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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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apeglm Resource Report Resource Website 1+ mentions |
apeglm (RRID:SCR_026951) | software resource, software toolkit | Software package provides Bayesian shrinkage estimators for effect sizes for variety of GLM models, using approximation of posterior for individual coefficients. | Bayesian shrinkage estimators, | NCI P01 CA142538; NHGRI R01 HG009125; NIEHS P30 ES010126; NIGMS R01 GM070335 |
PMID:30395178 | Free, Available for download, Freely available, | SCR_026951 | SciCrunch Registry | , Approximate Posterior Estimation for generalized linear model, Approximate posterior estimation for GLM | 2026-10-24 12:54:10 | 2 | ||||||||
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JaBba Resource Report Resource Website 1+ mentions |
JaBba (RRID:SCR_027134) | software application, software resource | Software tool to infer junction-balanced genome graphs with high fidelity. Builds genome graph based on junctions and read depth from whole genome sequencing, inferring optimal copy numbers for both vertices (DNA segments) and edges (bonds between segments). | Builds genome graph, junctions and read depth, infer junction-balanced genome graphs, whole genome sequencing, inferring optimal copy numbers, vertices and edges, DNA segments, bonds between segments, | NCI P01 CA91955; NCI P30 CA015704 |
PMID:33007263 | Free, Available for download, Freely available, | SCR_027134 | SciCrunch Registry | Junction Balance Analysis | 2026-10-24 12:54:14 | 1 | ||||||||
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Palantir Resource Report Resource Website 1+ mentions |
Palantir (RRID:SCR_027194) | algorithm resource, software resource, source code | Algorithm to align cells along differentiation trajectories. Models trajectories of differentiating cells by treating cell fate as probabilistic process and leverages entropy to measure cell plasticity along the trajectory. Generates high-resolution pseudo-time ordering of cells and, for each cell state, assigns probability of differentiating into each terminal state. | Trajectory, align cells along differentiation trajectories, | NCI P30 CA008748; NCI R01CA164729; NICHD DP1-HD084071 |
PMID:30899105 | Free, Available for download, Freely available | SCR_027194 | SciCrunch Registry | 2026-10-24 12:54:14 | 5 | |||||||||
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SeSAMe Resource Report Resource Website 10+ mentions |
SeSAMe (RRID:SCR_027388) | SeSAMe | software resource, software toolkit | Software R package for reducing artifactual detection of DNA methylation by Infinium BeadChips in genomic deletions. | reducing artifactual detection, DNA methylation, Infinium BeadChips, genomic deletions, | Michelle Lunn Hope Foundation ; NCI R01 CA170550; NCI U24 CA143882; NCI U24 CA210969; Ovarian Cancer Research Fund Grant ; Van Andel Research Institute |
PMID:30085201 | Free, Available for download, Freely available, | SCR_027388 | SciCrunch Registry | SEnsible Step-wise Analysis of DNA MEthylation | 2026-10-24 12:54:19 | 23 | |||||||
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CBaSE Resource Report Resource Website |
CBaSE (RRID:SCR_027765) | software application, software resource, source code | Software tool which derives gene-specific probabilistic estimates of the strength of negative and positive selection in cancer. | Cancer Genes, SNV, indel, gene-specific probabilistic estimates, strength of negative and positive selection, cancer | NCI U54 CA143874; NIGMS R01 GM078598; NIMH R01 MH101244 |
PMID:29106416 | Free, Available for download, Freely available | https://github.com/weghornlab/CBaSE, http://genetics.bwh.harvard.edu/cbase | SCR_027765 | SciCrunch Registry | Cancer Bayesian SElection estimation | 2026-10-24 12:54:30 | 0 | |||||||
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T Cell ExTRECT Resource Report Resource Website 1+ mentions |
T Cell ExTRECT (RRID:SCR_027742) | software resource, software toolkit, source code | Software R package to calculate T cell fractions from WES data from hg19 or hg38 aligned genomes. | T-cell, T cell receptor excision circle, WES data, hg19 or hg38 aligned genomes, | NCATS UL1TR000100; NCI P30CA023100; NCI R21CA177519; NCI U01CA196406; NHLBI U54HL108460; NIH Office of the Director DP5OD017937; NLM T15LM011271; NSF |
PMID:34497419 | Free, Available for download, Freely available | SCR_027742 | SciCrunch Registry | , T cell exome TREC, T cell exome T cell Receptor Excision Circle | 2026-10-24 12:54:27 | 1 | ||||||||
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CoMUT Resource Report Resource Website 1+ mentions |
CoMUT (RRID:SCR_027745) | software library, software resource, software toolkit, source code | Software Python library for creating comutation plots to visualize genomic and phenotypic information. Used for visualizing genomic and phenotypic information via comutation plots. | genomic DNA, phenotype, visualizing genomic and phenotypic information, comutation plots, | NCI R01 CA227388; NCI R37 CA222574; NCI U01 CA233100; NIGMS T32 GM008313; NSF |
PMID:32502231 | Free, Available for download, Freely available | SCR_027745 | SciCrunch Registry | 2026-10-24 12:54:27 | 4 | |||||||||
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Spectroscopic Imaging, VIsualization, and Computing (SIVIC) Resource Report Resource Website 1+ mentions |
Spectroscopic Imaging, VIsualization, and Computing (SIVIC) (RRID:SCR_027875) | SIVIC | software application, software resource | Software framework and application suite for processing and visualization of DICOM MR Spectroscopy data. Through the use of DICOM, SIVIC aims to facilitate the application of MRS in medical imaging studies. | DICOM MR Spectroscopy Workflows, data processing, data visualization, DICOM MR spectroscopy data, | NCI P01 CA11816; NCI RO1 CA127612; NIBIB P41EB013598 |
PMID:23970895 | Free, Available for download, Freely available | SCR_027875 | SciCrunch Registry | 2026-10-24 12:54:33 | 2 | ||||||||
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tximeta Resource Report Resource Website 1+ mentions |
tximeta (RRID:SCR_028005) | software resource, software toolkit | Software R package for reference sequence checksums for provenance identification in RNA-seq. Performs numerous annotation and metadata gathering tasks on behalf of users during the import of transcript counts and abundance from quantification tools such as salmon. Data are imported as SummarizedExperiment objects with associated GenomicRanges metadata. Correct metadata is added automatically via reference sequence digests, facilitating genomic analyses and assisting in computational reproducibility. | reference sequence checksums, provenance identification in RNA-seq, numerous annotation, metadata gathering, | NCI P01 CA142538; NHGRI R01 HG009937; NHGRI U41 HG004059; NIEHS P30 ES010126; NIMH R01 MH118349 |
PMID:32097405 | Free, Available for download, Freely available | SCR_028005 | SciCrunch Registry | Tximeta | 2026-10-24 12:54:34 | 1 | ||||||||
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HiTIMED Resource Report Resource Website |
HiTIMED (RRID:SCR_028180) | software application, software resource, source code | Software DNA methylation-based algorithm, to estimate cell proportions in tumor microenvironment. Profiles tumor, immune, and angiogenic components, allowing researchers to study tumor composition and its clinical implications using archival biospecimens. | estimate cell proportions, cell type resolution, tumor microenvironment, tumor-type-specific DNA methylation data, | NCI P30 CA168524; NCI P50 CA097257; NCI R01 CA207360; NCI R01CA216265; NIGMS P20 GM130423; NIGMS P20GM103428; NIGMS P20GM104416 |
PMID:36348337 | Free, Available for download, Freely available | SCR_028180 | SciCrunch Registry | Hierarchical Tumor Immune Microenvironment Epigenetic Deconvolution | 2026-10-24 12:54:37 | 0 | ||||||||
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somalier Resource Report Resource Website |
somalier (RRID:SCR_028167) | software application, software resource | Software application for rapid relatedness estimation for cancer and germline studies using efficient genome sketches extract informative sites, evaluate relatedness, and perform quality-control on BAM/CRAM/BCF/VCF/GVCF. Used for rapid relatedness estimation for cancer and germline studies using efficient genome sketches. | rapid relatedness estimation, cancer and germline studies, efficient genome sketches, quality control, | NCI P30CA04014; NCI R37CA246183; NCI U24CA209999; NHGRI R01HG009141; NHGRI R41HG010126 |
PMID:32664994 | Free, Available for download, Freely available | SCR_028167 | SciCrunch Registry | Somalier | 2026-10-24 12:54:38 | 0 | ||||||||
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OncoDB Resource Report Resource Website 50+ mentions |
OncoDB (RRID:SCR_028340) | data or information resource, database | Database offers integrated multi-omic data for patients across 33 cancer types. It encompasses gene expression, DNA methylation, somatic mutations, proteomic profiles, and chromatin accessibility, drawing from TCGA, GTEx, and CPTAC projects. Users can compare gene expression, DNA methylation, and protein levels between tumor and normal tissues, identifying differentially expressed genes and proteins, and examining gene-to-gene correlations. Provides oncogene mutation profiles and allows for survival analysis based on gene expression and methylation, linked to clinical parameters. Facilitates exploration of multi-omic correlations, such as gene expression with DNA methylation, and their variations with mutation status. Extends its analytical capabilities to include six major oncoviruses, offering insights into their impact on gene expression, methylation, and patient survival. | cancer patients data, gene expression, DNA methylation, somatic mutations, proteomic profiles, chromatin accessibility, | NCI R01CA287778; NIDCR R01DE026471; NIGMS R35GM141535 |
PMID:34718715 PMID:40995640 |
Free, Freely available, | SCR_028340 | SciCrunch Registry | OncoDB2.0 | 2026-10-24 12:54:43 | 84 | ||||||||
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BoneMarrowMap Resource Report Resource Website 1+ mentions |
BoneMarrowMap (RRID:SCR_028324) | software resource, software toolkit, source code | Software R package to enable rapid reference mapping and annotation of new scRNA-seq data across the spectrum of normal and malignant hematopoietic contexts. Single cell RNA-seq reference map of human hematopoietic development in the bone marrow, with balanced representation of hematopoietic stem and progenitor cells and differentiated populations. | bone marrow AML acute myeloid leukemia scRNA-seq, reference mapping and annotation, scRNA-seq data, hematopoietic context, reference map, human hematopoietic development, bone marrow, | NCI P30 CA021765; NCI R35 CA197695 |
PMID:40294241 | Free, Available for download, Freely available | SCR_028324 | SciCrunch Registry | 2026-10-24 12:54:43 | 5 | |||||||||
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MHCnuggets Resource Report Resource Website |
MHCnuggets (RRID:SCR_028674) | software application, software resource, source code | Software tool that predicts how protein pieces bind to Major Histocompatibility Complex (MHC) molecules. It uses deep learning to process peptide sequences, handle variable lengths, and evaluate both common and rare alleles. Used to predicts peptide-MHC binding. Can predict binding for common or rare alleles of MHC class I or II with a single neural network architecture. | MHC Class I and Class II neoantigen binding prediction, predict peptide-MHC binding, | Dutch Cancer Society International Translational Cancer Research ; NCI CA006973; NCI CA121113; NCI CA180950 |
PMID:31871119 | Free, Available for download, Freely available | SCR_028674 | SciCrunch Registry | 2026-10-24 12:54:48 | 0 | |||||||||
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chromap Resource Report Resource Website |
chromap (RRID:SCR_029148) | software application, software resource, source code | Software tool for alignment and preprocessing of high-throughput chromatin profiling sequencing data, including ATAC-seq, single-cell ATAC-seq, ChIP-seq, and Hi-C. Supports genomic read mapping, adapter trimming, duplicate removal, barcode correction, and quality control analysis, enabling efficient processing of bulk and single-cell sequencing datasets. Used for aligning and preprocessing high throughput chromatin profiles. | aligning and preprocessing high throughput chromatin profiles, chromatin profiling sequencing data, | NCI U01CA226196; NHGRI R01HG010040; NHGRI R01HG011139 |
PMID:34772935 | Free, Available for download, Freely available | SCR_029148 | SciCrunch Registry | 2026-10-24 12:54:59 | 0 | |||||||||
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SCSORS - Semi-Custom Synthesis On-line Request System Resource Report Resource Website 1+ mentions |
SCSORS - Semi-Custom Synthesis On-line Request System (RRID:SCR_005636) | SCSORS | material service resource, production service resource, reagent manufacture, service resource | ChemNavigator has extended its agreement with NCI to include the development of a new Semi-Custom Synthesis On-line Request System (SCSORS), funded mostly by NCI with additional financial support from the NIH Chemical Genomics Center (NCGC). The new SCSORS project will provide the NIH access to the world''s supply of synthetic chemistry available for drug discovery. Once fully formed, SCSORS will provide a strategy for all NIH scientists to circulate requests for specific chemical samples among thousands, if not tens of thousands, of synthetic chemists at suppliers registered in the system. Sample quantities will range from milligram up to kilogram scale requests. Suppliers will be provided tools that allow them to review these requests and make proposals to NIH scientists for the synthesis of substances. It is expected that using the SCSORS strategy will allow the NIH to acquire chemical samples at less than 10% of the internal cost of synthesis while offering access to world wide chemical expertise and diversity. Once fully implemented, SCSORS will become an archive of commercially accessible custom chemistry products for pharmaceutical research. It is expected that this database of commercially accessible substances will grow to over 250 million substances in the coming two years. | compound, pharmaceutical, chemistry, drug discovery, research | NCI | nlx_146249 | SCR_005636 | SciCrunch Registry | SCSORS Project, Semi-Custom Synthesis On-line Request System | 2026-10-24 12:45:30 | 1 | ||||||||
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CGAP GO Browser Resource Report Resource Website 1+ mentions |
CGAP GO Browser (RRID:SCR_005676) | CGAP GO Browser | data or information resource, data set, service resource | With the CGAP GO browser, you can browse through the GO vocabularies, and find human and mouse genes assigned to each term. GO data updated every few months. Platform: Online tool | gene, biological process, cellular component, molecular function, browser, ontology, ontology or annotation browser |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: Cancer Genome Anatomy Project |
NCI | Free for academic use | nlx_149116 | SCR_005676 | SciCrunch Registry | Cancer Genome Anatomy Project GO Browser | 2026-10-24 12:45:30 | 4 | ||||||
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WebArrayDB Resource Report Resource Website 1+ mentions |
WebArrayDB (RRID:SCR_005577) | WebArrayDB | analysis service resource, data analysis service, data or information resource, data repository, database, production service resource, service resource, software resource, storage service resource | An open source integrated microarray database and analysis suite that features convenient uploading of data for storage in a MIAME (Minimal Information about a Microarray Experiment) compliant fashion. It allows data to be mined with a large variety of R-based tools, including data analysis across multiple platforms. Different methods for probe alignment, normalization and statistical analysis are included to account for systematic bias. Student's t-test, moderated t-tests, non-parametric tests and analysis of variance or covariance (ANOVA/ANCOVA) are among the choices of algorithms for differential analysis of data. Users also have the flexibility to define new factors and create new analysis models to fit complex experimental designs. All data can be queried or browsed through a web browser. The computations can be performed in parallel on symmetric multiprocessing (SMP) systems or Linux clusters. | is listed by: OMICtools | Prostate Cancer Foundation ; Mary Kay Ash Foundation ; NIH ; NIAI R01AI034829; NIAI R01AI052237; NCI R01CA68822; NCI U01CA114810 |
PMID:19602526 | Open source, Account required, The software package is available for the use on a public web server or can be downloaded | OMICS_00782 | SCR_005577 | SciCrunch Registry | 2026-10-24 12:45:28 | 8 | |||||||
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PeptideMapper Resource Report Resource Website 1+ mentions |
PeptideMapper (RRID:SCR_005763) | PeptideMapper | data access protocol, software resource, web service | The PeptideMapper Web-Service provides alignments of peptide sequence alignments to proteins, mRNA, EST, and HTC sequences from Genbank, RefSeq, UniProt, IPI, VEGA, EMBL, and HInvDb. This mapping infrastructure is supported, in part, by the compressed peptide sequence database infrastructure (Edwards, 2007) which enables a fast, suffix-tree based mapping of peptide sequences to gene identifiers and a gene-focused detailed mapping of peptide sequences to source sequence evidence. The PeptideMapper Web-Service can be used interactively or as a web-service using either HTTP or SOAP requests. Results of HTTP requests can be returned in a variety of formats, including XML, JSON, CSV, TSV, or XLS, and in some cases, GFF or BED; results of SOAP requests are returned as SOAP responses. The PeptideMapper Web-Service maps at most 20 peptides with length between 5 and 30 amino-acids in each request. The number of alignments returned, per peptide, gene, and sequence type, is set to 10 by default. The default can be changed on the interactive alignments search form or by using the max web-service parameter. | peptide, sequence, protein, alignment, expressed sequence tag, mrna, est, htc, genbank, refseq, uniprot, ipi, vega, embl, hinvdb | has parent organization: Edwards Lab | NCI CA126189 | PMID:17437027 | nlx_149229 | SCR_005763 | SciCrunch Registry | PeptideMapper Web-Service, Peptide Mapper | 2026-10-24 12:45:32 | 4 | ||||||
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OligoGenome Resource Report Resource Website 1+ mentions |
OligoGenome (RRID:SCR_006025) | OligoGenome | data or information resource, database, resource | The Stanford Human OligoGenome Project hosts a database of capture oligonucleotides for conducting high-throughput targeted resequencing of the human genome. This set of capture oligonucleotides covers over 92% of the human genome for build 37 / hg19 and over 99% of the coding regions defined by the Consensus Coding Sequence (CCDS). The capture reaction uses a highly multiplexed approach for selectively circularizing and capturing multiple genomic regions using the in-solution method developed in Natsoulis et al, PLoS One 2011. Combined pools of capture oligonucleotides selectively circularize the genomic DNA target, followed by specific PCR amplification of regions of interest using a universal primer pair common to all of the capture oligonucleotides. Unlike multiplexed PCR methods, selective genomic circularization is capable of efficiently amplifying hundreds of genomic regions simultaneously in multiplex without requiring extensive PCR optimization or producing unwanted side reaction products. Benefits of the selective genomic circularization method are the relative robustness of the technique and low costs of synthesizing standard capture oligonucleotide for selecting genomic targets. | oligonucleotide, genome, probe, coding region, oligonucleotide sequence, chromosome | has parent organization: Stanford University; Stanford; California | NHGRI RC2 HG005570-01; NCI R21CA12848; NCI 5K08CA96879?6; NIDDK DK56339; NHGRI 2P01HG000205; NLM T15-LM007033; Doris Duke Clinical Foundation ; Reddere Foundation ; Liu Bie Ju Cha and Family Fellowship in Cancer ; Wang Family Foundation ; Howard Hughes Medical Foundation |
PMID:22102592 | nlx_151422 | SCR_006025 | SciCrunch Registry | Stanford Human Oligo Genome Project, Human OligoGenome Resource, Stanford Human Oligo Genome, Human Oligo Genome, Human OligoGenome | 2026-10-24 12:45:36 | 2 |
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