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https://delaney.shinyapps.io/CAIRN/

Web tool to graph all copy number alterations present in segment file. Custom data is permitted. Allows to display copy number alterations which overlap user specified region, to quantify number of amplified CNAs and deleted CNAs. Visualization tool to explore copy number alterations discovered in published cancer datasets. Intended to help oncology community observe of relative rates of amplification, deletion, and mutation of interesting genes and regions.

Proper citation: CAIRN (RRID:SCR_019101) Copy   

•   Source: SciCrunch Registry

https://github.com/jbelyeu/SV-plaudit

Software for rapidly curating structural variant (SVs) predictions. SV-plaudit provides a pipeline for creating image views of genomic intervals, automatically storing them in the cloud, deploying a website to view/score them, and retrieving scores for analysis.

Proper citation: SV-plaudit (RRID:SCR_016285) Copy   

•   Source: SciCrunch Registry

http://amp.pharm.mssm.edu/DGB/

Web based application to assist researchers with identifying drugs and small molecules that are predicted to maximally influence expression of mammalian gene of interest. Used to identify drugs and small molecules to regulate expression of target genes for research purpose only. Application for ranking drugs to modulate specific gene based on transcriptomic signatures.

Proper citation: Drug Gene Budger (RRID:SCR_016489) Copy   

•   Source: SciCrunch Registry

https://github.com/dpeerlab/phenograph

Software tool as clustering method designed for high dimensional single cell data. Algorithmically defines phenotypes in high dimensional single cell data. Used for large scale analysis of single cell heterogeneity.

Proper citation: Phenograph (RRID:SCR_016919) Copy   

•   Source: SciCrunch Registry

https://immunedb.readthedocs.io/en/latest/

Software system for storing and analyzing high throughput B and T cell immune receptor sequencing data. Comprised of web interface and of Python analysis tools to process raw reads for gene usage, infer clones, aggregate data, and run downstream analyses, or in conjunction with other AIRR tools using its import and export features.

Proper citation: ImmuneDB (RRID:SCR_017125) Copy   

•   Source: SciCrunch Registry

https://exrna-atlas.org

Software tool as data and metadata repository of Extracellular RNA Communication Consortium. Atlas includes small RNA sequencing and qPCR derived exRNA profiles from human and mouse biofluids. All RNAseq datasets are processed using version 4 of exceRpt small RNAseq pipeline. Atlas accepts submissions for RNAseq or qPCR data.

Proper citation: exRNA Atlas (RRID:SCR_017221) Copy   

•   Source: SciCrunch Registry

http://www.genepattern-notebook.org/

Interactive analysis notebook environment that streamlines genomics research by interleaving text, multimedia, and executable code into unified, sharable, reproducible “research narratives.” It integrates the dynamic capabilities of notebook systems with an investigator-focused, simple interface that provides access to hundreds of genomic tools without the need to write code.

Proper citation: GenePattern Notebook (RRID:SCR_015699) Copy   

•   Source: SciCrunch Registry

http://tissues.jensenlab.org

Database that integrates evidence on tissue expression from manually curated literature, proteomics and transcriptomics screens, and automatic text mining. It maps all evidence to common protein identifiers and Brenda Tissue Ontology terms, and further unifies it by assigning confidence scores that facilitate comparison of the different types and sources of evidence.

Proper citation: TISSUES (RRID:SCR_015665) Copy   

•   Source: SciCrunch Registry

http://amp.pharm.mssm.edu/LJP/

Interactive on line tool where signatures are tagged with user selected metadata and external transcript signatures are projected onto network. Browser to visualize signatures from breast cancer cell lines treated with single molecule perturbations.

Proper citation: LINCS Joint Project - Breast Cancer Network Browser (RRID:SCR_016181) Copy   

•   Source: SciCrunch Registry

https://github.com/QTIM-Lab/DeepNeuro

Software Python package for neuroimaging data. Framework to design and train neural network architectures. Used in medical imaging community to ensure consistent performance of networks across variable users, institutions, and scanners.

Proper citation: DeepNeuro (RRID:SCR_016911) Copy   

•   Source: SciCrunch Registry

https://github.com/qianli10000/mtradeR

Software R package implements Joint model with Matching and Regularization and simulation pipeline. Used to test association between taxa and disease risk, and adjusted for correlated taxa screened by pre-selection procedure in abundance and prevalence, individually.

Proper citation: mtradeR (RRID:SCR_022977) Copy   

•   Source: SciCrunch Registry

https://github.com/plaisier-lab/sygnal

Software pipeline to integrate correlative, causal and mechanistic inference approaches into unified framework that systematically infers causal flow of information from mutations to TFs and miRNAs to perturbed gene expression patterns across patients. Used to decipher transcriptional regulatory networks from multi-omic and clinical patient data. Applicable for integrating genomic and transcriptomic measurements from human cohorts.

Proper citation: SYGNAL (RRID:SCR_023080) Copy   

•   Source: SciCrunch Registry

https://github.com/Shenhav-and-Korem-labs/SCRuB

Software R package to help researchers address common issue of contamination in microbial studies. Well aware MiSeq decontamination program.

Proper citation: SCRuB (RRID:SCR_023518) Copy   

•   Source: SciCrunch Registry

https://github.com/genome/bam-readcount

Software tool that runs on BAM or CRAM file and generates low level information about sequencing data at specific nucleotide positions. Its outputs include observed bases, readcounts, summarized mapping and base qualities, strandedness information, mismatch counts, and position within the reads.

Proper citation: bam readcount (RRID:SCR_023653) Copy   

•   Source: SciCrunch Registry

https://www.sbpdiscovery.org/biomedical-research/shared-resources/cancer-metabolism

Facility that aims to investigate role of metabolism in cancer on cellular and organismal level, combining in vitro and in vivo analysis. Comprehensive metabolic facility, including stable isotope tracing and flux analysis. Provides analysis of metabolism using specialist instruments and methodologies, together with advice on planning experiments and analyzing data. All instruments and approaches are available on fee-for-service basis to Cancer Center scientists, but alsoto outside users. Samples for most services can be shipped, but Seahorse analyzer users need to be local so they can bring live cells for analysis.

Proper citation: Sanford Burnham Prebys Medical Discovery Institute Cancer Metabolism Core Facility (RRID:SCR_014873) Copy   

•   Source: SciCrunch Registry

http://www.salk.edu/science/core-facilities/integrative-genomics-and-bioinformatics-core/

Core facility established to assist the Salk community with integrating genomics data into their research. The primary focus of the core is to provide analysis support for next-generation sequencing applications.

Proper citation: Salk Institute Razavi Newman Integrative Genomics and Bioinformatics Core Facility (IGC) (RRID:SCR_014842) Copy   

•   Source: SciCrunch Registry

https://www.mdanderson.org/research/research-resources/core-facilities/functional-proteomics-rppa-core.html

Core provides technology for functional proteomics studies and centralized, standardized and quality controlled services locally and globally.

Proper citation: RPPA Core Facility (RRID:SCR_016649) Copy   

•   Source: SciCrunch Registry

https://voices.uchicago.edu/ucflow/

Core offers services in cytometry and antibody technology, helps to design projects, data acquisition, analysis and/or interpretation beyond routine practices,critical drafting and/or revision of manuscript for intellectual content purposes.

Proper citation: Chicago University Cytometry and Antibody Technology Core Facility (RRID:SCR_017760) Copy   

•   Source: SciCrunch Registry

https://www.mdanderson.org/research/research-resources/core-facilities/proteomics-facility.html

Facility provides mass spectrometry analysis of proteins. Provides access to mass spectrometry based proteomics technologies and services including Protein Identification, Molecular Weight Determination, Quantitative Protein Analysis, Post-translational Modification Analysis, LC or LC-MS Analysis, Equipment Usage, Additional Data Analysis:Bioinformatics, statistics, pathway analysis and Assistance preparing materials for manuscripts or grants.Consultations for custom assays for other MS Services are also available.

Proper citation: University of Texas MD Anderson Cancer Center Proteomics Core Facility (RRID:SCR_017731) Copy   

•   Source: SciCrunch Registry

https://www.med.unc.edu/microscopy/

Core provides training, assistance and services in light microscopy, electron microscopy and image analysis. UNC core facility that is part of Department of Pathology and Laboratory Medicine, and are light microscopy core for Lineberger Comprehensive Cancer Center.

Proper citation: University of North Carolina at Chapel Hill Microscopy Services Laboratory Core Facility (RRID:SCR_017913) Copy   

•   Source: SciCrunch Registry