Tools   Select Another Resource Report Type

https://CRAN.R-project.org/package=clustree

Software package which allows to produce clustering trees and visualize clusterings at different resolutions. Used in the analysis of large data sets to group together samples with similar properties.

Proper citation: clustree (RRID:SCR_016293) Copy   

•   Source: SciCrunch Registry
  

https://sourceforge.net/projects/next-ema/

Software for combined elementary flux mode and network-embedded thermodynamic analysis.

Proper citation: NExT-EMA (RRID:SCR_016291) Copy   

•   Source: SciCrunch Registry
  

https://www.hiv.lanl.gov/catnap

Analyze a database of HIV-1 IC50 and IC80 neutralization data from publicly-available sources, in conjunction with HIV-1 Envelope sequences. Access to an extensive databases of information about neutralizing antibodies and viruses used in published neutralization studies. Tool interfaces also allow input and analysis of user data. PMID: 26044712, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: CATNAP (RRID:SCR_016170) Copy   

•   Source: SciCrunch Registry
  

https://omictools.com/fluxmodecalculator-tool

Software for performing flux mode analysis in stoichiometric models. FluxModeCalculator enables large-scale elementary flux mode (EFM) computation and uses the OpenMP API to optimally exploit processor architectures with multiple cores., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: FluxModeCalculator (RRID:SCR_016290) Copy   

•   Source: SciCrunch Registry
  

http://amp.pharm.mssm.edu/l1000fwd/

Web application that provides interactive visualization of drug and small-molecule induced gene expression signatures. L1000FWD enables coloring of signatures by different attributes such as cell type, time point, concentration, as well as drug attributes such as MOA and clinical phase.

Proper citation: L1000 Fireworks Display (RRID:SCR_016175) Copy   

•   Source: SciCrunch Registry
  

https://beta.observablehq.com/

Web application for a code and text writing environment. It uses javascript and can be used to produce executable papers.

Proper citation: ObservableHQ (RRID:SCR_016173) Copy   

•   Source: SciCrunch Registry
  

https://hub.docker.com/r/biodepot/star-for-criu/

Software as an Hot Start software container for STAR alignment using CRIU (Checkpoint Restore in Userspace) tool to freeze the running container. Can be deployed to align RNA sequencing data. Used in the processing of biomedical big data for better reproducibility and reliability.

Proper citation: star-for-criu (RRID:SCR_016294) Copy   

•   Source: SciCrunch Registry
  

https://www.goldwave.com/goldwave.php

Software that enables users to digitally edit audio files. GoldWave can record, edit, and analyze audio for research-related purposes.

Proper citation: GoldWave (RRID:SCR_016189) Copy   

•   Source: SciCrunch Registry
  

http://www3.gehealthcare.com/en/products/categories/ep_recording/cardio_lab_recording_systems

Prucka CardioLab system delivers the EP data and visualization we need for electrophysiological study and catheter ablation.

Proper citation: Prucka CardioLab System (RRID:SCR_016180) Copy   

•   Source: SciCrunch Registry
  

http://amp.pharm.mssm.edu/LJP/

Interactive on line tool where signatures are tagged with user selected metadata and external transcript signatures are projected onto network. Browser to visualize signatures from breast cancer cell lines treated with single molecule perturbations.

Proper citation: LINCS Joint Project - Breast Cancer Network Browser (RRID:SCR_016181) Copy   

•   Source: SciCrunch Registry
  

https://github.com/ihmwg/IHM-dictionary

Software resource for a data representation for integrative/hybrid methods of modeling macromolecular structures.

Proper citation: IHM-dictionary (RRID:SCR_016186) Copy   

•   Source: SciCrunch Registry
  

https://pdb-dev.wwpdb.org

Data repository for integrative/hybrid structural models of macromolecules and their assemblies. This includes atomistic models as well as multi-scale models consisting of different coarse-grained representations.

Proper citation: PDB-Dev (RRID:SCR_016185) Copy   

•   Source: SciCrunch Registry
  

https://lifebit.ai/

Platform for computing management for data analysis on the cloud from the Lifebit company. Allows the computational analyses to be permanently linked to live analyses pipelines.

Proper citation: Lifebit Deploit (RRID:SCR_016428) Copy   

•   Source: SciCrunch Registry
  

http://ssadedin.github.io/ximmer/

Software to help users of targeted high throughput genomic sequencing data to accurately detect copy number variants (CNVs). Framework for running and evaluating other copy number detection tools.Used for evaluating and improving performance of CNV detection in exome and targeted sequencing data.

Proper citation: Ximmer (RRID:SCR_016427) Copy   

•   Source: SciCrunch Registry
  

http://conp.ca/

Web interface that facilitates open science for neuroscience community by simplifying global access to and sharing of datasets and tools. Portal internalizes typical data cycle of research project, beginning with data acquisition, followed by data processing with published tools, and ultimately publication of results with link to original dataset. Platform to form interactive network of collaborations in brain research, interdisciplinary student training, international partnerships, clinical translation and open publishing. Provides unified interface to Canadian neuroscience research community. Open neuroscience research with sharing of both data and methods, to create large-scale databases, development of standards for sharing, facilitation of advanced analytic strategies, open dissemination to global community of neuroscience data and methods, and establishment of training programs for next generation of computational neuroscience researchers.

Proper citation: Canadian Open Neuroscience Platform (RRID:SCR_016433) Copy   

•   Source: SciCrunch Registry
  

http://www.fftw.org/

Software as a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data (as well as of even/odd data, i.e. the discrete cosine/sine transforms or DCT/DST).

Proper citation: FFTW (RRID:SCR_016554) Copy   

•   Source: SciCrunch Registry
  

https://www.denovosoftware.com/?gclid=EAIaIQobChMI36rn3-Dd3AIV2ud3Ch27lw2oEAAYASAAEgLbRvD_BwE

Software tool for flow and image cytometry data analysis by De Novo Software company.

Proper citation: FCS Express (RRID:SCR_016431) Copy   

•   Source: SciCrunch Registry
  

https://www.mousephenotype.org/imits/

This resource has been replaced by GenTaR. Software tool for the planning of all IMPC mouse production. Allows IMPC production centers to record the progress of mouse production, cre-excision and to summarise the progress of phenotype data collection and transfer to the IMPC DCC. Stores all the mutation molecular structures made for the IKMC, catalogs of all IKMC products.

Proper citation: iMITS (RRID:SCR_016552) Copy   

•   Source: SciCrunch Registry
  

https://github.com/DepartmentofNeurophysiology/Analysis-tools-for-electrophysiological-somatosensory-cortex-databank/tree/master/Frozen%20Noise

Software analysis tools for electrophysiological somatosensory cortex databank. Allows to estimate the information content of spiking in single neuron resolution. It accompanies the open source intracellular recording database by Lantyer and colleagues.

Proper citation: Frozen Noise (RRID:SCR_016558) Copy   

•   Source: SciCrunch Registry
  

https://github.com/fbreitwieser/pavian

Software R package for interactive analysis of metagenomics classification results with a special focus on infectious disease diagnosis. Used for analyzing and visualization of metagenomics classification results from classifiers such as Kraken, Centrifuge and MetaPhlAn. Provides an alignment viewer for validation of matches to a particular genome.

Proper citation: Pavian (RRID:SCR_016679) Copy   

•   Source: SciCrunch Registry