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https://www.petermac.org/research/research-technologies/centre-for-advanced-histology-and-microscopy

Provides tools and expertise in bio image analysis, histology, and microscopy. Facility allows for the preparation, visualization, and quantification of biological samples at the cellular and sub cellular levels. Researchers can choose to utilize our instruments independently or collaborate with our skilled staff through our fee-for-service options.

Proper citation: Peter MacCallum Cancer Centre Advanced Histology and Microscopy Core Facility (RRID:SCR_025432) Copy   

•   Source: SciCrunch Registry

https://clinical-research-facility.ed.ac.uk/core-services/genetics

Core provides secure receipt, processing, archiving and analysis of biological samples. Offers support for clinical research from sample collection to genetic analysis, working to the principles of Good Clinical Practice for Laboratories. Facility provides access to genomic technologies and services including next-generation sequencing (Illumina), third-generation sequencing (PacBio and Oxford Nanopore), bespoke bioinformatics analysis, and genomics and bioinformatics training.

Proper citation: University of Edinburgh Genomics Core Facility (RRID:SCR_025433) Copy   

•   Source: SciCrunch Registry

https://github.com/toddstavish/puncta-analyzer

Software tool for detecting and quantifying punctate co-localization in multi-channel images.

Proper citation: Puncta Analyzer (RRID:SCR_025425) Copy   

•   Source: SciCrunch Registry

https://github.com/christopher-vollmers/C3POa

Software to detect DNA splint sequence raw reads. Computational pipeline for calling consensi on R2C2 nanopore data.

Proper citation: C3Poa (RRID:SCR_025484) Copy   

•   Source: SciCrunch Registry

https://github.com/dib-lab/TheGreatGenotyper

Software workflow begins by preprocessing short-read samples of raw data to create counting colored De Bruijn graph. Graph based method for population genotyping of small and structural variants. Population genotyping workflow.

Proper citation: The Great Genoytper (RRID:SCR_025487) Copy   

•   Source: SciCrunch Registry

https://medschool.cuanschutz.edu/cell-and-developmental-biology/em-core-facility

Service facility which provides instrumentation and image analysis on recharge basis. Offers full specimen preparation and imaging services. Specimen preparation for electron microscopy studies including negative staining, plastic embedding, ultramicrotome and immunogold.

Proper citation: University of Colorado School of Medicine Electron Microscopy Core Facility (RRID:SCR_025521) Copy   

•   Source: SciCrunch Registry

https://skera.how

Software Pacbio analysis tool. Deconcat PacBio reads.

Proper citation: Skera (RRID:SCR_025482) Copy   

•   Source: SciCrunch Registry

Ratings or validation data are available for this resource

https://github.com/zhangjunpeng411/SCOM

Software application to Pan-cancer characterization of ncRNA synergistic competition. Used to predict ncRNA synergistic competition network from gene expression data and predicted ncRNA-related ceRNA networks.

Proper citation: SCOM (RRID:SCR_023738) Copy   

•   Source: SciCrunch Registry

http://www.bios.unc.edu/research/genomic_software/Matrix_eQTL/

Software tool for ultra fast eQTL analysis via large matrix operations.

Proper citation: MatrixEQTL (RRID:SCR_025513) Copy   

•   Source: SciCrunch Registry

https://github.com/single-cell-genetics/cellsnp-lite

Software C/C++ tool for efficient genotyping bi-allelic SNPs on single cells. You can use cellsnp-lite after read alignment to obtain the snp x cell pileup UMI or read count matrices for each alleles of given or detected SNPs.

Proper citation: Cellsnp-lite (RRID:SCR_025515) Copy   

•   Source: SciCrunch Registry

https://cytekbio.com/pages/spectro-flo

Flow Cytometry acquisition software.

Proper citation: Cytek SpectroFlo (RRID:SCR_025494) Copy   

•   Source: SciCrunch Registry

https://gitlab.gwdg.de/MedBioinf/metabolomics/metaboserv

Browser based platform for selecting, exchanging, and visualizing metabolomics data with controlled data access. Used to facilitate collaborative metabolomics research and to enable researchers to make their experimental data findable, accessible, interoperable, and re-usable as defined by the FAIR principles.

Proper citation: MetaboSERV (RRID:SCR_025496) Copy   

•   Source: SciCrunch Registry

http://www.okazolab.com

Software for designing and running advanced behavioral experiments and neuroscientific studies.

Proper citation: EventIDE (RRID:SCR_025412) Copy   

•   Source: SciCrunch Registry

https://medicine.iu.edu/service-cores/facilities/medical-genomics

Provides high-throughput genomics services including: genomic DNA sequencing, transcriptome RNA sequencing, miRNA sequencing, methylome or targeted methylation sequencing, protein DNA/RNA interaction (ChIP-seq, ATAC-seq and CLIP-seq), 10x single cell or single nuclei sequencing, and SNP genotyping.

Proper citation: Indiana University School of Medicine Medical Genomics Core Facility (RRID:SCR_025533) Copy   

•   Source: SciCrunch Registry

https://www.seattlechildrens.org/research/resources/genomics-spatial-biology-colab/

Provides technology and service capabilities in long and short read sequencing, spatial transcriptomics, and single cell assays.

Proper citation: Seattle Children's Research Institute Genomics and Spatial Biology Collaborative Laboratory Core Facility (RRID:SCR_025490) Copy   

•   Source: SciCrunch Registry

https://github.com/qianyingw/pre-rob

Neural networks for RoB assessment in preclinical publications. BERT-model based automated tool that assesses bias of preclinical research studies.

Proper citation: pre-rob (RRID:SCR_025493) Copy   

•   Source: SciCrunch Registry

https://cancer.iu.edu/research/shared-facilities/bc2.html

Core offers services related to biospecimen and data collection in support of cancer research. Provides collection of well-annotated samples from patients with malignancy and normal controls to support studies exploring the biologic basis of cancer, move basic findings to clinic, and probe the biology underlying clinical and population phenomena.

Proper citation: Indiana University School of Medicine Biospecimen Collection and Banking Core Facility (RRID:SCR_025529) Copy   

•   Source: SciCrunch Registry

https://beadl.org

Universal framework for describing behavioral tasks. Language to abstract and standardize behavioral task descriptions on two layers. Graphical layer specifies elements to describe behavioral tasks as state machine in formal flow diagram and how task controlling system interacts with subject. This graphical layer has been designed to be easy to understand while retaining all aspects of behavioral task. The second layer is corresponding, XML-based description of task. This layer forms rigid, yet extensible foundation of BEADL and hides hardware implementation related details form graphical representation.BEADL-specific extension for Neurodata Without Borders data standard defines how behavioral outcomes of task are stored in NWB including corresponding BEADL task description.

Proper citation: BEADL:BEhavioral tAsk Description Language (RRID:SCR_025464) Copy   

•   Source: SciCrunch Registry

https://nwbinspector.readthedocs.io/en/dev/

Software Python-based package designed to asses quality of Neurodata Without Borders files and based on compliance with Best Practice. Meant as companion to PyNWB validator, which checks for strict schema compliance. Attempts to apply some commonsense rules and heuristics to find data components of file that pass validation, but are probably incorrect, or suboptimal, or deviate from best practices. In other words, while PyNWB validator focuses on compliance of structure of file with the schema, the inspector focuses on compliance of actual data with best practices. Meant as data review aid. It does not catch all best practice violations, and any warnings it does produce should be checked by knowledgeable reviewer.

Proper citation: NWB Inspector (RRID:SCR_025465) Copy   

•   Source: SciCrunch Registry

https://med.virginia.edu/genetically-engineered-murine-model-core/

Core provides services to produce and preserve genetically engineered mouse strains for animal model research.Supports animal model research endeavors, to advance genetic and reproductive technologies for model creation and preservation, and to serve as resource for design, development and derivation of customized mouse strains.

Proper citation: University of Virginia School of Medicine Genetically Engineered Murine Model Core Facility (RRID:SCR_025473) Copy   

•   Source: SciCrunch Registry