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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
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
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
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
https://www.unmc.edu/vcr/cores/vcr-cores/confocal-microscopy/index.html
Facility houses imaging technologies ranging from super resolution (~ 0.120 um to 0.020 um) to microscopic (~ 0.300 um) to mesoscopic (~ 1 um) biomedical imaging. Imaging specialists provide training and/or actively assist researchers collecting images across imaging instrumentation. Instrumentation includes Zeiss ELYRA PS.1 is inverted microscope for super resolution (SR) structured illumination microscopy (SIM) and single molecule localization microscopy (SMLM) including, PhotoActivated Localization Microscopy (PALM) using photo switchable/convertible fluorescent proteins, Total Internal Reflection Fluorescence (TIRF) and STochastic Optical Reconstruction Microscopy (STORM);Zeiss 800 CLSM with Airyscan is an inverted microscope dramatically increasing conventional confocal image resolution to ~180 nm using Airyscan technology; Zeiss 710 LSM is inverted microscope supporting most basic imaging applications, multi channel and spectral, co localization, live cell, 3D, and time series imaging; Zeiss Celldiscoverer 7 is widefield imaging system for automated, time lapse imaging of live samples; Zeiss Axioscan 7 is high performance whole slide scanning system for fluorescence, brightfield, and polarization imaging;Miltenyi Biotec Ultramicroscope II Light Sheet fluorescence microscope (LSFM) extends fluorescent imaging into true 3D, large scale volumetric imaging of intact tissues, organs, and small organisms. AMCF also houses several high-end data analysis workstations with premier image analysis software including HALO (Indica Labs) and IMARIS (Oxford Instruments) facilitating data rendering, analyses, and presentation options.
Proper citation: University of Nebraska Medical Center Advanced Microscopy Core Facility (RRID:SCR_022467) Copy
https://med.unr.edu/research/core-facilities-centers/high-spatial-temporal-resolution-imaging-core
Core provides high spatial and temporal resolution imaging methodologies and instrumentation for studying cellular structure, signaling pathways, and function in health and disease. Offers education, training and expertise in advising investigators in the use of the new technologies.
Proper citation: University of Nevada Reno School of Medicine High Spatial and Temporal Resolution Imaging Core Facility (RRID:SCR_024793) Copy
https://github.com/bioinform/somaticseq
Software accurate somatic mutation detection pipeline implementing stochastic boosting algorithm to produce somatic mutation calls for both single nucleotide variants and small insertions and deletions. NGS variant calling and classification.
Proper citation: SomaticSeq (RRID:SCR_024891) Copy
Web biological metadata server to view, store, and share your sample metadata in form of Portable Encapsulated Projects. PEPhub takes advantage of PEP biological metadata standard to store, edit, and access your PEPs in one place. Components include database where PEPs are stored; API to programmatically read and write PEPs in database; web based user interface to view and manage these PEPs via front end.
Proper citation: PEPhub (RRID:SCR_024892) Copy
https://github.com/xinhe-lab/GSFA
Software R package that performs sparse factor analysis and differential gene expression discovery simultaneously on single cell CRISPR screening data.
Proper citation: Guided Sparse Factor Analysis (RRID:SCR_025023) Copy
Web and command-line application to identify proteins with prion-like amino acid composition. Searches protein sequences to identify probable prion subsequences using hidden-Markov model algorithm.
Proper citation: PLAAC (RRID:SCR_024973) Copy
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
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
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
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
https://github.com/DerrickWood/kraken2
Software tool as second version of Kraken taxonomic sequence classification system.
Proper citation: kraken2 (RRID:SCR_026838) Copy
https://bioconductor.org/packages/release/bioc/html/apeglm.html
Software package provides Bayesian shrinkage estimators for effect sizes for variety of GLM models, using approximation of posterior for individual coefficients.
Proper citation: apeglm (RRID:SCR_026951) Copy
https://github.com/KrishnaswamyLab/PHATE
Software tool for visualizing high dimensional data using novel conceptual framework for learning and visualizing manifold to preserve both local and global distances.
Proper citation: PHATE (RRID:SCR_027119) Copy
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
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
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
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