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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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SigProfilerAssignment Resource Report Resource Website 1+ mentions |
SigProfilerAssignment (RRID:SCR_026899) | software application, software resource, source code | Software tool for assignment of known mutational signatures to individual samples and individual somatic mutations. | assignment of known mutational signatures, individual samples, individual somatic mutations, | Cancer Research UK Grand Challenge Award ; NIEHS R01ES030993; NIEHS R01ES032547; NCI R01CA269919; Packard Fellowship for Science and Engineering |
PMID:37502962 | Free, Available for download, Freely available, | SCR_026899 | 2026-02-16 09:51:16 | 3 | |||||||||
|
CLEAR Resource Report Resource Website |
CLEAR (RRID:SCR_027171) | software toolkit, source code, software resource | 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. | RNA-seq, cell experiment analysis for RNA-seq, | NCI P30 CA016058; NCI R50 CA211524; Ohio State University |
PMID:32039730 | GNU General Public License v3.0 | SCR_027171 | , CLEAR: Coverage-based Limiting-cell Experiment Analysis for RNA-seq, Coverage-based Limiting-cell Experiment Analysis for RNA-seq | 2026-02-16 09:51:19 | 0 | ||||||||
|
RAIDS (Robust Ancestry Inference using Data Synthesis) Resource Report Resource Website |
RAIDS (Robust Ancestry Inference using Data Synthesis) (RRID:SCR_027265) | RAIDS | software application, data processing software, data analysis software, software resource, simulation software | 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 | genetic ancestry, inference of genetic ancestry, cancer-derived molecular data, generate synthetic cancer-derived data, | NCI P30CA45508; NCI P20CA192996; NCI U01CA224013; NCI U01CA210240; NCI R01CA188134; NCI R01CA249002; NCI R01CA229699 |
PMID:36351074 | Free, Available for download, Freely Available | https://github.com/KrasnitzLab/RAIDS | SCR_027265 | , Robust Ancestry Inference using Data Synthesis (RAIDS), Robust Ancestry Inference using Data Synthesis | 2026-02-16 09:51:21 | 0 | ||||||
|
SEAHORSE Resource Report Resource Website |
SEAHORSE (RRID:SCR_027399) | database, data or information resource | Web-based database and search tool for exploratory data analysis in which we have pre-computed statistical associations between available data elements. Large-scale, open-access data sets such as the Genotype Tissue Expression Project (GTEx) and The Cancer Genome Atlas (TCGA) include multi-omic data on large numbers of samples along with extensive clinical and phenotypic information. Allows users to explore significant associations using tabulated summary statistics, data visualizations, and functional enrichment analyses (using RNA-seq data) for identified sets of genes. | Unexpected Correlations, Large Cohort Studies, Gene Expression, Gene Regulatory Networks, Correlations | NCI R35 CA220523; NHGRI R01 HG011393; NCI U24 CA231846 |
DOI:10.1101/2025.08.15.670514v1 | Free, Freely available, | SCR_027399 | Serendipity Engine Assaying Heterogeneous Omics Related Sampling Experiments | 2026-02-16 09:51:23 | 0 | ||||||||
|
BayesPrism Resource Report Resource Website 1+ mentions |
BayesPrism (RRID:SCR_027499) | software toolkit, source code, software resource | 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. | tumor microenvironment composition, gene expression deconvolution, analyze bulk RNA-seq data, estimate cell type-specific expression profiles, | NHGRI R01 HG009309; NCI U2C CA288284; NCI U54 CA209975 |
PMID:35469013 | Free, Available for download, Freely available | SCR_027499 | 2026-02-16 09:51:24 | 8 | |||||||||
|
CytoSPACE Resource Report Resource Website 1+ mentions |
CytoSPACE (RRID:SCR_027634) | software application, software resource, source code | 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. | Optimal mapping of scRNA-seq data to spatial transcriptomics data, assigning single cells from scRNA-seq, spatial transcriptomics coordinates, optimization framework, mapping, scRNA-seq data, spatial transcriptomics data, | American Association for Cancer Research ; Norwegian Cancer Society ; NCI R01CA255450; NCI R00CA187192; NCI R21CA238971; Virginia and D. K. Ludwig Fund for Cancer Research ; Donald E. and Delia B. Baxter Foundation |
PMID:36879008 | Free, Available for download, Freely available | https://github.com/digitalcytometry/cytospace | SCR_027634 | 2026-02-16 09:51:26 | 8 |
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