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https://github.com/vanallenlab/comut

Software Python library for creating comutation plots to visualize genomic and phenotypic information. Used for visualizing genomic and phenotypic information via comutation plots.

Proper citation: CoMUT (RRID:SCR_027745) Copy   

•   Source: SciCrunch Registry

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

Software R package for analysing multiple omics datasets in the context of molecular pathways, biological processes and other types of gene sets.Method that first prioritises genes through multi-omics data fusion and then identifies enriched pathways with gene-level evidence from input datasets.

Proper citation: ActivePathways (RRID:SCR_027736) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/release/data/annotation/html/BSgenome.Hsapiens.UCSC.hg38.html

Software R package containing the full genomic sequences for Homo sapiens as provided by UCSC (genome hg38, based on assembly GRCh38.p14 since 2023/01/31).

Proper citation: BSgenome Hsapiens UCSC hg38 (RRID:SCR_027738) Copy   

•   Source: SciCrunch Registry

https://smirnovgroup.wordpress.ncsu.edu/e580-a-shared-x-q-band-instrument/

Bruker ELEXSYS-E580 pulse X-/Q-band instrument offers state-of-the-art capabilities for both standard and cutting-edge EPR spectroscopy across a broad range of sample types and experimental needs. High-performance Electron Paramagnetic Resonance (EPR) spectrometer used for advanced research in chemistry, materials science, biochemistry, and physics, enabling studies of paramagnetic molecules, protein structures, quantum states, and materials by combining X-band (9-10 GHz) and Q-band (34 GHz) frequencies for high-resolution, sensitive pulse techniques.

Proper citation: Bruker: ELEXSYS-E580 pulse X-/Q-band system (RRID:SCR_027754) Copy   

•   Source: SciCrunch Registry

https://github.com/cancerit/telomerecat

Software R package for estimating average telomere length (TL) for paired end, whole genome sequencing (WGS) sample.Telomere computational analysis tool.

Proper citation: Telomerecat (RRID:SCR_027747) Copy   

•   Source: SciCrunch Registry

http://bionlp.bcgsc.ca/cancermine/

Text-mined and routinely updated database of drivers, oncogenes and tumor suppressors in different types of cancer.

Proper citation: CancerMine (RRID:SCR_027748) Copy   

•   Source: SciCrunch Registry

https://github.com/Zhao-Lab-UW/SAMS-Semi-Automatic-MEA-Spike-sorting-pipeline-

Software MATLAB-based application for spike sorting multi-electrode array (MEA) recordings. Used for efficient, reproducible spike sorting in high-throughput neuronal culture experiments. SAMS performs batched automated spike sorting processes and also allows the users to review and correct any clusters or spike assignments.

Proper citation: Semi-Automated MEA Spike Sorting (SAMS) (RRID:SCR_027843) Copy   

•   Source: SciCrunch Registry

https://github.com/BioDepot/SpatialProteomics

Software graphical and containerized spatial proteomics workflow. End-to-end containerized spatial proteomics analysis workflow with QuPath integration. Consists of cell segmentation, batch correction, unsupervised clustering, validation of clusters on the image, and cell type clustering results visualization.

Proper citation: SpatialProteomics (RRID:SCR_027835) Copy   

•   Source: SciCrunch Registry

https://github.com/zhoujt1994/scHiCluster

Software Python package for single-cell chromosome contact data analysis. It includes the identification of cell types (clusters), loop calling in cell types, and domain and compartment calling in single cells. Facilitates visualization and comparison of single-cell 3D genomes.

Proper citation: scHiCluster (RRID:SCR_027854) Copy   

•   Source: SciCrunch Registry

https://opensourcephysics.github.io/tracker-website/

Software video analysis and modeling tool developed within the Open Source Physics (OSP) Java framework. Allows frame-by-frame tracking of anatomical landmarks and articulated structures from video recordings, enabling the extraction of time-dependent kinematic variables such as displacement, velocity, and acceleration. Tracker is well suited for biomechanical analyses of articulated systems, as it supports joint-based rotations, reference-frame definition, and the export of quantitative motion data for further post-processing.

Proper citation: Tracker (RRID:SCR_027845) Copy   

•   Source: SciCrunch Registry

https://www.mskcc.org/

World-renowned institution dedicated to ending cancer through expert, compassionate patient care, pioneering research, and education for adults and children with all types of cancer, combining cutting-edge science with a holistic approach to treatment and support. Its mission focuses on innovative diagnosis and treatment (surgery, chemo, radiation, immunotherapy), supportive care (nursing, counseling, rehab), and training future cancer leaders.

Proper citation: Memorial Sloan Kettering Cancer Center (RRID:SCR_027785) Copy   

•   Source: SciCrunch Registry

https://ccg.uni-koeln.de/

Represents central facility and does not operate for profit, engaging in academic research collaborations and service provision on collaborative basis. Provides infrastructure for all kinds of sequencing, gene mapping and whole genome association studies in complex diseases as well as the validation of copy number variations.

Proper citation: University of Cologne Center for Genomics (CCG) Core Facility (RRID:SCR_027822) Copy   

•   Source: SciCrunch Registry

https://www.mskcc.org/research/ski/core-facilities/biostatistics

Core provides expertise on study design and statistical analysis. Devoted to developing and understanding ways to derive scientific inferences from quantitative data and to developing methods for achieving this aim. The staff are highly trained in this field and experienced in all of the specialized areas of statistical techniques including clinical trials methodology, survival analysis, epidemiologic methods, analysis of genomics data, statistical genetics, methods for diagnostic medicine, health services research, survivorship, evidence-based medicine and psychometric methods.

Proper citation: Memorial Sloan Kettering Cancer Center Biostatistics Core Facility (RRID:SCR_027821) Copy   

•   Source: SciCrunch Registry

https://neurojson.io/

Web application for human-readable, searchable neuroimaging datasets using universally accessible JSON format and URL-based RESTful APIs. NeuroJSON.io is built upon highly scalable document-store NoSQL database technologies, specifically, open-source Apache CouchDB engine, that can handle millions of datasets without major performance penalties. Provides fine-grained data search capabilities to allow users to find, preview and re-combine complex data records from public datasets before download.

Proper citation: NeuroJSON.io (RRID:SCR_027793) Copy   

•   Source: SciCrunch Registry

https://liana-py.readthedocs.io/en/latest/

Software framework that adapts and extends existing methods and knowledge to study cell-cell communication in single-cell, spatially-resolved, and multi-modal omics data. All-in-one framework for cell-cell communication inference.

Proper citation: LIANA+ (RRID:SCR_027830) Copy   

•   Source: SciCrunch Registry

https://github.com/HarmonizedMRI/Functional

Software application for vendor-neutral, open-source acquisition and reconstruction protocols for fully harmonized multi-site functional MRI studies.

Proper citation: Functional (RRID:SCR_027832) Copy   

•   Source: SciCrunch Registry

https://github.com/schwartzlab-methods/CellNEST

Software tool to decipher patterns of communication. Used to relay-network communication detection that identifies putative ligand–receptor–ligand–receptor communication. Detects T cell homing signals in human lymph nodes, identifies aggressive cancer communication in lung adenocarcinoma and colorectal cancer, and predicts new patterns of communication that may act as relay networks in pancreatic cancer.

Proper citation: CellNEST (RRID:SCR_027883) Copy   

•   Source: SciCrunch Registry

https://bican-bg.vercel.app/

Portal that allows users to explore taxonomy-guided genome selections, visualize epigenetic assays, and analyze chromatin data across basal ganglia cell populations identified by the BRAIN Initiative Cell Atlas Network (BICAN) with an interactive research platform. The portal allows for investigation of several key epigenetic assays including associated with active enhancers and promoters, repressed genes, and constitutive heterochromatin. Used to analyze complex genomic and epigenomic data from the brain, helping identify specific cell types, understand gene regulation, and map disease-related molecular events, ultimately aiding in understanding neurological disorders like Alzheimer's, autism, and depression by revealing what goes wrong at the cellular level, leading to better gene therapies.

Proper citation: BICAN Basal Ganglia Epigenome Explorer (RRID:SCR_027887) Copy   

•   Source: SciCrunch Registry

http://pl64.com

Software versatile all-purpose image and graphics editor for Windows, macOS, and Linux (via Wine) that combines raster (bitmap) and vector editing, making it a strong, affordable alternative to Adobe Photoshop, with features like layers, masks, color management (CMYK, Lab, 16-bit), batch processing, and web tools, presented in a comprehensive yet sometimes retro-looking interface . You can edit images or optimize them for the web, but you can also prepare print-ready PDF data.

Proper citation: Photoline (RRID:SCR_027878) Copy   

•   Source: SciCrunch Registry

https://camera.niehs.nih.gov/

Interactive database and user interface providing online access to validated alternative methods for U.S. regulatory and other contexts of use. Central hub and unified resource of validated alternative methods that enhances accessibility to validation study reports, data, protocols / SOPs, and information on regulatory guidance.Users can filter searches by alternative method types, defined approaches, Test Method Endpoint, and regulatory guidance.

Proper citation: Collection of Alternative Methods for Regulatory Application (CAMERA) (RRID:SCR_027893) Copy   

•   Source: SciCrunch Registry