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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
Core provides expertise, services, education, and instrumentation to enhance biomedical research through LC-MS/MS-based proteomics. Services are offered for protein identification; characterization of post-translational modifications; and quantitative proteomics to identify differentially expressed/degraded proteins, regulated sites of post-translational modification, protein-protein interactions, and protein targets of drugs identified in phenotypic screens. Analyses include sample preparation, LC-MS/MS, database searching, generation of reports, and assistance with data interpretation. Faculty and staff assist with experimental design and development/optimization of customized methodology for analysis of post-translationally modified peptides (e.g. phosphorylation and O-GlcNAc modification, N- and O-linked glycosylation, Cys modifications including S-glutathionylation, and glycation of Lys and Arg). Quantitative approaches including metabolic labeling (SILAC), isobaric tagging (iTRAQ/TMT), and label free proteomics (LFQ) are performed on Orbitrap Elite or Orbitrap Fusion Lumos Mass Spectrometers. Developes methodology to identify alterations in post-translational modifications that impact signal transduction, transcription, translation, and response to therapeutics with goal of enabling investigators to discover molecular mechanisms underlying disease progression and therapeutic response.
Proper citation: South Carolina Medical University Mass Spectrometry Core Facility (RRID:SCR_017959) Copy
https://vbrn.org/proteomics-services/
Provides central resource of mass spectrometry based proteomics technologies to identify, characterize and quantify target proteins in various biological and biomedical samples. Provides mass spectrometry expertise for analyzing proteins and peptides for proteomics studies, support for data analysis from proteomics measurements, training in proteomics methods, and experimental design.
Proper citation: Vermont University Proteomics Core Facility (RRID:SCR_018667) Copy
https://www.unh.edu/research/welcome-university-instrumentation-center
University wide core facility offers NMR,SEM including FIB, EBS, EBSD, Tensile Stage,Confocal,X-Ray Photoelectron Spectroscopy,X-Ray Microscope aka Micro CT, Expert analysis of research and industrial samples,Training in scientific instrument operation and data analysis, Maintenance, repair, and calibration of instruments,Specialty instrument engineering design and application services,Facilitation of access to scientific instruments throughout the university.
Proper citation: University of New Hampshire University Instrumentation Center Core Facility (RRID:SCR_021101) Copy
https://pepatac.databio.org/en/latest/
Software standardized pipeline for ATAC-seq data analysis with serial alignments. Leverages unique features of ATAC-seq data to optimize for speed and accuracy, and provides several unique analytical approaches. Downstream analysis is simplified by standard definition format, modularity of components, and metadata APIs in R and Python. Restartable, fault-tolerant, and can be run on local hardware, using any cluster resource manager, or in provided Linux containers. We also emphasize the advantage of aligning to the mitochondrial genome serially, which improves alignment and quality control metrics. Includes quality control plots, summary statistics, and variety of data formats.
Proper citation: PEPATAC (RRID:SCR_024758) Copy
https://github.com/TaliaferroLab/LABRAT
Software application to quantify usage of alternative polyadenylation and cleavage sites in RNAseq data and identify genes whose usage of these sites varies across experimental conditions.
Proper citation: LABRAT (RRID:SCR_025006) Copy
https://reprint-apms.org/?q=chooseworkflow
Database of Mass Spectrometry contaminants and pipeline for Affinity Purification coupled with Mass Spectrometry analysis. Contaminant repository for affinity purification mass spectrometry data. Database of standardized negative controls. Used to identify protein-protein interactions.
Proper citation: CRAPome (RRID:SCR_025008) Copy
https://apps.cytoscape.org/apps/stringapp
Software application for network analysis and visualization of proteomics data. Cytoscape app that makes it easy to import STRING networks into Cytoscape, retains appearance and many of features of STRING, and integrates data from associated databases.
Proper citation: Cytoscape StringApp (RRID:SCR_025009) Copy
https://sourceforge.net/p/mageck/wiki/Home/
Software tool to identify important genes from genome-scale CRISPR-Cas9 screens. Used for prioritizing single-guide RNAs, genes and pathways in genome-scale CRISPR/Cas9 knockout screens.
Proper citation: MAGeCK (RRID:SCR_025016) Copy
Software framework to find and re-analyze public Mass Spectrometry data. Used to find uniformly formatted public MS/MS data in the Global Natural Product Social Molecular Networking Platform (GNPS) via formatted metadata. New or previously collected data can be added provided they adhere to the ReDU metadata standards (the implemented drag-and-drop validator is applicable to any scientific data) and data are available in GNPS/MassIVE.
Proper citation: ReDU (RRID:SCR_025105) Copy
https://github.com/mwang87/MassQueryLanguage
Software application for universal searching of Mass Spectrometry data. Open source MS query language for flexible and mass spectrometer manufacturer-independent mining of MS data. Implements common MS terminology to build consensus vocabulary to search for MS patterns in single mass spectrometry run. Enables set of mass spectrometry patterns to be queried directly from raw data.
Proper citation: MassQL (RRID:SCR_025106) Copy
https://fmug.amaral.northwestern.edu/
Software data-driven tool to identify understudied genes and characterize their tractability. Users submit list of human genes and can filter these genes down based on list of factors. Code to generate Find My Understudied Genes app for Windows, iOS and macOS platforms.
Proper citation: Find My Understudied Genes (RRID:SCR_025047) Copy
https://github.com/willtownes/glmpca
Software R package for dimension reduction of non-normally distributed data. Generalized PCA for non-normally distributed data.
Proper citation: glmpca (RRID:SCR_025517) Copy
https://github.com/bmvdgeijn/WASP/
Software allele-specific pipeline for unbiased read mapping and molecular QTL discovery. Allele-specific software for robust molecular quantitative trait locus discovery.
Proper citation: WASP (RRID:SCR_025497) Copy
https://discover.nci.nih.gov/rsconnect/cellminercdb/
Web application integrating cancer cell line pharmacogenomics. Enables exploration and analysis of cancer cell line pharmacogenomic data across different sources. Focuses on cancer patient-derived human cell line molecular and pharmacological data. CellMinerCDB (v1.2) includes several improvements.
Proper citation: CellMinerCDB (RRID:SCR_025649) Copy
https://bioxtas-raw.readthedocs.io/en/latest/
Software tool as GUI based Python program for reduction and analysis of small-angle X-ray solution scattering (SAXS) data.Small-angle scattering data reduction and analysis. Available on Windows, macOS (and OS X), and Linux.
Proper citation: BioXTAS RAW (RRID:SCR_025769) Copy
https://github.com/DevonsMo/IJOQ/releases
Software Python tool for fully automated analysis of cell-cell junction integrity. Used for fluorescence microscopy analysis.
Proper citation: Intercellular Junction Organization Quantification (RRID:SCR_026026) Copy
https://github.com/ay-lab/mustache
Software tool for multi-scale detection of chromatin loops from Hi-C and Micro-C contact maps in high resolutions (10kbp all the way to 500bp and even more). Used to detect chromatin loops caused by interaction of DNA segments with variable size.
Proper citation: Mustache (RRID:SCR_026110) Copy
https://github.com/open2c/cooltools
Software suite of computational tools that enables flexible, scalable, and reproducible analysis of high-resolution contact frequency data. Provides suite of computational tools with paired python API and command line access, which facilitates workflows either on high-performance computing clusters or via custom analysis notebooks. As part of the Open2C ecosystem, cooltools also provides detailed introductions to key concepts in Hi-C-data analysis with interactive notebook documentation.
Proper citation: cooltools (RRID:SCR_026118) Copy
https://github.com/WGLab/LongReadSum
Software fast and flexible QC and signal summarization tool for long read sequencing data.
Proper citation: LongReadSum (RRID:SCR_026408) Copy
Software Python library for deep probabilistic analysis of single-cell and spatial omics data. Used for probabilistic modeling and analysis of single-cell omics data, built on top of PyTorch and AnnData.
Proper citation: scvi-tools (RRID:SCR_026673) Copy
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