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https://github.com/jorgemasgomez/almondcv2

Software repository provides open-source implementation of RGB imaging workflow for morphological and morphometric analysis of fruits and seeds.

Proper citation: almondcv2 (RRID:SCR_027064) Copy   

•   Source: SciCrunch Registry

https://github.com/mskcc/vcf2maf

Software tool to convert Virtual Contact File into Mutation Annotation Format, where each variant is annotated to only one of all possible gene isoforms.

Proper citation: vcf2maf (RRID:SCR_027063) Copy   

•   Source: SciCrunch Registry

https://www.meshlab.net/

Software application used for processing and editing 3D triangular meshes. Provides tools for editing, cleaning, repairing, inspecting, rendering, texturing, and converting meshes. This makes it suitable for variety of tasks related to 3D data, including preparing models for 3D printing.

Proper citation: Meshlab (RRID:SCR_027065) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/web/packages/clusterCrit/index.html

Software package for computing collection of clustering validation or quality criteria and partition comparison indices.

Proper citation: clusterCrit (RRID:SCR_027219) Copy   

•   Source: SciCrunch Registry

https://github.com/DZeevi-Lab/TinkerHap

Software accurate read-based phasing tool that integrates multiple methodologies to enhance phasing accuracy. Used to efficiently phase genomic data by linking sequencing reads across heterozygous sites, extending haplotype blocks, and incorporating pre-phased data when available. Read-based phasing algorithm with integrated multi-method support for enhanced accuracy.

Proper citation: TinkerHap (RRID:SCR_027235) Copy   

•   Source: SciCrunch Registry

https://github.com/dpeerlab/Palantir/

Algorithm to align cells along differentiation trajectories. Models trajectories of differentiating cells by treating cell fate as probabilistic process and leverages entropy to measure cell plasticity along the trajectory. Generates high-resolution pseudo-time ordering of cells and, for each cell state, assigns probability of differentiating into each terminal state.

Proper citation: Palantir (RRID:SCR_027194) Copy   

•   Source: SciCrunch Registry

https://biodare2.ed.ac.uk/

Data analysis resource and repository for biological data related to circadian rhythms, sharing public data from over 10,000 experiments (in 2025). The main features of BioDare2 are: fast analysis of rhythmic data (rhythm detection and period, phase, amplitude), timeseries processing, attractive visualizations, simple data description, data sharing with permalinks, easy data uploads and a modern UI.

Proper citation: BioDare2 (RRID:SCR_027193) Copy   

•   Source: SciCrunch Registry

https://github.com/Arcadia-Science/ProteinCartography

Software pipeline to build similarity maps of protein space. Identifies proteins related to query protein using sequence- and structure-based searches, compares all protein structures, and creates navigable map that can be used to look at protein relationships and make hypotheses about function.

Proper citation: ProteinCartography (RRID:SCR_027230) Copy   

•   Source: SciCrunch Registry

https://github.com/Yonghao-Holden/TEProf3

Software pipeline to detect Transposable Elements transcripts. Used to identify TE-derived promoters and transcripts using transcriptomic data from multiple sources, including short-read RNA-seq data, long-read RNA-seq data and single cell RNA-seq data.

Proper citation: TEProf3 (RRID:SCR_027288) Copy   

•   Source: SciCrunch Registry

https://github.com/omicscodeathon/emimr

Software application for identifying transcriptomic and epigenomic changes.

Proper citation: EMImR (RRID:SCR_027327) 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.umichttml.org/

Core enables the use of primary human organoids as tissue models for discovery, translation and regenerative medicine by providing:access to high-quality, well-characterized neonatal through adult human organoid lines from multiple organs for investigators studying human development and disease; access to detailed protocols; access to specialized, quality controlled and batch-tested reagents; expertise, guidance and training; help obtaining data;help establishing organoid lines;letters of support for grant submissions.

Proper citation: University of Michigan Human Organoid Core Facility (RRID:SCR_027333) Copy   

•   Source: SciCrunch Registry

https://mranalysis.cn/

Web-based platform providing integrated and standardized Mendelian Randomization analysis workflow. This includes GWAS data quality assessment, power/ sample size estimation, MR analysis, SNP-to-gene enrichment analysis, and data visualization. Interactive R Shiny application designed for Mendelian randomization analysis.

Proper citation: MRanalysis (RRID:SCR_027338) Copy   

•   Source: SciCrunch Registry

https://github.com/janjoy/BTE-RAG

Software application for BTE RAG implementation for DMDB QA datasets. Provides implementation of BTE-RAG framework, designed specifically for retrieval-augmented question answering (QA) in biomedical contexts. BTE-RAG leverages explicit mechanistic knowledge retrieval from BioThings Explorer (BTE) to significantly enhance the accuracy and reliability of large language models (LLMs) on biomedical benchmarks.

Proper citation: BTE-RAG (RRID:SCR_027297) Copy   

•   Source: SciCrunch Registry

https://www.merative.com/real-world-evidence/real-world-data-analytics#skiptheform-marketscan

Employer-sourced medical and drugs claims database of the under-65 working population and their dependents, as well as 65+ with Medicare supplemental insurance paid by employers.

Proper citation: MarketScan by Merative (RRID:SCR_027329) Copy   

•   Source: SciCrunch Registry

https://www.janelia.org/support-team/janelia-experimental-technology

Core team designs, builds and tests instruments, tools, and software that enable novel scientific investigation. Offers expertise in Data acquisition and analysis; Machine vision and image processing; Precision machining; Embedded systems design and programming; Laser, microscopy, and optical imaging systems engineering; Custom circuit design; Novel sensor systems; Lab automation, robotics and motion control; Mechanical design, machined and/or fabricated components and assemblies; Process automation.

Proper citation: Howard Hughes Medical Institute at Janelia Research Campus Janelia Experimental Technology jET Core Facility (RRID:SCR_027301) Copy   

•   Source: SciCrunch Registry

https://www.iqm.unicamp.br/institucional/infraestrutura/cemuiq/liafq/

Laboratory for Physicochemical Analysis of IQ-UNICAMP houses equipment for a range of analytical techniques:Thermal Analysis comprises techniques that measure the physical or chemical properties of a substance, or its reaction products, under controlled temperature variation;Atomic Spectrometry enables multi-element determination in solution samples;Elemental Analysis is used to determine the Carbon, Hydrogen, and Nitrogen content in solid and viscous samples.Nitrogen Physisorption is a technique used to determine the surface area and pore size of solid materials.

Proper citation: State University of Campinas LIAFQ-IQ Laboratory of Physicochemical Analysis Core Facility (RRID:SCR_027389) Copy   

•   Source: SciCrunch Registry

https://github.com/calebclayreagor/DELAY

Software application as convolutional neural network for inference of gene-regulatory relationships across pseudotime-ordered single-cell trajectories. Used for depicting pseudotime-lagged causality for accurate gene-regulatory inference.

Proper citation: DELAY (RRID:SCR_027302) Copy   

•   Source: SciCrunch Registry

https://github.com/NikolayOskolkov/MCWorkflow

Software application as computational workflow for detecting coordinates of microbial-like or human-like sequences in eukaryotic and procaryotic reference genomes.

Proper citation: MCWorkflow (RRID:SCR_027305) Copy   

•   Source: SciCrunch Registry

https://pypi.org/project/transformers/

Software framework for machine learning models in text, computer vision, audio, video, and multimodal model, for both inference and training.

Proper citation: Transformers (RRID:SCR_027381) Copy   

•   Source: SciCrunch Registry