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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.
https://github.com/rbundschuh/CLEAR
Software workflow that identifies reliably quantifiable transcripts in limiting-cell RNA-seq (lcRNA-seq) data for differentially expressed genes (DEG) analysis. Coverage-based Limiting-cell Experiment Analysis for RNA-seq.
Proper citation: CLEAR (RRID:SCR_027171) Copy
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
https://bioconductor.org/packages/RAIDS/
Software R package to enable genetic ancestry inference from various cancer sequence sources (RNA, Exome, and Whole-Genome sequences). This package also implements simulation algorithm that generates synthetic cancer-derived data. Used for accurate and robust inference of genetic ancestry from cancer-derived molecular data across genomic platforms
Proper citation: RAIDS (Robust Ancestry Inference using Data Synthesis) (RRID:SCR_027265) Copy
https://bioconductor.org/packages/release/bioc/html/GenVisR.html
Software R package for visualizing genomics data. Provides a user-friendly, flexible and comprehensive suite of tools for visualizing complex genomic data in three categories (small variants, copy number alterations and data quality) for multiple species of interest.
Proper citation: GenVisR (RRID:SCR_027559) Copy
https://github.com/Danko-Lab/BayesPrism
Software R package for fully Bayesian inference of tumor microenvironment composition and gene expression deconvolution. Used to analyze bulk RNA-seq data and estimate cell type-specific expression profiles.
Proper citation: BayesPrism (RRID:SCR_027499) Copy
https://cytospace.stanford.edu/
Software tool for assigning single cells from scRNA-seq to spatial transcriptomics coordinates via optimization framework. Supports high-resolution cell/spot alignment, capacity-constrained/domain-aware placement, and outputs per-cell/per-spot assignments and probabilities for downstream visualization and analysis. Used for optimal mapping of scRNA-seq data to spatial transcriptomics data.
Proper citation: CytoSPACE (RRID:SCR_027634) Copy
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