on allelic frequencies, phylogenetic trees, file conversions.

Proper citation: Populations (RRID:SCR_024175) Copy   

•   Source: SciCrunch Registry
  

https://rniftilib.r-forge.r-project.org/

Software R package provides R-interface to the NIfTI reference implementation the niftilib C-library.

Proper citation: rniftilib (RRID:SCR_024296) Copy   

•   Source: SciCrunch Registry
  

http://wwwmgs.bionet.nsc.ru/mgs/systems/rsnp/

A system of databases which stores information on the influence of mutations in regulatory gene regions . This tool helps recognize protein binding sites that are being altered by mutation. It has four cross-linked sub databases that focus on specific aspects including: (1) the effect of single nucleotide mutations in regulatory gene regions and their interaction with nuclear proteins; (2) references to original publications on the subject; (3) the experimental details of these publications; and (4) the protocols of these experiments. This resource is aimed at providing information to further research on the influence of specific sequence alterations on disease susceptibility, drug resistance and healthcare.

Proper citation: rSNP Guide (RRID:SCR_000087) Copy   

•   Source: SciCrunch Registry