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https://nbcc.lunenfeld.ca/facilities/next-gen-sequencing
Core provides both short and long read sequencing capabilities for analysis of gene function and expression.Facility specializes in functional genomics and single cell biology. Services include consultation, sample preparation (especially for spatial and single cell applications), quality control, sequencing analysis, bioinformatics support, and assistance with grant and publication writing related to the services. Applications include:gene function analysis - pooled CRISPR screening, multiplexed barcode screens; whole genome sequencing - both short- and long-read sequencing; bulk gene expression profiling; single cell biology (single cells and single nuclei); spatial profiling; pathogen detection and profiling.
Proper citation: Lunenfeld-Tanenbaum Research Institute Network Biology Collaborative Centre Next-Generation Sequencing Core Facility (RRID:SCR_025385) Copy
https://www.uni.lu/lcsb-en/facilities/rodent-facility/
Assist researchers in development and analysis of various in vivo neurodegenerative and cancer models including humanized and germ-free animals. Facility has capacity to house different transgenic and germ-free mouse strains in more than 2500 IVC cages within SOPF breeding barrier.
Proper citation: University of Luxembourg LCSB Rodent Platform Core Facility (RRID:SCR_025267) Copy
https://CRAN.R-project.org/package=ggvenn
Software R package to draw venn diagram by ggplot2.
Proper citation: ggvenn (RRID:SCR_025300) Copy
https://github.com/MontpellierRessourcesImagerie/imagej_macros_and_scripts/wiki/Wound-Healing-Tool
Software tool to analyze scratch assays. It measures the area of wound in cellular tissue on stack of images representing time-series.
Proper citation: Wound Healing Tool (RRID:SCR_025260) Copy
https://inrae.github.io/pgd-mmdt/
Web ecosystem for sharing metadata. Designed to annotate datasets by creating metadata file to attach to storage space. Allows users to add descriptive metadata to datasets produced within collective of research unit, platform, multi-partner project, etc. to fit to data management plan about data organization and documentation, data storage and frictionless metadata sharing.
Proper citation: Maggot (RRID:SCR_025261) Copy
https://lambada.icm-institute.org
Reference atlas of the developing post-natal mouse brain. Provides data and annotations on distribution of cells and gene expression in mouse brain.
Proper citation: LAMBADA (RRID:SCR_025382) Copy
https://sites.dartmouth.edu/cqb/projects-and-cores/data-analytics-core/
Core offers statistical analysis of genomics data. Provides suite of standardized analysis pipelines for common data types like RNA-seq, ATAC-seq, and genome assembly. For more complex datasets, such as single-cell genomics, provides tailored analysis solutions. Core team assists with all project stages, from experimental design to publication support and data management. GDSC hosts several multi-day bioinformatics workshops designed to introduce fundamental concepts for analysis of genomics data.
Proper citation: Dartmouth Genomic Data Sciences Core Facility (RRID:SCR_025383) Copy
https://medinform.jmir.org/2015/4/e35
Algorithm for generating unique study identifiers in distributed and validatable fashion, in multicenter research. Light-weight, block chain style resource identifier generation for tracking resource linkage, provenance, utilization, and visualization. NHash has unique set of properties: (1) it is a pseudonym serving the purpose of linking research data about study participant for research purposes; (2) it can be generated automatically in completely distributed fashion with virtually no risk for identifier collision; (3) it incorporates set of cryptographic hash functions based on N-grams, with combination of additional encryption techniques such as shift cipher; (d) it is validatable (error tolerant) in the sense that inadvertent edit errors will mostly result in invalid identifiers.
Proper citation: NHash Identifier (RRID:SCR_025313) Copy
https://nbcc.lunenfeld.ca/facilities/high-throughput-screening
Provides instrumentation and expertise for the automation of laboratory processes. Facility has automated screening platforms and accessory equipment to enable flexible and scalable in vitro and in vivo assays including organoids. Services include access to chemical and genome-wide siRNA libraries, assay development and implementation, and data analysis. Applications include drug discovery and lead validation; ELISA-based assays for immune surveillance; protein biomarker discovery using OLINK proteomics technology; multiplexed barcode screening assays.
Proper citation: Lunenfeld-Tanenbaum Research Institute Network Biology Collaborative Centre High-Throughput Screening Core Facility (RRID:SCR_025390) Copy
https://biotech.illinois.edu/cmto
Facility, couples cytometry with microscopy, genomics and proteomics using instrumentation, expertise and services. Utilizes advanced super resolution microscopy techniques to gain understanding of cell sorting, analysis and enable cutting-edge spatial and single cell and multi-omics services.
Proper citation: University of Illinois at Urbana-Champaign Roy J. Carver Biotechnology Center Cytometry and Microscopy to Omics Core Facility (RRID:SCR_025272) Copy
https://pypi.org/project/goatools/0.4.7/
Software Python library for Gene Ontology analysis. Performs gene ontology enrichment analyses to determine over- and under-represented terms.
Proper citation: goatools (RRID:SCR_025305) Copy
Provides catalogue of confirmed and predicted DNA replication origin sites. At present this is limited to budding yeast and fission yeast. Data have been collated as culmination of number of genome-wide studies to identify location of replication origins throughout budding yeast genome. In addition to genome-wide studies data from large number of other origin mapping and characterization studies have been included.
Proper citation: OriDB (RRID:SCR_025365) Copy
https://shop.sartorius.com/ca/p/incucyte-ai-cell-health-analysis-software-module/BA-04871#
Software for analysis to determine live versus dead cells – no fluorescent dyes needed.
Proper citation: Incucyte Cell-By-Cell Analysis Software Module (RRID:SCR_025367) Copy
https://hillmanresearch.upmc.edu/research/facilities/in-vivo-imaging/
Provides novel quantitative imaging techniques that trace biomarkers of molecular events associated with effective cancer therapy.
Proper citation: University of Pittsburgh Hillman Cancer Center In Vivo Imaging Core Facility (RRID:SCR_025360) Copy
Web interactive browser to visualize data and perform gene set enrichment analysis along with gene and SNP lookup. Web interface used to query STARNET datasets and downstream analysis which includes RNAseq from 7 tissues: blood, free internal mammary artery (MAM), atherosclerotic aortic root (AOR), subcutaneous fat (SF), visceral abdominal fat (VAF), skeletal muscle (SKLM), and liver (LIV). Paired SNP genotyping data is included and utilized for tissue expression quantitative trait loci (eQTL), CAD heritability (H2), co-expression networks and gene regulatory networks.
Proper citation: STARNET (RRID:SCR_025238) Copy
https://bioinformatics.sph.harvard.edu/
Provides single point of contact for Harvard researchers interested in bioinformatics support, applying genomic approaches together with established and developing methodologies from epidemiology, environmental health, biostatistics and bioinformatics to improve human health.Services include analysis all types of next-generation sequencing data from RNA-seq and single cell RNA-seq to variant sequencing (exome or whole genome), to ChIP-seq or bisulfite sequencing. Offers bioinformatics training program for Harvard researchers interested in learning basic data skills and analysis of high-throughput sequencing data.
Proper citation: Harvard University Chan School of Public Health Bioinformatics Core Facility (RRID:SCR_025373) Copy
https://mriresearch.med.ubc.ca/
Facility consist of Philips 3.0 Tesla MRI scanner for studies on humans, Bruker small bore 9.4 Tesla MRI scanner, and computing facility for image archival and analysis. Scanners are entirely dedicated to research, and MR scanning is carried out on cost recovery basis. The scanners were selected to cater to a very broad range of in vivo applications and the Imaging Centre staff is trained to support any research projects that the scanners can accommodate.
Proper citation: University of British Columbia MRI Research Core Facility (RRID:SCR_025374) Copy
https://knightadrc.wustl.edu/professionals-clinicians/request-center-resources/
Provides on request resources including Data: clinical and cognitive measures as well as MRI and amyloid imaging scans; Tissue: frozen brain tissue, paraffin brain sections, antemortem CSF, DNA, fibroblast, dermal fibroblasts, plasma (fasting and non-fasting) and iPSC; Participants: eligible participants may be invited to enroll in research of other investigators after appropriate review. Researchers can use the request portal to review Center guidelines and policies; view available data and tissue; access data tables and codebooks; and submit request for resources.
Proper citation: Washington University School of Medicine Knight ADRC Request Center Resources Core Facility (RRID:SCR_025254) Copy
https://CRAN.R-project.org/package=forestmodel
Software R package that produces forest plots using 'ggplot2' from models produced by functions such as stats::lm(), stats::glm() and survival::coxph().
Proper citation: forestmodel (RRID:SCR_025250) Copy
https://github.com/ezrabru/POLCAM-Live
Software for live processing of polarisation camera images.
Proper citation: POLCAM-Live (RRID:SCR_025342) Copy
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