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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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SIMS Resource Report Resource Website 1+ mentions |
SIMS (RRID:SCR_025787) | software application, software resource | Software label transfer tool for single-cell RNA sequencing analysis. Scalable, Interpretable Modeling for Single-cell RNA-seq data classification. | label transfer, single-cell RNA sequencing analysis, single-cell RNA-seq data classification, | Schmidt Futures ; NHGRI 1RM1HG011543; NSF ; NIMH 1U24MH132628; University of California Office of the President ; QualcommInstitute |
PMID:38823397 | Free, Available for download, Freely available | SCR_025787 | scalable, interpretable machine learning for single cell | 2026-08-04 09:45:53 | 2 | ||||||||
|
UpSetR Resource Report Resource Website 50+ mentions |
UpSetR (RRID:SCR_026112) | software resource, software toolkit, source code | Software R package for visualization of intersecting sets and their properties. | visualization of intersecting sets, | NHGRI R00 HG007583; NHGRI U54HG007963; NCI U01 CA198935 |
PMID:28645171 | Free, Available for download, Freely available | https://cran.rstudio.com/web/packages/UpSetR/ | SCR_026112 | 2026-08-04 09:45:54 | 72 | ||||||||
|
cooltools Resource Report Resource Website 10+ mentions |
cooltools (RRID:SCR_026118) | software resource, software toolkit, source code | Software suite of computational tools that enables flexible, scalable, and reproducible analysis of high-resolution contact frequency data. Provides suite of computational tools with paired python API and command line access, which facilitates workflows either on high-performance computing clusters or via custom analysis notebooks. As part of the Open2C ecosystem, cooltools also provides detailed introductions to key concepts in Hi-C-data analysis with interactive notebook documentation. | enables reproducible analysis, high-resolution contact frequency data, paired python API, | NIGMS R35 GM143116; NHGRI UM1 HG011536; NHGRI R01 HG003143 |
PMID:38709825 | Free, Available for download, Freely available | SCR_026118 | 2026-08-04 09:45:55 | 25 | |||||||||
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NovoBreak Resource Report Resource Website 1+ mentions |
NovoBreak (RRID:SCR_026032) | software application, software resource, source code | 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. | discover somatic and germline structural variation, structural variation breakpoints, whole-genome sequencing data, local assembly, breakpoint detection, cancer genomes, | NCI R01 CA172652; NHGRI U41 HG007497; NCI P30 CA016672 |
PMID:27892959 | Free, Available for download, Freely available, | SCR_026032 | 2026-08-04 09:45:54 | 1 | |||||||||
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SAFARI Resource Report Resource Website 1+ mentions |
SAFARI (RRID:SCR_026028) | SAFARI | software application, software resource, source code | C++ software program for alignment of ancient DNA to a pangenome reference graph. Used to recover more alignments from ancient DNA samples, which suffer from characteristic substitution patterns due to chemical damage. | Pangenomics, ancient DNA, alignment, recover alignments from ancient DNA samples, characteristic substitution patterns, chemical damage, | Novo Nordisk Data Science Investigator ; NHGRI R01HG010485; NHGRI U41HG010972; NHGRI U01HG010961 |
PMID:39415996 | Free, Available for download, Freely available, | SCR_026028 | Sensitive Alignments from a RYmer Index | 2026-08-04 09:45:55 | 1 | |||||||
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AACR GENIE cBioPortal Resource Report Resource Website 10+ mentions |
AACR GENIE cBioPortal (RRID:SCR_026217) | portal, organization portal, data or information resource, consortium | 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. | International data-sharing consortium, generating an evidence base, precision cancer medicine, integrating clinical-grade cancer genomic data, clinical outcome data, cancer patients, | NCI CA008748; Howard Hughes Medical Institute ; NCI 5U01CA168394; NCI 5P50CA098258; NCI 5P50CA083639; NHGRI U54HG008100; NCI U24CA210950; NCI U24CA209851; NCI 2P30CA006516; NCI 5P30CA068485; NCI CA006973; NCI CA121113; NCI CA180950 |
PMID:28572459 | Restricted | SCR_026217 | 2026-08-04 09:45:56 | 13 | |||||||||
|
LongReadSum Resource Report Resource Website 1+ mentions |
LongReadSum (RRID:SCR_026408) | software application, software resource, source code | Software fast and flexible QC and signal summarization tool for long read sequencing data. | signal summarization, quality control, long read sequencing data, | NHGRI F31HG013259; NHGRI HG013359; NIGMS GM132713 |
PMID:39211184 | Free, Available for download, Freely available, | SCR_026408 | 2026-08-04 09:45:58 | 1 | |||||||||
|
GenomicKB Resource Report Resource Website |
GenomicKB (RRID:SCR_026591) | knowledge base, knowledge graph, database, data or information resource | Database that uses knowledge graph to consolidate genomic datasets and annotations. Graph database for researchers to explore and investigate human genome, epigenome, transcriptome, and 4D nucleome. Genomic entities and relationships are represented as diverse nodes and edges with properties. | genomic datasets and annotations, human genome, epigenome, transcriptome, 4D nucleome, | NHGRI R35HG011279 | PMID:36318240 | Free, Freely available | SCR_026591 | Genomic Knowledgebase | 2026-08-04 09:46:00 | 0 | ||||||||
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Bigtools Resource Report Resource Website |
Bigtools (RRID:SCR_026627) | software toolkit, software resource, software library, source code | Software library and associated tools for reading and writing bigwig and bigbed files. High-performance BigWig and BigBed library in Rust. | BigWig, BigBed, Rust, reading and writing bigwig and bigbed files, | NHGRI UM1 HG011536 | PMID:38837370 | Free, Available for download, Freely available | SCR_026627 | 2026-08-04 09:46:01 | 0 | |||||||||
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chromvar Resource Report Resource Website 10+ mentions |
chromvar (RRID:SCR_026570) | data processing software, source code, data analysis software, software resource, software application, software toolkit | Software R package for analyzing sparse chromatin-accessibility data by estimating gain or loss of accessibility within peaks sharing the same motif or annotation while controlling for technical biases. Enables accurate clustering of scATAC-seq profiles and characterization of known and de novo sequence motifs associated with variation in chromatin accessibility. Used for analysis of sparse chromatin accessibility data from single cell or bulk ATAC or DNAse-seq data. | analyzing sparse chromatin-accessibility data, analysis of sparse chromatin accessibility data, single cell, bulk ATAC, DNAse-seq data, | is used by: pychromVAR | NHGRI P50HG007735; NIAID U19AI057266; Rita Allen Foundation ; Harvard Society of Fellows ; Broad Institute Fellowship |
PMID:28825706 | Free, Available for download, Freely available | SCR_026570 | chromatin Variability Across Regions | 2026-08-04 09:46:01 | 11 | |||||||
|
Borzoi Resource Report Resource Website 1+ mentions |
Borzoi (RRID:SCR_026619) | software resource, software toolkit, source code | 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. | Borzoi models access, convolutional neural networks, predict RNA-seq coverage, | Common Fund of the Office of the Director ; NCI ; NHGRI ; NHLBI ; NIDA ; NIMH ; NINDS |
PMID:39779956 | Free, Available for download, Freely available | SCR_026619 | 2026-08-04 09:46:02 | 1 | |||||||||
|
NetworkDataCompanion Resource Report Resource Website 1+ mentions |
NetworkDataCompanion (RRID:SCR_026532) | software toolkit, software resource, source code, software library | 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. | TCGA and GTEx data analysis, TCGA data processing, filtering and mapping gene, normalization and cleaning, | NCI R35CA220523; NCI U24CA231846; NCI P50CA127003; NHGRI R01HG011393; NHGRI R01HG125975; NHLBI P01HL114501; NHLBI T32HL007427; NHLBI K01HL166376; American Lung Association |
PMID:39574772 | Free, Available for download, Freely available | SCR_026532 | 2026-08-04 09:46:00 | 1 | |||||||||
|
scvi-tools Resource Report Resource Website 10+ mentions |
scvi-tools (RRID:SCR_026673) | data processing software, source code, data analysis software, software resource, software application, software library, software toolkit | Software Python library for deep probabilistic analysis of single-cell and spatial omics data. Used for probabilistic modeling and analysis of single-cell omics data, built on top of PyTorch and AnnData. | probabilistic analysis, single-cell omics data, spatial omics data, | NIGMS R35GM124916; Chan-Zuckerberg Foundation ; NHGRI T32HG000047 |
PMID:35132262 | Free, Available for download, Freely available | https://github.com/scverse/scvi-tools | SCR_026673 | single-cell variational inference tools | 2026-08-04 09:46:03 | 31 | |||||||
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RFMix Resource Report Resource Website 1+ mentions |
RFMix (RRID:SCR_027030) | software application, software resource | Software tool for local ancestry and admixture inference. Discriminative Modeling Approach for Rapid and Robust Local-Ancestry Inference. | Discriminative Modeling, local ancestry and admixture inference, | NLM LM007033; NHGRI 2R01HG003229; NSF |
PMID:23910464 | Restricted | SCR_027030 | 2026-08-04 09:46:08 | 5 | |||||||||
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Phenotype Data Collection Toolkits Resource Report Resource Website |
Phenotype Data Collection Toolkits (RRID:SCR_026924) | software resource, software toolkit, source code | Software suite of data collection toolkits that cover range of biomedical research fields. These toolkits provide data collection forms that can be used to build research database and can facilitate phenotype standardisation and harmonisation efforts on African continent and larger user community. | data collection forms, build research database, facilitate phenotype standardisation, | NHGRI U24HG006941 | PMID:37766808 | Free, Available for download, Freely available | SCR_026924 | 2026-08-04 09:46:08 | 0 | |||||||||
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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 | 2026-08-04 09:46:12 | 0 | ||||||||
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GenVisR Resource Report Resource Website 10+ mentions |
GenVisR (RRID:SCR_027559) | software resource, software toolkit | 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. | visualizing genomics data, genomics, genomics data, small variants, copy number alterations, data quality, multiple species, | NHGRI K99HG007940; NCI K22CA188163 |
PMID:27288499 | Free, Available for download, Freely available | SCR_027559 | 2026-08-04 09:46:14 | 41 | |||||||||
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BayesPrism Resource Report Resource Website 1+ mentions |
BayesPrism (RRID:SCR_027499) | software resource, software toolkit, source code | 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 | 2026-08-04 09:46:13 | 8 | |||||||||
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Scooby Resource Report Resource Website |
Scooby (RRID:SCR_028110) | software application, software resource, source code | Software aplication to predict scRNA-seq coverage and scATAC-seq insertion profiles along the genome at single-cell resolution. It leverages the pre-trained multi-omics profile predictor Borzoi as a foundation model, equips it with a cell-specific decoder, and fine-tunes its sequence embeddings. | convolutional neural networks, predict RNA-seq coverage, scATAC-seq insertion profiles, Borzoi, cell-specific decoder, | European Research Council ; Gene Regulation Observatory at the Broad Institute of MIT & Harvard ; NHLBI 5P01HL131477; NHGRI UM1 HG011986; NHLBI DP2 HL151353; German Research Foundation |
PMID:41125796 | Free, Available for download, Freely available | SCR_028110 | 2026-08-04 09:46:21 | 0 | |||||||||
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CivicDb Resource Report Resource Website |
CivicDb (RRID:SCR_028055) | knowledge base, database, data or information resource | Open-access, community-driven knowledgebase designed to crowdsource and curate evidence on the clinical significance of cancer-related genomic variants. It helps researchers and clinicians interpret tumor DNA mutations to guide precision medicine. | clinical significance of cancer-related genomic variants, cancer-related genomic variants, genomic variants, | is related to: ClinGen | NCI U01CA209936; NCI U24CA237719; NCATS UL1TR002345; NHGRI U41 HG008735; NHGRI R00HG010157; NHGRI R00HG007940; NCI K22CA188163 |
PMID:36373660 | Free, Freely available, | SCR_028055 | , Clinical Interpretation of Variants in Cancer, CIViCdb | 2026-08-04 09:46:23 | 0 |
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