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

http://www.flir.jp/instruments/display/?id=54865

Software application for thermography for FLIR Systems. It has a basic thermal image analysis function including color palette and image adjustment function. Used to analyse the thermographic measurement data.

Proper citation: FLIR tools (RRID:SCR_016330) 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

http://www.nitrc.org/projects/mica/

Software toolbox based on FSL command line tools that performs masked independent component analysis and related analyses in an integrated way within a spatially restricted subregion of the brain. Used for investigating functional connectivity in functional magnetic resonance imaging data in the field of neuroimaging.

Proper citation: masked ICA (mICA) Toolbox (RRID:SCR_016349) Copy   

•   Source: SciCrunch Registry

https://www.lungmap.net/

Portal for lung histochemistry data. For structural and molecular data regarding normal perinatal and postnatal lung development in the mouse and human. For public sharing of data sets, establishing a repository of young human lung tissues obtained through organ donor organizations, and developing a comprehensive lung ontology .Contains lung images and transcriptomic, proteomic, and lipidomic human and mouse data and provides scientific information to stimulate interest in research careers. Used to serve as a research resource and public education tool.

Proper citation: LungMap (RRID:SCR_016347) 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

https://gotrack.msl.ubc.ca/

Open source web-based system and database that provides access to historical records and trends in the Gene Ontology (GO) and GO annotations (GOA). Used for monitoring changes in the Gene Ontology and their impact on genomic data analysis.

Proper citation: GOTrack (RRID:SCR_016399) 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/cortex-lab/Suite2P

Software package for processing two-photon recordings. Available together with a graphical user interface that allows manual curation of the results. Used in two-photon microscopy for the analysis of data from two-photon imaging. Registers raw movies, detects active cells, extracts their calcium traces and infers their spike times.

Proper citation: Suite2P (RRID:SCR_016434) Copy   

•   Source: SciCrunch Registry

https://emcore.ucsf.edu/cryoem-software

Software tool for anisotropic correction of beam-induced motion for improved cryo-electron microscopy. Used to describe the sample motion as a local deformation that varies smoothly throughout the exposure. A program running on Linux.

Proper citation: MotionCor2 (RRID:SCR_016499) Copy   

•   Source: SciCrunch Registry

http://www.mediacy.com/imagepro

Software platform to perform image processing, analysis, and data reporting for microscope-based research and quality inspection.

Proper citation: Image Pro (RRID:SCR_016497) Copy   

•   Source: SciCrunch Registry

https://www.humancellatlas.org

Software tool as a catalog of comprehensive reference of human cells based on their stable properties, transient features, locations and abundances. Map to show the relationships among its elements. Open data international collaborative project involving diverse scientific communities to provide a framework for understanding cellular dysregulation in human disease.

Proper citation: Human Cell Atlas (RRID:SCR_016530) Copy   

•   Source: SciCrunch Registry

http://bioconductor.org/packages/release/bioc/html/MetaCyto.html

Software tool for automated meta-analysis of mass and flow cytometry data. Provides functions for preprocessing, automated gating and meta-analysis of cytometry data and collection of cytometry data from the ImmPort database.

Proper citation: MetaCyto (RRID:SCR_016415) Copy   

•   Source: SciCrunch Registry

http://www.broadcvdi.org/

Platform for analysis of the genetics of cardiovascular disease.Used for searching and analysis of human genetic information linked to myocardial infarction, atrial fibrillation and related traits while protecting the integrity and confidentiality of the data.

Proper citation: Cardiovascular Disease Knowledge Portal (RRID:SCR_016536) Copy   

•   Source: SciCrunch Registry

http://www.cyto.purdue.edu/cdroms/micro1/7_spon/vaytek/voxblast.htm

Software application for science and medicine which offers 3-D Measurement, 3-D Volume Visualization, and 3-D Rendering for any 3-D data. It accepts stacks of registered 2-D images and creates 3-D projections from any viewpoint.

Proper citation: VoxBlast (RRID:SCR_016491) Copy   

•   Source: SciCrunch Registry

https://omabrowser.org/oma/

Web based database interface for orthology prediction for the inference of orthologs among complete genomes. Used to relate genes across many species., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: OMA Orthology database (RRID:SCR_016425) Copy   

•   Source: SciCrunch Registry

https://github.com/mpi2/HARP

Software as a cross platform application for automating the processing of μCT and OPT image data. Used for standarization of embryo images prior to export to the PhenoDCC. Capable of processing other image modalities and specimens. Can be download as a stand alone release.

Proper citation: HARP (RRID:SCR_016546) Copy   

•   Source: SciCrunch Registry

https://github.molgen.mpg.de/MPIBR-coattia/MatlabMain/tree/master/behaviorAnalysis/code/NSKtoolbox/externalToolboxes/kCSDv1

Software tool for analyzing recordings from multielectrodes. Source code for the Matlab implementation of the Kernel Current Source Density method. The method operates in one-, two-, and three-dimensional space to perform nonparametric estimation of transmembrane current sources from local field potentials recorded from arbitrarily distributed electrodes.

Proper citation: kCSD-Matlab (RRID:SCR_016424) Copy   

•   Source: SciCrunch Registry