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https://github.com/PaulingLiu/scibet

Software tool as supervised cell type identifier that accurately predicts cell identity for newly sequenced single cells.

Proper citation: SciBet (RRID:SCR_024743) Copy   

•   Source: SciCrunch Registry

https://github.com/bioinfodlsu/rice-pilaf

Web app for post-GWAS/QTL analysis that performs slew of novel bioinformatics analyses to cross GWAS/QTL mapping results with host of publicly available rice databases.

Proper citation: RicePilaf (RRID:SCR_024945) Copy   

•   Source: SciCrunch Registry

https://github.com/bpucker/NAVIP

Software tool for functional impact prediction for sequence variants. Neighborhood-Aware Variant Impact Predictor (NAVIP) considers all variants within a given protein coding sequence when predicting the functional consequences.

Proper citation: NAVIP (RRID:SCR_024838) Copy   

•   Source: SciCrunch Registry

https://www.ucl.ac.uk/ion/research/research-departments/clinical-and-movement-neurosciences/centres-and-projects/queen-4

Platform for archival digital glass slide collection containing digital whole slide images from Lewy body disorders: Parkinson’s Disease, Parkinson’s Disease with Dementia and Dementia with Lewy Bodies, and control cases.E stained post-mortem brain tissues from patients with neurodegenerative diseases and controls.

Proper citation: QSBB Digital Pathology Resource (RRID:SCR_025020) Copy   

•   Source: SciCrunch Registry

https://inrae.github.io/pgd-mmdt/

Web ecosystem for sharing metadata. Designed to annotate datasets by creating metadata file to attach to storage space. Allows users to add descriptive metadata to datasets produced within collective of research unit, platform, multi-partner project, etc. to fit to data management plan about data organization and documentation, data storage and frictionless metadata sharing.

Proper citation: Maggot (RRID:SCR_025261) Copy   

•   Source: SciCrunch Registry

https://github.com/PhysiMeSS/PhysiMeSS

PhysiCell add-on which allows users to simulate ECM components as agents. PhysiCell addon for extracellular matrix modelling.

Proper citation: PhysiMeSS (RRID:SCR_025455) Copy   

•   Source: SciCrunch Registry

https://github.com/gobics/cocopye

Software tool for quality assessment of microbial genomes. Used to predict completeness and contamination of bacterial and archaeal genomes. Provides taxonomic classification of the input. Feature-based learning and prediction of genome quality indices.

Proper citation: CoCoPyE (RRID:SCR_025756) Copy   

•   Source: SciCrunch Registry

https://mouseinfo.kr/

Center to develop genetically engineered mice, analyze mouse phenotypes, and establish nationwide infrastructure for mouse research. South Korean government designated KMPC as principal organization for preclinical trials using mice and hamsters.

Proper citation: Korea Mouse Phenotyping Center (RRID:SCR_026052) Copy   

•   Source: SciCrunch Registry

http://firebrowse.org/

Portal provides access to cancer genomic data from variety of analyses: clinical, copy number, miR, miRseq, mRNA, mRNAseq, mutation and pathway analyses. Provides comprehensive suite of interdependent analyses of those data, including: correlations, clustering, and GISTIC and MutSigCV. Companion portal to the Broad Institute GDAC Firehose analysis pipeline, and was developed to cull and analyze data generated by The Cancer Genome Atlas (TCGA), which characterizes and identifies genomic patterns in human cancer models.

Proper citation: FireBrowse (RRID:SCR_026320) Copy   

•   Source: SciCrunch Registry

https://github.com/Neural-Systems-at-UIO/WebWarp

Web application for nonlinear refinement of image registration after WebAlign.

Proper citation: WebWarp (RRID:SCR_026759) Copy   

•   Source: SciCrunch Registry

https://github.com/Neural-Systems-at-UIO/WebAlign

Web application for 2D image registration to 3D atlas. Used for user guided affine spatial registration (anchoring) of sectional image data, typically high resolution histological images, to 3D reference atlas space. Can generate user defined cut planes through atlas templates that match orientation of cutting plane of 2D experimental images (atlas maps).

Proper citation: WebAlign (RRID:SCR_026758) Copy   

•   Source: SciCrunch Registry

https://github.com/Breeding-Insight/BIGapp

Species-agnostic web-based application for processing genotypic data in no-code RShiny user-friendly interface. Allows users without coding experience to process genetic data in all genome ploidy ranges and for multiallelic data, starting from number of input formats (including VCF). Also allows to perform downstream QC analyses (e.g., PCA) and run genomic analysis (e.g., Linkage mapping, QTL analysis, genome-wide association studies (GWAS), and genomic selection (GS).

Proper citation: BIGapp (RRID:SCR_026676) Copy   

•   Source: SciCrunch Registry

https://github.com/ngyuilun/EC-LMGraph

Software tool, which combine graph deep learning and protein language model, for accurate enzyme function and catalytic site prediction.

Proper citation: EC-LMGraph (RRID:SCR_027317) Copy   

•   Source: SciCrunch Registry

https://www.mcw.edu/departments/pathology-and-laboratory-medicine/research/mcw-tissue-bank

College of American Pathologists-accredited biorepository that collects, processes, securely stores, and distributes human biospecimens (tissues and blood products) for medical research. Tissue Bank that is a CAP-accredited biorepository supporting four human consent programs. Provides fresh and frozen tissue and biological materials with known preanalytical variables to researchers as well as provides specialized processing and imaging services.

Proper citation: Medical College of Wisconsin Tissue Bank (RRID:SCR_027842) Copy   

•   Source: SciCrunch Registry

https://github.com/mzlab-research/SMIntegration

Software open-source platform for integrated analysis of spatial transcriptomics and metabolomics data. It integrates spatial pattern recognition, differential comparison, network construction, and functional annotation into a unified workflow. Enables to explore gene-metabolite co-regulation mechanisms through an intuitive web interface, revealing spatial heterogeneity in tissue development and disease progression.

Proper citation: SMIntegration (RRID:SCR_027925) Copy   

•   Source: SciCrunch Registry

http://www.laureateinstitute.org/

Clinical neuroscience research institute in Tulsa, Oklahoma, dedicated to identifying biological markers and developing advanced interventions for mental health conditions, including disorders of mood, anxiety, eating, and substance use.

Proper citation: Laureate Institute for Brain Research; Oklahoma; USA (RRID:SCR_028639) Copy   

•   Source: SciCrunch Registry

http://www.computationalbioenergy.org/parallel-meta.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 30,2023. Open source pipeline for metagenomic data analysis, which enables efficient and parallel analysis of multiple metagenomic datasets and visualization of results for multiple samples. Can perform rapid data mining among microbial community data for comparative taxonomic and functional analysis.

Proper citation: Parallel-META (RRID:SCR_000121) Copy   

•   Source: SciCrunch Registry

https://simtk.org/home/aspf

Scalable particle fluid simulation code for Lagrangian particle-based fluid simulation. This adaptive sampling strategy allows using smaller (and thus more) particles in geometrically complex regions, while less particles are used for thick flat fluid volumes. Additionally, a novel distance-based particle surface definition is implemented which hides the particle granularity and allows dynamic resampling near the fluid-air interface. The code is implemented in C++ and should compile on Linux.

Proper citation: Adaptively Sampled Particle Fluids (RRID:SCR_000083) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/bait/

Software to create strand inheritance plots in data derived from the Strand-Seq sequencing protocol. The software is designed to be flexible with a range of species, and basic template folders can called to read in species-specific data.

Proper citation: BAIT (RRID:SCR_000511) Copy   

•   Source: SciCrunch Registry

http://fulxie.0fees.us/?type=reference&ckattempt=1

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 1,2023. Web-based tool for evaluating and screening reference genes from extensive experimental datasets. It integrates major computational programs (geNorm, Normfinder, BestKeeper, and the comparative delta-Ct method) to compare and rank the tested candidate reference genes. Based on the rankings from each program, it assigns an appropriate weight to an individual gene and calculated the geometric mean of their weights for the overall final ranking., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: RefFinder (RRID:SCR_000472) Copy   

•   Source: SciCrunch Registry