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https://ngdc.cncb.ac.cn/databasecommons/

Curated catalog of worldwide biological databases to provide landscape of biological databases throughout the world and enable easy retrieval and access to specific collection of databases of interest. Catalog of worldwide biological databases as well as their curated meta information and derived statistics.

Proper citation: Database Commons (RRID:SCR_023661) Copy   

•   Source: SciCrunch Registry

https://github.com/vpc-ccg/svict

Software tool for detecting structural variations from cell free DNA containing low dilutions of circulating tumor DNA.

Proper citation: SViCT (RRID:SCR_023656) Copy   

•   Source: SciCrunch Registry

https://github.com/emo-bon/MetaGOflow

Software pipeline for marine Genomic Observatories data analysis. Used to address challenges of analysis of European Marine Omics Biodiversity Observation Network data.

Proper citation: metaGOflow (RRID:SCR_023674) Copy   

•   Source: SciCrunch Registry

http://www.proteomesoftware.com/products/scaffold/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 1,2023. Visualize and validate complex MS/MS proteomics experiments

Proper citation: Scaffold (RRID:SCR_014321) Copy   

•   Source: SciCrunch Registry

https://www.10xgenomics.com/instruments/xenium-analyzer

Xenium Analyzer offers subcellular profiling of 100s to 1,000s of RNA targets alongside multiplexed protein, in fresh, frozen or FFPE tissue.

Proper citation: 10x Genomics: Xenium Analyzer (RRID:SCR_023910) Copy   

•   Source: SciCrunch Registry

https://github.com/eMetaboHUB/Forum-LiteraturePropagation

Method extending ’guilt by association’ principle to literature information by using Bayesian framework to suggest diseases associated with overlooked metabolites.

Proper citation: Forum Literature Propagation (RRID:SCR_023874) Copy   

•   Source: SciCrunch Registry

https://www.akoyabio.com/

Spatial biology company offering solutions for high parameter tissue analysis from discovery through clinical and translational research, enabling development of more precise therapies for immuno-oncology and other drug development applications.

Proper citation: Akoya Biosciences (RRID:SCR_023774) Copy   

•   Source: SciCrunch Registry

https://www.akoyabio.com/phenocycler/instrument/

PhenoCycler-Fusion system is integrated platform combining automated, ultrahigh-plex cycling platform, Akoya PhenoCycler, and its high-speed imaging platform, PhenoImager (formerly Phenoptics), into end-to-end, integrated workflow.

Proper citation: Akoya Biosciences: PhenoCycler-Fusion (RRID:SCR_023773) Copy   

•   Source: SciCrunch Registry

https://www.shoprainin.com/Pipettes/Single-Channel-Manual-Pipettes/Pipet-Lite-XLS-LTS/Pipet-Lite-LTS-Pipette-L-1000XLS%2B/p/17014382

Pipet-Lite™ XLS+ manual single-channel pipette, 100-1000 μL, uses LTS™ LiteTouch™ tips. Accurate and precise, ergonomic, autoclavable liquid end, rugged and durable (L-1000XLS+)

Proper citation: Rainin: Pipet-Lite LTS Pipette L-1000XLS+ (RRID:SCR_023894) Copy   

•   Source: SciCrunch Registry

https://www.shoprainin.com/Pipettes/Single-Channel-Manual-Pipettes/Pipet-Lite-XLS-LTS/Pipet-Lite-LTS-Pipette-L-200XLS%2B/p/17014391

Pipet-Lite™ XLS+ manual single-channel pipette, 20-200 μL, uses LTS™ LiteTouch™ tips. Accurate and precise, ergonomic, autoclavable liquid end, rugged and durable (L-200XLS+)

Proper citation: Rainin: Pipet-Lite LTS Pipette L-200XLS+ (RRID:SCR_023892) Copy   

•   Source: SciCrunch Registry

https://www.nikon.com/company/news/2018/0319_nsim_s_01.html

Microscope enables super solution imaging of live cells at ten times the speed of conventional SIM. Powered by ECLIPSE Ti2-E Inverted Research Microscope, taking advantage of its advanced optics, stability and features.

Proper citation: Nikon: N-SIM S Super Resolution Microscope (RRID:SCR_023803) Copy   

•   Source: SciCrunch Registry

https://www.hitachi-keu.com/en-gb/iv/hv-f203gvscl.html

High resolution 1/1.8" 3 CCD Progressive Scan Color Camera with 1600 x 1200 pixel (UXGA) that is installed in the ZEISS Axioscan Z1 slide scanner. Integrated functions include electronic shutter from 1/30s to 1/100000s, Long term Integration up to 4s, AGC, external Trigger, Auto Shading, 6 Colour Masking, Frame-On-Demand Function, White Balance, AGC, Black Level Adjustment and Partial Scan Function.

Proper citation: Hitachi: 16-bit 3-CCD color camera HV-F203GV / HV-F203SCL (RRID:SCR_023888) Copy   

•   Source: SciCrunch Registry

https://www.cytivalifesciences.com/en/us/shop/protein-analysis/spr-label-free-analysis/spr-systems/biacore-4000-surface-plasmon-resonance-system-p-06144

High throughput Surface Plasmon Resonance system with high quality interaction data for better informed decision making in antibody selection, drug discovery and more., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Cytiva: Biacore 4000 (RRID:SCR_023766) Copy   

•   Source: SciCrunch Registry

https://de.moleculardevices.com/products/microplate-readers/multi-mode-readers/spectramax-id3-id5-readers

Microplate reader to measure absorbance, fluorescence and luminescence.

Proper citation: Molecular Devices: SpectraMax iD3 multi-mode microplate reader (RRID:SCR_023920) Copy   

•   Source: SciCrunch Registry

https://www.sanger.ac.uk/science/tools/caf

Software tools for manipulating Common Assembly Format files text format for describing sequence assemblies,that can be downloaded from the Sanger ftp site.

Proper citation: caftools (RRID:SCR_023982) Copy   

•   Source: SciCrunch Registry

https://data.broadinstitute.org/alkesgroup/BOLT-LMM/

Software statistical tool for identifying genetic associations. Used for genome wide association studies in large cohorts.

Proper citation: BOLT-LMM (RRID:SCR_023978) Copy   

•   Source: SciCrunch Registry

https://quint-workflow.readthedocs.io/en/latest/QUINTintro.html

Software workflow includes suite of various software to form analysis pipeline of atlas-based quantifuication of labbeled features in histological images from mouse or rat brain. This workflow also suggests and explains with instructional videos the way these software work together. Used for quantification and spatial analysis of labelling in series of rodent brain section images based on available 3D reference atlases.

Proper citation: QUINT (RRID:SCR_023856) Copy   

•   Source: SciCrunch Registry

https://github.com/brainglobe/brainreg-segment

Software tool for manual segmentation of regions/objects within the brain. Brainreg-segment will only work if the user registers their data with brainreg first. Used for segmentation of 3D shapes in common anatomical space.

Proper citation: Brainreg-segment (RRID:SCR_023853) Copy   

•   Source: SciCrunch Registry

http://contra.stanford.edu/contrafold/

Software novel secondary structure prediction method based on conditional log-linear models, a flexible class of probabilistic models which generalize upon SCFGs by using discriminative training and feature-rich scoring. Used for sequence prediction.

Proper citation: CONTRAfold (RRID:SCR_023994) Copy   

•   Source: SciCrunch Registry

http://ingenium.home.xs4all.nl/dicom.html

Software for DICOM training and testing,Demonstration and research image archives,Image format conversion from scanner with DICOM network access,DICOM image viewing and slide making, DICOM image selection, (limited) editing, and splitting and merging of series, Advanced scriptable image modification, filtering, forwarding and conversion, DICOM caching and archive merging, DICOM web access for viewing and data management (scriptable),Connection to Lua IDE for all sorts of DICOM manipulation.

Proper citation: Conquest DICOM (RRID:SCR_023993) Copy   

•   Source: SciCrunch Registry