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https://mageewomens.org/for-researchers/core-facilities/momiforresearchers

Core provides collection of obstetric biological materials from prenatal visits through delivery along with annotated clinical information. In addition to specimen access, MOMI staff can provide study design assistance as needed.

Proper citation: Magee-Womens Research Institute Magee Obstetric Medical and Infant Database and Biobank Core Facility (RRID:SCR_025230) Copy   

•   Source: SciCrunch Registry

https://github.com/Nextomics/NextPolish

Software tool to fix base errors SNV/Indel in genome generated by noisy reads. Used to correct error bases in reference genome.

Proper citation: NextPolish (RRID:SCR_025232) Copy   

•   Source: SciCrunch Registry

https://github.com/tjiangHIT/cuteSV

Software tool for long read based human genomic structural variation detection. Collects signatures of various types of SVs and employs clustering-and-refinement method to analyze signatures to implement sensitive SV detection.cuteSV2 is upgraded version of cuteSV.

Proper citation: cuteSV (RRID:SCR_025233) Copy   

•   Source: SciCrunch Registry

https://github.com/GoekeLab/m6anet

Software Python tool for detection of m6A from direct RNA-Seq data. Leverages multiple instance learning framework to detect m6a modifications from Nanopore Direct RNA Sequencing data.

Proper citation: m6anet (RRID:SCR_025234) Copy   

•   Source: SciCrunch Registry

https://hillmanresearch.upmc.edu/research/facilities/biostatistics/

Provides statistical and computational methods for design, execution, analysis, and reporting of cancer-related research studies and trials including biomarker analysis and grant development.

Proper citation: University of Pittsburgh Hillman Cancer Center Biostatistics Core Facility (RRID:SCR_025355) Copy   

•   Source: SciCrunch Registry

https://github.com/STOmics/StereoSiTE

Software Python package for analysis and visualization of spatial transcriptomics data. Framework to spatially and quantitatively profile the cellular neighborhood organized iTME.

Proper citation: StereoSiTE (RRID:SCR_025236) Copy   

•   Source: SciCrunch Registry

https://hillmanresearch.upmc.edu/research/facilities/cancer-genomics/

Supports genomics and transcriptomics platforms including nucleic acid extraction, sample QC, next-generation library preparation and sequencing. Specializes in paraffin-embedded tissue samples.

Proper citation: University of Pittsburgh Hillman Cancer Center Cancer Genomics Core Facility (RRID:SCR_025357) Copy   

•   Source: SciCrunch Registry

https://github.com/PuttickMacroevolution/MCMCTreeR

Software R package to estimate distribution values for temporal node constraints and prepare input files for MCMCtree. Helps users choose parameters to reflect age information for prior age distributions, visualise time priors, and produce output files ready to be used in MCMCtree. Used to prepare MCMCtree analyses and visualize posterior ages on trees.

Proper citation: MCMCtreeR (RRID:SCR_025348) Copy   

•   Source: SciCrunch Registry

https://www.yworks.com/products/yed

Software desktop application as general purpose diagramming program with multi-document interface. Cross-platform Java application to generate high-quality diagrams. Runs on Windows, Linux, Mac OS, and other platforms that support Java Virtual Machine.

Proper citation: yEd (RRID:SCR_025325) Copy   

•   Source: SciCrunch Registry

https://www.lifexsoft.org/

Software for calculation of radiomic features for medical images. Enables calculation of conventional, histogram based, textural, and shape features from PET, SPECT, MR, CT, and US images, or from any combination of imaging modalities. Dedicated to researchers, radiologists, nuclear medicine physicians and oncologists to give access to 306 histogram, textural and shape indices in addition to conventional indices and where users can change calculation options.

Proper citation: LIFEx (RRID:SCR_025284) Copy   

•   Source: SciCrunch Registry

https://github.com/schwartzlab-methods/too-many-cells-interactive

Web browser-based JavaScript application for visualizing hierarchical cellular populations as interactive radial tree. Allows users to explore, filter, and manipulate hierarchical data structures through intuitive interface while also enabling batch export of high-quality custom graphics.

Proper citation: TooManyCellsInteractive (RRID:SCR_025315) Copy   

•   Source: SciCrunch Registry

https://github.com/tovaroe/GBMatch_CNN/

Software tool for predicting TS and risk from glioblastoma whole slide images. Used to predict risk scores and transcriptional subtypes from whole slide images of glioblastomas.

Proper citation: GBMatch_CNN - GBMPredictor (RRID:SCR_025316) Copy   

•   Source: SciCrunch Registry

https://compbio.uth.edu/FusionGDB2/

Functional annotation database of human fusion genes.FusionGDB 2.0 has updates of contents such as up-to-date human fusion genes, fusion gene breakage tendency score with FusionAI deep learning model based on 20 kb DNA sequence around BP, investigation of overlapping between fusion breakpoints with human genomic features across cellular role's categories, transcribed chimeric sequence and following open reading frame analysis with coding potential based on deep learning approach with Ribo-seq read features, and rigorous investigation of protein feature retention of individual fusion partner genes in protein level.

Proper citation: FusionGDB2 (RRID:SCR_025299) Copy   

•   Source: SciCrunch Registry

https://github.com/muzafferarikan/gNOMO2

Software as comprehensive and modular pipeline for integrated multi-omics analyses of microbiomes. Enables integration of taxonomic and functional analyses in microbiome multi-omics data.

Proper citation: gNOMO2 (RRID:SCR_025293) Copy   

•   Source: SciCrunch Registry

https://www.bruker.com/en/products-and-solutions/preclinical-imaging/paravision-360.html

Software for preclinical imaging integrated with Bruker MRI spectrometers. Used with Bruker MRI, PET/MR, and PET/CT instruments. Enables easy and high throughput imaging. All images, protocols, and subjects are in one location with inherent co-registration, image fusion, data processing, and analysis.

Proper citation: ParaVision 360 (RRID:SCR_025295) Copy   

•   Source: SciCrunch Registry

https://cryoem.bio.purdue.edu/

Facility provides access to instrumentation enabling users to collect data for high-resolution single particle reconstructions and tomographic studies of cells and larger complexes.

Proper citation: Purdue University Cryo-Electron Microscopy Core Facility (RRID:SCR_025545) Copy   

•   Source: SciCrunch Registry

https://huygens.science.uva.nl/VolcaNoseR/

Web app for creating, exploring, labeling and sharing volcano plots . The plot can be annotated to show genes/proteins based on their top ranking or based on user input.

Proper citation: VolcaNoseR (RRID:SCR_025419) Copy   

•   Source: SciCrunch Registry

https://merc.unl.edu/

Provides range of evaluation and data services to support client needs.Through consulting, evaluation, methodology, and training, we work to fill gaps and improve and empower data driven decision making.At the proposal stage of grants, we can design evaluation plans to meet your project needs, with the associated narrative text, budget, and letter of collaboration, as needed. We can also fill gaps post-award, or provide support with internal funding. We can assist with logic models, Broader Impacts, methodologies, needs assessments, survey design and implementation, support with Institutional Review Board applications, and trainings in our areas of expertise.

Proper citation: University of Nebraska-Lincoln Methodology and Evaluation Research Core Facility (RRID:SCR_025551) Copy   

•   Source: SciCrunch Registry

https://freimann.nd.edu/

Home to virtually all laboratory animals. Services include Procurement, Animal care, Breeding, Training,Limited procedures for research.

Proper citation: Notre Dame Freimann Life Science Center Core Facility (RRID:SCR_025552) Copy   

•   Source: SciCrunch Registry

https://cbg-ethz.github.io/V-pipe/

Software pipeline for analysis of next-generation sequencing data derived from intra-host and environmental viral populations. Designed for analysing NGS data of short viral genomes. Used for assessing viral genetic diversity from high-throughput data.

Proper citation: V-pipe (RRID:SCR_025399) Copy   

•   Source: SciCrunch Registry