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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
https://github.com/bmvdgeijn/WASP/
Software allele-specific pipeline for unbiased read mapping and molecular QTL discovery. Allele-specific software for robust molecular quantitative trait locus discovery.
Proper citation: WASP (RRID:SCR_025497) Copy
https://github.com/willtownes/glmpca
Software R package for dimension reduction of non-normally distributed data. Generalized PCA for non-normally distributed data.
Proper citation: glmpca (RRID:SCR_025517) Copy
https://bioxtas-raw.readthedocs.io/en/latest/
Software tool as GUI based Python program for reduction and analysis of small-angle X-ray solution scattering (SAXS) data.Small-angle scattering data reduction and analysis. Available on Windows, macOS (and OS X), and Linux.
Proper citation: BioXTAS RAW (RRID:SCR_025769) Copy
https://github.com/DevonsMo/IJOQ/releases
Software Python tool for fully automated analysis of cell-cell junction integrity. Used for fluorescence microscopy analysis.
Proper citation: Intercellular Junction Organization Quantification (RRID:SCR_026026) Copy
https://github.com/ay-lab/mustache
Software tool for multi-scale detection of chromatin loops from Hi-C and Micro-C contact maps in high resolutions (10kbp all the way to 500bp and even more). Used to detect chromatin loops caused by interaction of DNA segments with variable size.
Proper citation: Mustache (RRID:SCR_026110) Copy
https://github.com/open2c/cooltools
Software suite of computational tools that enables flexible, scalable, and reproducible analysis of high-resolution contact frequency data. Provides suite of computational tools with paired python API and command line access, which facilitates workflows either on high-performance computing clusters or via custom analysis notebooks. As part of the Open2C ecosystem, cooltools also provides detailed introductions to key concepts in Hi-C-data analysis with interactive notebook documentation.
Proper citation: cooltools (RRID:SCR_026118) Copy
https://github.com/WGLab/LongReadSum
Software fast and flexible QC and signal summarization tool for long read sequencing data.
Proper citation: LongReadSum (RRID:SCR_026408) Copy
Software Python library for deep probabilistic analysis of single-cell and spatial omics data. Used for probabilistic modeling and analysis of single-cell omics data, built on top of PyTorch and AnnData.
Proper citation: scvi-tools (RRID:SCR_026673) Copy
https://github.com/williamslab/ped-sim
Software tool to simulate pedigree structures. Used for simulating relatives that can utilize either sex-specific or sex averaged genetic maps and also either model of crossover interference or traditional Poisson model for inter-crossover distances.
Proper citation: ped-sim (RRID:SCR_026957) Copy
https://github.com/RGLab/CytoML
Software R package that enables cross-platform import, export, and sharing of gated cytometry data. It currently supports Cytobank, FlowJo, Diva, and R, allowing users to import gated cytometry data from commercial platforms into R.
Proper citation: CytoML (RRID:SCR_027485) Copy
https://github.com/wyang17/SQuIRE
Software RNA-seq analysis pipeline that provides quantitative and locus-specific picture of Transposable Elements expression.
Proper citation: SQuIRE (RRID:SCR_027719) Copy
https://github.com/zfyuan/EpiProfile2.0_Family
Software tool for processing Epi-Proteomics mass spectrometry data. Discriminates isobaric histone peptides using distinguishing fragment ions in their tandem mass spectra and extracts the chromatographic area under the curve using previous knowledge about peptide retention time. Nanoflow liquid chromatography coupled with high resolution tandem mass spectrometry-based quantification tool for histone peptides, which can also be adapted to analyze nonhistone protein samples. EpiProfile 2.0 is extended version of v1.0 for enhanced quantification of histone peptides based on LC-MS/MS analysis.
Proper citation: EpiProfile (RRID:SCR_028224) Copy
Web-based application to trace tumor tissue of origin in primary and metastasized cancers.
Proper citation: HiTAIC (RRID:SCR_028181) Copy
Provides manufacturing micro- and nanofluidic devices for biomedical research, equipment and resources for applications with micro- and nanofabrication needs. Facility conisists of ISO class 7 cleanroom space, housing tools and materials for techniques including photolithography, nano-imprint lithography, plasma (dry) etching (ICP-RIE), wet etching, thin film deposition, scanning electron microscopy (VP-SEM), atomic force microscopy, contact angle goniometry, ellipsometry, profilometry, wafer dicing, wire bonding, laser ablation and engraving, 3D printing, hot embossing, and COMSOL software for device modeling. In addition, the facility has numerous microscopes for general inspection, ovens and furnaces, ultrapure water, and dedicated process fume hoods.
Proper citation: University of Kansas Nanofabrication Core Facility (RRID:SCR_028756) Copy
https://cpvb.org/service-cores/services/
Core provides investigators with access to specialized expertise in primary cell isolation, ex vivo organ function assessment, histology, and advanced tissue imaging. The Core supports cardiovascular, pulmonary, and vascular research through customized experimental services, consultation, and rigorous functional and molecular analyses that accelerate mechanistic discovery and translational research.
Proper citation: Ocean State Research Institute Providence VA Medical Center Cell Isolation and Organ Function Core Facility (RRID:SCR_028797) Copy
https://aimrc.uark.edu/data-science-core/
Core specializes in artificial intelligence-based approaches to elucidate relationships between large imaging, bioenergetics, genomic, and proteomic data sets. Provided services include: 1) foundational training for those getting started with high-performance computing and Arkansas Research Platform (ARP), 2) training and support for the collaborative use of a 508 TB data storage server exclusively maintained for and catering to AIMRC researchers, 3) training for Python programming, basic data mining, and machine learning, 4) training and support for using open-source deep learning based biomedical imaging resources (e.g., ZeroCostDL4Mic and Bioimage Model Zoo), and 5) customized solutions for deep learning based and large foundational models based biomedical imaging analysis, multi-omics data integration and analysis, and quantitative analysis pipelines for large data sets.
Proper citation: University of Arkansas AIMRC Data Science Core Facility (RRID:SCR_028681) Copy
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