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https://scimap.xyz

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://github.com/hms-dbmi/UpSetR

Software R package for visualization of intersecting sets and their properties.

Proper citation: UpSetR (RRID:SCR_026112) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://oncotree.mskcc.org/

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   

•   Source: SciCrunch Registry

https://genie.cbioportal.org/

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://pathoman.mskcc.org/

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/release/bioc/html/signifinder.html

Software R package designed to streamline collection and use of cancer transcriptional signatures across bulk, single-cell, and spatial transcriptomics data. Used for collection and implementation of public transcriptional cancer signatures.

Proper citation: signifinder (RRID:SCR_027141) Copy   

•   Source: SciCrunch Registry

https://ki.mit.edu/sbc/nanocore

Provides instruments for materials and nanomaterials research and full service TEM and cryoTEM sample preparation and imaging. Conducts CLEM and cryoCLEM workflows utilizing cryoFluorescence, cryoSEM and cryoFIB with focus on bio samples.Provides equipment and expertise to work with nanomaterials for characterization and imaging purpose. Core imaging capabilities include high performance field emission transmission electron microscope equipped with STEM, EELS, EDS and cryo-imaging, high performance field emission scanning electron microscope and focused ion beam equipped with STEM and cryo-imaging, cryo-fluorescent confocal microscope for CLEM workflows, and atomic force microscope equipped with liquid cell. Instrumentation for material characterization includes high throughputdynamic light scattering, nanoparticle sizing and counting, and rheometry.

Proper citation: Massachusetts Institute of Technology Swanson Biotechnology Center Nanotechnology Materials Core Facility (RRID:SCR_018674) Copy   

•   Source: SciCrunch Registry

https://www.uhcancercenter.org/research/shared-resources/genomics-and-bioinformatics

Core offers central service that uses genomic technologies combined with expert data analysis.Provides genomic analyses and bioinformatics as well as technical and scientific consultation,collaboration and initial data interpretation to all UH faculty with priority given to Cancer Center members with federal funding for cancer related projects. Offers expertise in molecular biology, genetics, genomics and bioinformatics, and can provide project planning, advice, and troubleshooting at all phases of the project.Genomic analysis services include DNA/RNA isolation, plating, and quality analysis, custom genotyping, Real-Time qPCR-based gene expression, copy number and methylation assays, pyrosequencing, Affymetrix and Illumina microarray based assays,Next Generation Sequencing on NextSeq500, iSeq100, NanoString nCounter analysis.

Proper citation: University of Hawaii at Manoa Cancer Center Genomics and Bioinformatics Shared Resource Core Facility (RRID:SCR_019085) Copy   

•   Source: SciCrunch Registry

https://www.lsi.umich.edu/science/centers-technologies/center-structural-biology

Comprehensive structural biology resource.Provides high throughput protein laboratory for protein engineering, protein purification facilities for small- and large-scale protein production, macromolecular crystallization and crystallography laboratories for solving crystal structures of biological molecules, and X-ray facility with access to high energy synchrotron radiation. Provides expert guidance to researchers through every stage of project, collaborating and consulting with researchers who use the facilities. Service categories are Chemical, Material and Protein Characterization, Molecular Biology. Services include Cloning, Crystallization, Differential thermal analysis, Drug development, NMR (small molecule), PCR, Protein crystallography, Protein engineering, Protein production, Structure determination, Xray.

Proper citation: University of Michigan Center for Structural Biology Core Facility (RRID:SCR_021065) Copy   

•   Source: SciCrunch Registry

https://cami.northwestern.edu/

Provides access to range of preclinical imaging modalities and support services. These include MRI, nuclear imaging (PET, SPECT, and CT), in vivo bioluminescence and fluorescence imaging, animal housing and prep spaces, and tissue culture. Image analysis services are available, as are software packages (JIM, Amira, Matlab) and a workstation for users to perform their own data analysis. Imaging services can be provided for investigators' own animal models, or animal models can be supplied by the Developmental Therapeutics Core.

Proper citation: Northwestern University Center for Advanced Molecular Imaging Core Facility (RRID:SCR_021192) Copy   

•   Source: SciCrunch Registry

https://www.feinberg.northwestern.edu/sites/cam/

Core offers instrumentation and services for study of biological processes at whole animal, tissue, cellular and subcellular levels. This includes light microscopy, electron microscopy and image analysis. Light microscopy offerings include super resolution microscopy (MINFLUX, STED, NSPARC, SORA), fluorescent laser scanning and spinning disk microscopy, fluorescent lifetime imaging, automated high throughput tissue cytometry, atomic force microscopy, laser capture microdissection, mutliphoton imaging, and whole animal bioluminescent and fluorescent imaging. Electron microscopy includes sample prep and imaging for TEM, SEM, platinum replicas, immuno gold and CLEM. We also provide microinjection equipment, chambers for stable live cell observation, and anesthesia equipment. CAM provides training on numerous different instrument platforms, consultation on experiment design, as well as digital image processing and image analysis.CAM is one of two Nikon Imaging Centers in the US, allowing us access and excellent support from Nikon to develop innovative solutions for the cutting edge imaging needs of users.

Proper citation: Northwestern University Feinberg School of Medicine Center for Advanced Microscopy and Nikon Imaging Center Core Facility (RRID:SCR_020996) Copy   

•   Source: SciCrunch Registry