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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.
Software tools for interactive viewing and fast sharing of large image data. Comprises Minerva Author, a tool to create and annotate images, and Minerva Story, a narrative image viewer for web hosting. Used for interpreting and interacting with complex images, organized around guided analysis approach. Enables fast sharing of large image data that is stored on Amazon S3 and viewed using zoomable image viewer implemented using OpenSeadragon, making it ideal for integration into multi-omic browsers for data dissemination of tissue atlases.
Proper citation: Minerva (RRID:SCR_024750) Copy
Software toolkit for analyzing spatial molecular data. Underlying framework is generalizable to spatial datasets mapped to XY coordinates. Package uses anndata framework making it easy to integrate with other popular single-cell analysis toolkits. It includes preprocessing, phenotyping, visualization, clustering, spatial analysis and differential spatial testing. Python based implementation efficiently deals with large datasets of millions of cells.
Proper citation: scimap (RRID:SCR_024751) 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
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/GregorySchwartz/too-many-cells
Software suite of tools, algorithms, and visualizations focusing on relationships between cell clades. This includes new ways of clustering, plotting, choosing differential expression comparisons. Identifies and visualizes relationships of single-cell clades.
Proper citation: TooManyCells (RRID:SCR_025328) 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://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://www.borch.dev/uploads/screpertoire/
Software R toolkit for analyzing single-cell immune repertoire profiling. Used for single-cell immune receptor analysis.
Proper citation: scRepertoire (RRID:SCR_025691) Copy
https://github.com/hms-dbmi/UpSetR
Software R package for visualization of intersecting sets and their properties.
Proper citation: UpSetR (RRID:SCR_026112) Copy
https://github.com/NCI-CGR/PLP_prediction_workflow/tree/autogvp
Software tool integrates ClinVar variant annotation with modified InterVar classification approach, based on American College of Medical Genetics-Association for Molecular Pathology guidelines, to output germline variant classification. Since AutoGVP input only requires VCF file, it can facilitate large-scale, clinically focused classification of germline sequence variants.
Proper citation: AutoGVP (RRID:SCR_026107) Copy
https://github.com/czc/nb_distribution
Software tool to discover somatic and germline structural variation breakpoints in whole genome sequencing data. Can report accurate breakpoints of Deletions, Duplications, Inversions and Translocations. Designed for Illumina paired-end data. Local assembly for breakpoint detection in cancer genomes.
Proper citation: NovoBreak (RRID:SCR_026032) Copy
Community-driven cancer classification platform encompassing rare and common cancers that provides clinically relevant and appropriately granular cancer classification for clinical decision support systems and oncology research. Cancer classification system for precision oncology.
Proper citation: OncoTree (RRID:SCR_026218) Copy
International data-sharing consortium focused on generating an evidence base for precision cancer medicine by integrating clinical-grade cancer genomic data with clinical outcome data of cancer patients treated at multiple institutions worldwide.
Proper citation: AACR GENIE cBioPortal (RRID:SCR_026217) Copy
https://github.com/katerinakazantseva/strainy
Software tool for phasing and assembly of bacterial strains from long-read sequencing data (either Oxford Nanopore or PacBio). Given reference (or collapsed de novo assembly) and set of aligned reads as input, tool produces multi-allelic phasing, individual strain haplotypes and strain-specific variant calls. Used for phasing and assembly of strain haplotypes from long-read metagenome sequencing.
Proper citation: Strainy (RRID:SCR_026430) Copy
https://github.com/dviraran/xCell
Software R package for generating cell type scores and R scripts for development of xCell. Web tool that performs cell type enrichment analysis from gene expression data for immune and stroma cell types. Used for Cell types enrichment analysis.
Proper citation: xCell (RRID:SCR_026446) Copy
Web application to automate germline genomic variant curation from clinical sequencing based on ACMG guidelines. Aggregates multiple tracks of genomic, protein and disease specific information from public sources.
Proper citation: PathoMAN (RRID:SCR_026552) Copy
https://github.com/QuackenbushLab/NetworkDataCompanion
Software R library of utilities for performing analyses on TCGA and GTEx data using the Network Zoo. Streamlines routine steps in TCGA data processing, including filtering and mapping gene and sample identifiers between modalities and allows modality-specific data transformation, such as normalization and cleaning.
Proper citation: NetworkDataCompanion (RRID:SCR_026532) Copy
https://github.com/calico/borzoi
Software package to access the Borzoi models, which are convolutional neural networks trained to predict RNA-seq coverage at 32bp resolution given 524kb input sequences.
Proper citation: Borzoi (RRID:SCR_026619) Copy
https://petab.readthedocs.io/en/latest/
Repository contains PEtab specifications and additional documentation. Data format for specifying parameter estimation problems in systems biology. SBML and TSV based data format for parameter estimation problems in systems biology. Human- and computer- readable format for representing parameter estimation problems in systems biology.
Proper citation: PEtab (RRID:SCR_026915) Copy
https://github.com/AlexandrovLab/SigProfilerAssignment
Software tool for assignment of known mutational signatures to individual samples and individual somatic mutations.
Proper citation: SigProfilerAssignment (RRID:SCR_026899) Copy
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