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https://github.com/jmchandonia/CORAL

Software tool as framework for rigorous self validated data modeling and integrative, reproducible data analysis.

Proper citation: CORAL (RRID:SCR_022711) Copy   

•   Source: SciCrunch Registry
  

https://github.com/FRED-2/OptiType

Software tool for precision HLA typing from next generation sequencing data.

Proper citation: OptiType (RRID:SCR_022279) Copy   

•   Source: SciCrunch Registry
  

https://bioconductor.org/packages/SNPRelate/

Software R package as parallel computing toolset for relatedness and principal component analysis of SNP data.

Proper citation: SNPRelate (RRID:SCR_022719) Copy   

•   Source: SciCrunch Registry
  

https://github.com/B-UMMI/LMAS

Automated workflow enabling benchmarking of traditional and metagenomic prokaryotic de novo assembly software using defined mock communities. Results are presented in interactive HTML report where selected global and reference specific performance metrics can be explored.

Proper citation: LMAS (RRID:SCR_022251) Copy   

•   Source: SciCrunch Registry
  

https://github.com/bpucker/KIPEs

Software tool as automatic approach for identification of players in biosynthesis pathway. Used for automatic annotation of flavonoid biosynthesis steps in new transcriptome of genome sequence assembly. Various enzymes of entire metabolic networks can be identified if sufficient knowledge about functionally relevant amino acids is available.Combines comprehensive sequence similarity analyses with inspection of functionally relevant amino acid residues and domains in subjected peptide sequences.

Proper citation: Knowledge based Identification of Pathway Enzymes (RRID:SCR_022370) Copy   

•   Source: SciCrunch Registry
  

https://ptc.bocsci.com/services/protac-diastereomer-design-negative-control.html

Service to design PROTAC diastereomer to meet new drug discovery goals.

Proper citation: BOC Sciences PROTAC diastereomer Design negative control Service Resource (RRID:SCR_022249) Copy   

•   Source: SciCrunch Registry
  

https://ptc.bocsci.com/services/protac-design-based-on-bioinformatics.html

Provides PROTAC design based on bioinformatics services to customers to meet new drug discovery goals. Used for analysis of large scale multi group data to discover potential drug targets based on biological network characteristics, multi gene chip, proteome, metabolome data.

Proper citation: BOC Sciences PROTAC Design based on Bioinformatics (RRID:SCR_022248) Copy   

•   Source: SciCrunch Registry
  

https://commons.cri.uchicago.edu/pcdc/

PCDC brings together clinical, genomic, and imaging data from institutions around the world to transform pediatric cancer research and outcomes. Headquartered at University of Chicago, PCDC works with international leaders in pediatric cancers and National Cancer Institute to develop and apply uniform data standards that facilitate collection, combination, and analysis of data from many different sources. PCDC Consortium developes common core data dictionary and common governance structure spanning pediatric cancers neuroblastoma, soft tissue sarcoma, acute myeloid leukemia, acute lymphoblastic leukemia, germ cell tumors, bone tumors, and Hodgkin lymphoma to enable innovative cross disease research as well as set standard for future cancer data commons endeavors.

Proper citation: Pediatric Cancer Data Commons (RRID:SCR_022369) Copy   

•   Source: SciCrunch Registry
  

https://ptc.bocsci.com/services/linker-design-and-optimization-services.html

Provides Linker Design and Optimization services to meet new drug discovery goals.

Proper citation: BOC Sciences Linker Design and Optimization Services Service Resource (RRID:SCR_022247) Copy   

•   Source: SciCrunch Registry
  

https://bioconductor.org/packages/release/bioc/html/multiHiCcompare.html

Software package for removing biases across multiple Hi-C datasets. Properly handles Hi-C-specific decay of chromatin interaction frequencies with increasing distance between interacting regions.

Proper citation: multiHiCcompare (RRID:SCR_022368) Copy   

•   Source: SciCrunch Registry
  

http://sanger-pathogens.github.io/snp-sites/

Software tool to find SNP sites from multi-FASTA alignment file. Can output results in multiple formats for downstream analysis.

Proper citation: SNP-sites (RRID:SCR_022265) Copy   

•   Source: SciCrunch Registry
  

https://www.zeiss.com/microscopy/us/products/confocal-microscopes/lsm-900-with-airyscan-2.html

Laser scanning confocal microscope for multiplex imaging and analysis., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Zeiss: LSM 900 with Airyscan 2 (RRID:SCR_022263) Copy   

•   Source: SciCrunch Registry
  

https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/refs/heads/main/PDF/SCR_022262.pdf

System for efficient transfection of a variety of hard-to transfect cell lines and primary cells. Using certified aluminium electrode cuvettes this single cuvette system is capable of transfecting various substrates in a low throughput format.

Proper citation: Lonza: Nucleofector 2b Device (RRID:SCR_022262) Copy   

•   Source: SciCrunch Registry
  

https://www.u-toyama.ac.jp/

Japanese national university in Toyama Prefecture established in 1949. University of Toyama has three campuses, namely Gofuku, Sugitani, and Takaoka campuses.

Proper citation: University of Toyama; Toyama; Japan (RRID:SCR_022751) Copy   

•   Source: SciCrunch Registry
  

https://www.ncbi.nlm.nih.gov/refseq/about/nonredundantproteins/

Non-redundant RefSeq protein records are currently provided for archaeal and bacterial RefSeq genomes, with exception of selected reference genomes, by NCBI prokaryotic genome annotation pipeline. This scope definition may change in the future to include additional RefSeq sub-kingdoms or other organism groups and some GenBank conceptual translation protein records may provide cross-links to RefSeq non-redundant proteins.

Proper citation: RefSeq non-redundant proteins (RRID:SCR_022748) Copy   

•   Source: SciCrunch Registry
  

https://orthovenn2.bioinfotoolkits.net/home

Web server for whole genome comparison and annotation of orthologous clusters across multiple species.Works on any operating system with modern browser and Javascript enabled. Used to identify orthologous gene clusters and supports user define species to upload customized protein sequences. Interactive graphic tool which provides Venn diagram view for comparing multiple species protein sequences.

Proper citation: OrthoVenn2 (RRID:SCR_022504) Copy   

•   Source: SciCrunch Registry
  

https://edspace.american.edu/openbehavior/project/pavca/

Project related to tracking behavior. Used to identify subgroups of individuals that differentially attribute incentive value to food cue. Includes apparatus for studying Pavlovian conditioned approach behavior. Customized rat PavCA chambers are constructed based on modular devices purchased from Med-Associates. Code used to operate equipment and collect data was written using Med-Associates’ MEDSTATE programming language. This program is then loaded into Med-PC V operating program, also created by Med-Associates.

Proper citation: PavCA project (RRID:SCR_022508) Copy   

•   Source: SciCrunch Registry
  

https://en.wikipedia.org/wiki/Surgisphere

American healthcare analytics company established in 2008. Originally textbook marketing company, it came under scrutiny in May 2020 after it had provided large datasets of COVID-19 patients which were subsequently found to be extremely unreliable. The questionable data was used in studies published in The Lancet and The New England Journal of Medicine in May 2020. On 15 June 2020, company website was taken offline.

Proper citation: Surgisphere (RRID:SCR_022759) Copy   

•   Source: SciCrunch Registry
  

http://hollywood.mit.edu/exonscan/

Software framework for modeling sequence motifs based on maximum entropy principle.

Proper citation: ExonScan Web Server (RRID:SCR_022516) Copy   

•   Source: SciCrunch Registry
  

https://github.com/SGDDNB/ShinyCell

Software R package to create interactive Shiny based web applications to visualise single cell data via visualising cell information and/or gene expression on reduced dimensions e.g. UMAP, visualising coexpression of two genes on reduced dimensions, visualising distribution of continuous cell information e.g. nUMI / module scores using violin plots / box plots, visualising composition of different clusters / groups of cells using proportion plots and visualising expression of multiple genes using bubbleplots / heatmap.Shiny Interactive Web Apps for Single-Cell Data.

Proper citation: ShinyCell (RRID:SCR_022756) Copy   

•   Source: SciCrunch Registry