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https://github.com/SlicerMorph/SlicerMorph

Open and extensible platform to retrieve, visualize and analyse 3D morphology.Extension to import microCT data and conduct 3D morphometrics in Slicer. Used for data import, visualization, measurement, annotation, and geometric morphometric analysis on 3D data, including volumetric scans (CTs and MRs) and 3D surface scans, all within the 3D Slicer application.

Proper citation: SlicerMorph (RRID:SCR_024674) Copy   

•   Source: SciCrunch Registry

https://github.com/conda/conda-package-handling

Software to create and extract conda packages of various formats.

Proper citation: conda-package-handling (RRID:SCR_023991) Copy   

•   Source: SciCrunch Registry

https://bic.nd.edu/

Offers instrumentation dedicated to characterizing biomolecular conformations and interactions, as well as equipment for isolation and purification of macromolecules for subsequent detailed biophysical analysis.

Proper citation: University of Notre Dame ND Biophysics Instrumentation Core Facility (RRID:SCR_023867) Copy   

•   Source: SciCrunch Registry

https://www.uml.edu/research/crf/ourlabs/microscopy-core-lab.aspx

Core offers micro-imaging and micro-analysis solutions by providing access to several photon-, scanned probe-, ion beam-, and electron beam-based imaging and analytical instruments, services, and technical expertise for characterization of materials including nano-engineered materials, microelectronics, photonics, biomaterials, and others with applications in life sciences, drug discovery, environmental and energy research. Consultative services are also available.

Proper citation: University of Massachusetts Lowell Microscopy Core Facility (RRID:SCR_024677) Copy   

•   Source: SciCrunch Registry

http://faculty.washington.edu/maga/SCRI_MicroCT/

Shared instrument facility that has a Bruker Skyscan 1272 ex-vivo microCT that is capable of X-ray imaging at sub-microb resolution. The instrument can optionally be equipped with a 16-sample sample changer to automate the scanning queue. Core provides visualization and image analysis support for researchers, using open-source 3D Slicer biomedical imaging suite.

Proper citation: Seattle Children's Research Institute Micro Computed Tomography Imaging and Visualization Lab Core Facility (RRID:SCR_024678) Copy   

•   Source: SciCrunch Registry

http://www.cbcb.umd.edu/software/ELPH/index.shtml

Software tool as general purpose Gibbs sampler for finding motifs in set of DNA or protein sequences.Takes as input a set containing sequences, and searches through them for the most common motif, assuming that each sequence contains one copy of the motif. Used to find patterns such as ribosome binding sites (RBSs) and exon splicing enhancers (ESEs).

Proper citation: ELPH (RRID:SCR_024011) Copy   

•   Source: SciCrunch Registry

https://gitlab.com/tjobbertjob/ms-review-paper

Variability analysis of proteomics data used for deep learning.

Proper citation: ms-variability-analysis (RRID:SCR_024531) Copy   

•   Source: SciCrunch Registry

https://github.com/PacificBiosciences/unanimity

Software to generate highly accurate single molecule consensus reads.

Proper citation: CCS (RRID:SCR_024379) Copy   

•   Source: SciCrunch Registry

https://github.com/cancerit/alleleCount

Software package to prevent code duplication. Support code for NGS copy number algorithms. Generates count of coverage of each allele ACGT at that location given any filter settings.

Proper citation: alleleCount (RRID:SCR_023961) Copy   

•   Source: SciCrunch Registry

https://github.com/KanduriC/simAIRR

Software tool for simulation of antigen experienced adaptive immune receptor repertoire datasets for benchmarking of machine learning methods.

Proper citation: simAIRR (RRID:SCR_023956) Copy   

•   Source: SciCrunch Registry

https://github.com/ejcorn/mouse_abi_tool

Software tool to pull gene expression from Allen Brain Institute API in same annotation space as structural connectome.

Proper citation: Mouse_abi_tool (RRID:SCR_023831) Copy   

•   Source: SciCrunch Registry

https://boc.wisc.edu/

Core provides instrumentation for light and fluorescence based microscopy, including epifluorescence, confocal, and super-resolution imaging.Provides access to and training on basic and advanced light microscopy techniques. Expertise and advice is available for the design of experiments involving these techniques.

Proper citation: University of Wisconsin-Madison Biochemistry Optical Core Facility (RRID:SCR_023952) Copy   

•   Source: SciCrunch Registry

https://neuroscience.stanford.edu/research/neuroscience-community-labs/koret-human-neurosciences-community-laboratory

Core for collaborative human neuroscience research provides access to technology and expertise to high density electroencephalography recording and transcranial magnetic stimulation studies in human subjects.

Proper citation: Stanford University Koret Human Neurosciences Community Laboratory Core Facility (RRID:SCR_024528) Copy   

•   Source: SciCrunch Registry

https://www.sdstate.edu/genomics-sequencing-facility

Facility offers custom sequencing services from DNA/RNA extractions to sequencing using Illumina and Oxford Nanopore platforms. Projects examples include bulk RNAseq, 3\'RNASeq, Single Cell transcriptomics (10X Genomics), Genome sequencing, and amplicon sequencing (ie 16SRNA, genotyping). Services include experimental design and bioinformatics data analysis.

Proper citation: South Dakota State University Genomics Sequencing Core Facility (RRID:SCR_023959) Copy   

•   Source: SciCrunch Registry

https://github.com/mateidavid/fast5

Software C++ library for accessing Oxford Nanopore Technologies sequencing data.

Proper citation: Fast5 Library (RRID:SCR_024023) Copy   

•   Source: SciCrunch Registry

https://em-lab.berkeley.edu/

Imaging core and shared resource facility. Provides electron microscopy services, education, and training. Equipped with high resolution transmission electron microscopes, scanning electron microscopes, high pressure freezer and ancillary sample preparation equipment. The equipment can provide nanometer scale analysis for biological, chemical and materials science. Offers Project consultation, Education and training for new users, Equipment for trained users who anticipate having long term EM projects, Full service microscopy.

Proper citation: University of California at Berkeley Electron Microscope Laboratory Core Facility (RRID:SCR_024544) Copy   

•   Source: SciCrunch Registry

https://health.uconn.edu/cell-analysis-modeling/microscopy-facility/

CCAM Microscopy Facility provides access to equipment for quantitative fluorescence imaging applications. Instruments include laser scanning confocal microscopes equipped with 34 channel highefficiency QUASAR detectors. One of these microscopes supports nonlinear optical excitation, fluorescence correlation spectroscopy, and fluorescence lifetime imaging microscopy. Additionally, there is a light sheet microscope available for micro/mesoscale 3D imaging. The Zeiss Elyra 7 microscope is capable of total internal reflection fluorescence microscopy and supports several super resolution techniques such as lattice structured illumination microscopy, stochastic optical reconstruction microscopy, 3D photoactivated localization microscopy, and DNA points accumulation for imaging in nanoscale topography.

Proper citation: University of Connecticut Health Center for Cell Analysis and Modeling Microscopy Core Facility (RRID:SCR_024655) Copy   

•   Source: SciCrunch Registry

https://github.com/TADA-A/TADA-A/tree/master

Software statistical framework for mapping risk genes from de novo mutations in whole genome sequencing studies.

Proper citation: TADA-A (RRID:SCR_024538) Copy   

•   Source: SciCrunch Registry

http://mayoresearch.mayo.edu/center-for-individualized-medicine/medical-genome-facility.cfm

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 23,2026. Medical Genome Facility includes Cytogenetics Core, Genome Analysis Core and Proteomics Core. Available services include Sanger DNA sequencing, genotyping, gene expression and cytogenetic analysis, biospecimens accessioning and processing, tissue and cell molecular analysis, RNA interference, and oligonucleotide synthesis. Provides Illumina HiSeq2000 platforms and Pacific Biosciences RS single molecule real-time sequencer.Offers applied research services for development of innovative, personalized tests and treatments, especially with regard to biomarkers.

Proper citation: Mayo Clinic Medical Genome Core Facility (RRID:SCR_024632) Copy   

•   Source: SciCrunch Registry

https://biom-format.org/

Software provides command line interface and Python API for working with Biological Observation Matrix files.

Proper citation: python-biom-format (RRID:SCR_024193) Copy   

•   Source: SciCrunch Registry