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https://www.zeiss.com/microscopy/int/products/microscope-software/zen.html

Software package for ZEISS light microscopy systems. Universal user interface for every imaging system from ZEISS to assist to acquire images, process images, visualize big data by GPU powered 3D engine, analyze images via Machine Learning-based tools, correlate between light-light or light-electron microscopes, store raw data in secure format locally or in the cloud., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: ZEN-ZEISS Efficient Navigation (RRID:SCR_021725) Copy   

•   Source: SciCrunch Registry
  

http://rna.informatik.uni-freiburg.de/MutaRNA/Input.jsp

Web server predicts and visualizes mutation induced structure changes of single nucleotide polymorphism in RNA sequence. This covers changes in accessibility (single strandedness) of molecule, its intra molecular base pairing potential and its base pairing probabilities. One of Freiburg RNA tools.

Proper citation: MutaRNA (RRID:SCR_021723) Copy   

•   Source: SciCrunch Registry
  

https://www.nature.com/articles/nprot.2014.131

Software tool calculates direction autocorrelation, plots and calculates other essential parameters to analyze cell migration in two dimensions: it displays cell trajectories individually and collectively, and it calculates average speed and mean square displacements (MSDs) to assess the area explored by cells over time.

Proper citation: DiPer (RRID:SCR_021720) Copy   

•   Source: SciCrunch Registry
  

https://www.cancer.gov/about-cancer/treatment/drugs

Portal to find consumer friendly information about drugs for cancer and conditions related to cancer. The list is in alphabetical order by generic name and brand name.

Proper citation: NIH NCI list of FDA approved cancer drugs (RRID:SCR_021841) Copy   

•   Source: SciCrunch Registry
  

https://github.com/kukionfr/VAMPIRE_open

Software tool for analysis of cell and nuclear morphology from fluorescence or bright field images. Enables profiling and classification of cells into shape modes based on equidistant points along cell and nuclear contours. Robust method to quantify cell morphological heterogeneity.

Proper citation: VAMPIRE (RRID:SCR_021721) Copy   

•   Source: SciCrunch Registry
  

https://github.com/Murali-group/SARS-CoV-2-network-analysis

Software tool to predict human proteins that interact with SARS-CoV-2 proteins and trace provenance of predictions.

Proper citation: SARS-CoV-2 network analysis (RRID:SCR_021811) Copy   

•   Source: SciCrunch Registry
  

https://www.mayo.edu/research/labs/tissue-repair-mechanobiology/software

Software tool to calculate 2D tractions exerted by adherent cell on its substrate. Used in field of mechanobiology to study contractile responses of variety of cell types.

Proper citation: TractionsForAll (RRID:SCR_021819) Copy   

•   Source: SciCrunch Registry
  

https://manualzz.com/doc/6543996/drosophila-activity-monitoring-system-user-s-guide

Software tool used in Drosophila Activity Monitor system to scann data for errors. Also allows user to extract data from monitor files and bin data in different lengths.

Proper citation: Trikinetics DAM FileScan (RRID:SCR_021817) Copy   

•   Source: SciCrunch Registry
  

https://github.com/VisionandCognition/NHP-pycortex

Software tool as adaptation for NHP brains and pipelines. Pycortex python based toolkit for surface visualization of fMRI data.

Proper citation: NHP pycortex (RRID:SCR_021815) Copy   

•   Source: SciCrunch Registry
  

https://www.ebi.ac.uk/eqtl

Catalog provides uniformly processed gene expression and splicing QTLs from all available public studies on human. Expression and splicing QTLs recomputed from public datasets.

Proper citation: eQTL Catalogue (RRID:SCR_021700) Copy   

•   Source: SciCrunch Registry
  

https://github.com/jtamames/SqueezeMeta

Software tool as fully automated pipeline for metagenomic analysis. Used for metagenomics covering all steps of analysis. Features several characteristics including co-assembly procedure or co-assembly of unlimited number of metagenomes via merging of individual assembled metagenomes, both with read mapping for estimation of abundances of genes in each metagenome. Includes binning and bin checking for retrieving individual genomes.

Proper citation: SqueezeMeta (RRID:SCR_021821) Copy   

•   Source: SciCrunch Registry
  

https://bioconductor.org/packages/BASiCS/

Software tool for Bayesian analysis of single cell sequencing data. Used to perform statistical analyses of single cell RNA sequencing datasets in context of supervised experiments.

Proper citation: Bayesian Analysis of Single Cell Sequencing (RRID:SCR_021829) Copy   

•   Source: SciCrunch Registry
  

https://www.mpi.nl/

Institute is entirely devoted to psycholinguistics – the study of how we produce and understand language, and how we acquire these skills as first or second language learners. The only institution in the world entirely dedicated to psycholinguistics, and is also one of only three among total of 90 within the Max Planck Society to be located outside Germany.

Proper citation: Max Planck Institute for Psycholinguistics; Nijmegen; Netherlands (RRID:SCR_021706) Copy   

•   Source: SciCrunch Registry
  

https://omgenomics.com/circa/

Software tool used to plot circular plots and visualize genomic data along genomic locations.

Proper citation: Circa (RRID:SCR_021828) Copy   

•   Source: SciCrunch Registry
  

https://archive.mpi.nl/tla/elan

Software annotation tool for audio and video recordings. Annotation can be sentence, word or gloss, comment, translation or description of any feature observed in media. Annotations can be created on multiple layers. Tiers can be hierarchically interconnected. Annotation can either be time-aligned to media or it can refer to other existing annotations. Content of annotations consists of Unicode text and annotation documents are stored in XML format (EAF).

Proper citation: ELAN (RRID:SCR_021705) Copy   

•   Source: SciCrunch Registry
  

http://www.psychencode.org/

Collaboration between research institutes working to provide framework of regulatory genomic elements in individuals with neuropsychiatric disorders.Collaboration has resulted in comprehensive set of manuscripts published in Science providing new insights into biology of developing, adult, and diseased human brain.Manuscripts are organized around three flagship articles, first analyzing human development, second studying disease transcriptomes, and third integrating tissue and single cell data with deep learning approaches.

Proper citation: PsychENCODE (RRID:SCR_021760) Copy   

•   Source: SciCrunch Registry
  

https://scicrunch.org/ResourceWatch

Knowledgebase of biomedical research resources. Repository for storing validation and problematic information about variety of entities within biomedical domain, such as antibodies, cell lines, etc. Enables researchers to submit their own claims about specific entity to make validation/problematic information F.A.I.R. (Findable, Accessable, Interoperable, Reuseable).

Proper citation: Biomed Resource Watch (RRID:SCR_021761) Copy   

•   Source: SciCrunch Registry
  

https://rescognito.com/

Platform for recognizing and promoting Open Research. Open online service that aims to offer fairer and more democratic platform for recognizing researcher contributions.Allows researchers to openly acknowledge colleagues for meaningful contributions to research process, such as Publication, Mentoring,Teaching,Data sharing,Reproducibility practices, Sharing negative results, Participation in discussion groups,Software development, Clinical trials management, Leadership, Community outreach, Public engagement. ORCID iDs, DOIs, grant IDs and other persistent identifiers are used where available as links to appropriate contributions.

Proper citation: Rescognito (RRID:SCR_021874) Copy   

•   Source: SciCrunch Registry
  

https://github.com/igordot/sns

Set of automated workflows for common sequencing based (Illumina) protocols, such as RNA-seq, ChIP-seq, ATAC-seq, WGBS/RRBS methylation, whole genome/exome/targeted variant detection, and contaminant screening. Sequencing data analysis pipelines.

Proper citation: Seq-N-Slide (RRID:SCR_021752) Copy   

•   Source: SciCrunch Registry
  

https://bitbucket.org/dries_decap/halvadeforspark/

Software implements germline and somatic variant calling pipelines based on best practices pipelines from Broad Institute using Spark framework. Produces VCF output file which contains single nucleotide polymorphisms (SNPs) and short insertions and deletions (indels) when supported by used tools. Program requires Spark on either local cluster with one or more nodes, Amazon EMR cluster or Docker image to run.

Proper citation: Halvade Somatic (RRID:SCR_021771) Copy   

•   Source: SciCrunch Registry