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https://www.une.edu/research/cobre/histology

Core provides access to expertise, training and specialized instrumentation related to tissue processing, sectioning, staining, immunohistochemistry and microscopy. Offers services and training related to image analysis and image analysis software to guide investigators in choosing best methods for presenting their data.Services include Trimming of wet tissues,Tissue processing into paraffin, OCT and paraffin embedding, Sectioning of paraffin-embedded/frozen tissues, Routine and special histochemical staining, Immunohistochemistry/Immunofluorescence, Antibody optimization, Brightfield/ widefield/ confocal microscopy, Image capture and image analysis.Core has cryostats, microtomes and microscopes available for reservation.

Proper citation: University of New England COBRE Histology and Imaging Core Facility (RRID:SCR_017885) Copy   

•   Source: SciCrunch Registry
  

http://proteomics.northwestern.edu/collaborate

Core offers multiple types of experiments from simple protein identification to protein quantitation. Performs traditional bottom-up proteomics, where proteins are digested with enzyme prior to analysis and intact, top-down proteomics analyses. Services include proteins identification after in-gel or in-solution digestion, top-down mass spectrometry to preserve post-translationally modified forms of proteins present in vivo by measuring them intact, IP-MS Pulldown,BioID service to identify target of biotin ligase that has been tagged onto their protein via traditional cloning methods,Untargeted Quantitative Peptide Proteomics,Targeted Quantitative Peptide Proteomics,Epiproteomic Histone Modification Panel A,Epiproteomic Histone Modification Panel B,Untargeted Metabolomics,Phosphoproteomics,PTM Scan,ChIP-MS.

Proper citation: Northwestern University Proteomics Core Facility (RRID:SCR_017945) Copy   

•   Source: SciCrunch Registry
  

https://lmf.mdibl.org/

Core provides professional scientific expertise in light microscopy. Offers access to hardware and software as well as expert guidance at any step of imaging project, from experimental design to image analysis.Comprises eight microscope systems including two laser scanning confocal microscopes including one Olympus inverted confocal microscope system (FV1000) and one Zeiss inverted confocal microscope system (LSM-980) equipped with Airy scan 2 for super resolution and 2-photon technology for in-vivo deep imaging with temperature controlled chamber. One spinning disk confocal including Nikon inverted spinning disk microscope system with incubation chamber (Eclipse Ti with Yokogawa disk CSU-W1), two Zeiss widefield microscopes for brightfield and epifluorescence illumination (Zeiss Apotome and Zeiss Colibri), three macroscopes systems to observe large samples or complete model organisms in brightfield and epifluorescence including one Olympus stereomicroscope system (MVX10) and two Zeiss stereomicroscope systems (SteREO Discovery V12), fully automated and one AxioZoom V16 , fully automated with ApoTome attachment.

Proper citation: Mount Desert Island Biological Laboratory Light Microscopy Core Facility (RRID:SCR_019166) Copy   

•   Source: SciCrunch Registry
  

https://jcesom.marshall.edu/research/office-of-research-and-graduate-education/core-facilities/genomics/

Core provides services including high throughput next generation sequencing (NGS) to support whole genome, whole exome, RNA-Seq, single cell RNA-Seq, microbiome and global chromatin and methylation studies, biostatistical and bioinformatic support for NGS projects, access to DNA/RNA sequence analysis software, automated Sanger DNA sequencing, genotyping and RNA/DNA quality assessment, access to shared instrumentation such as plate readers, real time thermal cyclers, Agilent Bioanalyzers, fluorimeters, and spectrophotometers.

Proper citation: Marshall University School of Medicine Genomics Core Facility (RRID:SCR_018885) Copy   

•   Source: SciCrunch Registry
  

https://aideepmed.com/COACH/

Web application for protein-ligand binding site prediction. Starting from given structure of target proteins, COACH will generate complementray ligand binding site predictions using two comparative methods, TM-SITE and S-SITE, which recognize ligand-binding templates from the BioLiP protein function database by binding-specific substructure and sequence profile comparisons.

Proper citation: COACH (RRID:SCR_027684) Copy   

•   Source: SciCrunch Registry
  

https://github.com/cytoscape/RCy3

Software R package in Bioconductor that communicates with Cytoscape via its REST API, providing access to the full feature set of Cytoscape from within the R programming environment. RCy3 has been redesigned to streamline its usage and future development as part of a broader Cytoscape Automation effort.Network biology using Cytoscape from within R.

Proper citation: RCy3 (RRID:SCR_027668) Copy   

•   Source: SciCrunch Registry
  

https://weghornlab.org/software.html

Software tool which derives gene-specific probabilistic estimates of the strength of negative and positive selection in cancer.

Proper citation: CBaSE (RRID:SCR_027765) Copy   

•   Source: SciCrunch Registry
  

https://github.com/vanallenlab/comut

Software Python library for creating comutation plots to visualize genomic and phenotypic information. Used for visualizing genomic and phenotypic information via comutation plots.

Proper citation: CoMUT (RRID:SCR_027745) Copy   

•   Source: SciCrunch Registry
  

https://github.com/SalasLab/HiTIMED

Software DNA methylation-based algorithm, to estimate cell proportions in tumor microenvironment. Profiles tumor, immune, and angiogenic components, allowing researchers to study tumor composition and its clinical implications using archival biospecimens.

Proper citation: HiTIMED (RRID:SCR_028180) Copy   

•   Source: SciCrunch Registry
  

https://oncodb.org/

Database offers integrated multi-omic data for patients across 33 cancer types. It encompasses gene expression, DNA methylation, somatic mutations, proteomic profiles, and chromatin accessibility, drawing from TCGA, GTEx, and CPTAC projects. Users can compare gene expression, DNA methylation, and protein levels between tumor and normal tissues, identifying differentially expressed genes and proteins, and examining gene-to-gene correlations. Provides oncogene mutation profiles and allows for survival analysis based on gene expression and methylation, linked to clinical parameters. Facilitates exploration of multi-omic correlations, such as gene expression with DNA methylation, and their variations with mutation status. Extends its analytical capabilities to include six major oncoviruses, offering insights into their impact on gene expression, methylation, and patient survival.

Proper citation: OncoDB (RRID:SCR_028340) Copy   

•   Source: SciCrunch Registry
  

https://polymerscreen.yale.edu

Open access web app that allows users to search for optimal condition for extraction of membrane proteins into membrane active polymers which allows for retention of native membrane environment around target protein.

Proper citation: MAP Database Guide for Membrane Protein Solubilization (RRID:SCR_025656) Copy   

•   Source: SciCrunch Registry
  

https://pypi.org/project/SpaGCN/

Software graph convolutional network to integrate gene expression and histology to identify spatial domains and spatially variable genes. SpaGCN integrates information from gene.

Proper citation: SpaGCN (RRID:SCR_025978) Copy   

•   Source: SciCrunch Registry
  

https://github.com/zhouhj1994/LinDA

Software linear models for differential abundance analysis of microbiome compositional data. Used to tackle compositional effects in differential abundance analysis. It fits linear regression models on centered log2-ratio transformed data, identifies bias term due to transformation and compositional effect, and corrects bias using mode of regression coefficients. It could fit mixed-effect models.

Proper citation: LinDA (RRID:SCR_025966) Copy   

•   Source: SciCrunch Registry
  

https://github.com/YingMa0107/CARD/

Software R package for spatial transcriptomics. Deconvolution method that combines cell-type-specific expression information from single-cell RNA sequencing (scRNA-seq) with correlation in cell-type composition across tissue locations.

Proper citation: Conditional AutoRegressive Deconvolution (RRID:SCR_026310) Copy   

•   Source: SciCrunch Registry
  

https://autodocksuite.scripps.edu/adt/

Software graphical user interface to help to set up which bonds will treated as rotatable in the ligand and to analyze dockings. Used for automated docking with selective receptor flexibility. Designed to predict how small molecules, such as substrates or drug candidates, bind to receptor of known 3D structure.

Proper citation: AutoDockTools (RRID:SCR_026401) Copy   

•   Source: SciCrunch Registry
  

https://github.com/spreka/biomagdsb

Software tool as parameter-free deep learning framework for nucleus segmentation using image style transfer. Cell segmentation tool.

Proper citation: NucleAIzer (RRID:SCR_026500) Copy   

•   Source: SciCrunch Registry
  

https://github.com/compgenomics/MeTPeak

Software package for finding the location of m6A sites in MeRIP-seq data.

Proper citation: MeTPeak (RRID:SCR_026533) Copy   

•   Source: SciCrunch Registry
  

https://github.com/agshumate/Liftoff

Software genome annotation lift-over tool capable of mapping genes between two assemblies of the same or closely related species. Aligns genes from reference genome to target genome and finds the mapping that maximizes sequence identity while preserving the structure of each exon, transcript and gene. Used for accurate mapping of gene annotations.

Proper citation: Liftoff (RRID:SCR_026535) Copy   

•   Source: SciCrunch Registry
  

https://endomap.hms.harvard.edu/

Structural interactome viewer. Interactive database of endosomal protein-protein interactions identified by cross-linking mass spectrometry and modeled by AlphaFold multimer. Structural protein interactome of human early endosomes.

Proper citation: EndoMap (RRID:SCR_026690) Copy   

•   Source: SciCrunch Registry
  

https://github.com/DerrickWood/kraken2

Software tool as second version of Kraken taxonomic sequence classification system.

Proper citation: kraken2 (RRID:SCR_026838) Copy   

•   Source: SciCrunch Registry