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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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L1000 Characteristic Direction Signature Search Engine Resource Report Resource Website 1+ mentions |
L1000 Characteristic Direction Signature Search Engine (RRID:SCR_016177) | L1000CDS2 | data access protocol, data or information resource, data set, database, service resource, software resource, web service | LINCS L1000 characteristic direction signatures search engine. Software tool to find consensus signatures that match user’s input gene lists or input signatures. Underlying dataset is LINCS L1000 small molecule expression profiles generated at Broad Institute by Connectivity Map team. Differentially expressed genes of these profiles were calculated using multivariate method called Characteristic Direction. | signature, gene, dataset, ligand, characteristic, expression, benchmark |
is related to: LINCS Joint Project - Breast Cancer Network Browser has parent organization: Icahn School of Medicine at Mount Sinai; New York; USA |
NCI U54 CA189201; NHLBI U54 HL127624 |
PMID:28413689 | Free, Freely available | SCR_016177 | 2026-09-03 04:53:49 | 8 | |||||||
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Harmonizome Resource Report Resource Website 100+ mentions |
Harmonizome (RRID:SCR_016176) | data or information resource, data processing software, data visualization software, database, software application, software resource, web application | Web application that allows for searching, visualization, and prediction about genes and proteins. It contains a collection of processed datasets gathered to serve and mine knowledge about genes and proteins from major online resources. | gene, protein, visualization, search, prediction, functional | BD2K-LINCS Data Coordination and Integration Center ; Illuminating the Druggable Genome ; Knowledge Management Center ; NCI U54 CA189201; NHLBI U54 HL127624; NIGMS R01 GM098316 |
PMID:27374120 | Freely available, Free, Available for download | SCR_016176 | 2026-09-03 04:53:37 | 142 | |||||||||
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ConsensusClusterPlus Resource Report Resource Website 100+ mentions |
ConsensusClusterPlus (RRID:SCR_016954) | data analysis software, data processing software, software application, software resource | Software written in R for determining cluster count and membership by stability evidence in unsupervised analysis. Provides quantitative and visual stability evidence for estimating the number of unsupervised classes in a dataset with item tracking, item consensus and cluster consensus plots. | cluster, count, stability, evidence, unsupervised, analysis, , bio.tools |
is listed by: Bioconductor is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
NCI F32CA142039; NCI U24 CA126554; Thomas G. Labrecque Foundation |
PMID:20427518 | Free, Available for download, Freely available | biotools:consensusclusterplus | https://bio.tools/consensusclusterplus | SCR_016954 | 2026-09-03 04:54:20 | 196 | ||||||
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dcmqi Resource Report Resource Website 1+ mentions |
dcmqi (RRID:SCR_016933) | dcmqi | data processing software, image processing software, software application, software library, software resource, software toolkit | Software library to help with the conversion between imaging research formats and the standard DICOM representation for image analysis results. Used to implement conversion of the data stored in commonly used research formats into the standard DICOM representation. Available as a precompiled binary package for every major operating system, as a Docker image, and as an extension to 3D Slicer. | DICOM, converter, medical, image, computing, quantitative, analysis, clinical, data, metadata, radiology, standard, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Harvard University; Cambridge; United States |
NCI U24 CA180918; NIBIB P41 EB01589; NIBIB P41 EB015902; NIBIB R01 EB014955 |
PMID:29092948 | Free, Available for download, Freely available, Tutorial available | biotools:dcmqi | https://github.com/QIICR/dcmqi, https://bio.tools/dcmqi | SCR_016933 | DICOM for Quantitative Imaging, The Digital imaging and Communications in Medicine for Quantitative Imaging, Digital imaging and Communications in Medicine for Quantitative Imaging, DCMQI | 2026-09-03 04:53:58 | 4 | ||||
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MARRVEL Resource Report Resource Website 10+ mentions |
MARRVEL (RRID:SCR_016871) | MARRVEL | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | Web tool to search multiple public variant databases simultaneously and provide a unified interface to facilitate the search process. Used for integration of human and model organism genetic resources to facilitate functional annotation of the human genome. Used for analysis of human genes and variants by cross-disciplinary integration of records available in public databases to facilitate clinical diagnosis and basic research. | integration, database, model, genetic, resource, functional, annotation, genome, data, analysis, dataset, rare, variant, exploration, bio.tools |
uses: OMIM uses: ClinVar uses: DECIPHER uses: Geno2MP uses: Database of Genomic Variants is used by: Hypothesis Center is listed by: bio.tools is listed by: Debian |
Baylor College of Medicine Medical Scientist Training Program ; Belfer Foundation ; CPRIT RP170387; Houston Endowment ; Huffington Foundation ; NCI P30 CA06516; NCRR R24 RR032668; NHGRI U01 HG007709; NIGMS R01 GM067761; NIGMS R01 GM067858; NIGMS R01 GM084947; NIGMS R01 GM120033; NIH Office of the Director R24 OD021997; NIH Office of the Director R24 OD022005; NINDS 1U54NS093793; NINDS U54 NS093793; NSF DMS 1263932; Simons Foundation ; T T Chao Family Foundation ; The Robert and Janice McNair Foundation |
PMID:28502612 | Free, Public, Freely available | biotools:marrvel | https://bio.tools/marrvel | SCR_016871 | Model organism Aggregated Resources for Rare Variant ExpLoration | 2026-09-03 04:54:15 | 25 | ||||
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Markov Affinity based Graph Imputation of Cells Resource Report Resource Website 50+ mentions |
Markov Affinity based Graph Imputation of Cells (RRID:SCR_022371) | MAGIC | data analysis software, data processing software, software application, software resource | Software tool for imputing missing values restoring structure of large biological datasets.Method that shares information across similar cells, via data diffusion, to denoise cell count matrix and fill in missing transcripts. | imputing missing values, restoring structure, shares information across similar cells, denoise cell count matrix, fill in missing transcripts | American Cancer Society ; NCI P30 CA008748; NCI R01 CA164729; NICHD DP1 HD084071; Simons SFARI grants |
PMID:29961576 | Free, Available for download, Freely available | SCR_022371 | 2026-09-03 04:58:27 | 86 | ||||||||
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miQC Resource Report Resource Website 1+ mentions |
miQC (RRID:SCR_022697) | data analysis software, data processing software, software application, software resource | Software tool as flexible, probablistic metrics for quality control of scRNA-seq data. Adaptive probabilistic framework for quality control of single-cell RNA-sequencing data. Data driven QC metric that jointly models proportion of reads mapping to mtDNA and number of detected genes with mixture models in probabilistic framework to predict which cells are low quality in given dataset. | scRNA-seq data quality control, QC metric, low quality data prediction, single cell RNA-sequencing data | Academy of Finland ; Cancer Foundation Finland ; European Union Horizon 2020 research and innovation program ; NCI CA237170; NHGRI HG009007 |
PMID:34428202 | Free, Available for download, Freely available | SCR_022697 | 2026-09-03 04:58:45 | 4 | |||||||||
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Minimum Information about Tissue Imaging Resource Report Resource Website |
Minimum Information about Tissue Imaging (RRID:SCR_022830) | MITI | consortium, data or information resource, narrative resource, organization portal, portal, standard specification | Consortium provides guidelines for highly multiplexed tissue images. Standard that applies best practices developed for genomics and other microscopy data to highly multiplexed tissue images and traditional histology. Data and metadata standards consistent with Findable, Accessible, Interoperable, and Reusable (FAIR) standards that guide data deposition, curation and release. | Data and metadata standards, FAIR, tissue imaging, minimum information standard, guidelines for highly multiplexed tissue images | NCI U2C CA233195; NCI U2C CA233238; NCI U2C CA233254; NCI U2C CA233262; NCI U2C CA233280; NCI U2C CA233284; NCI U2C CA233285; NCI U2C CA233291; NCI U2C CA233303; NCI U2C CA233311; NCI U54 CA225088 |
PMID:35277708 | Free, Freely available | https://github.com/miti-consortium/MITI | SCR_022830 | MITI Consortium | 2026-09-03 04:58:56 | 0 | ||||||
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caHUB Resource Report Resource Website |
caHUB (RRID:SCR_009657) | caHUB | data or information resource, narrative resource, standard specification | THIS RESOURCE IS NO LONGER IN SERVICE. Documented July 5, 2018. A national center for biospecimen science and standards to advance cancer research and treatment. It was created in response to the critical and growing need for high-quality, well-documented biospecimens for cancer research. The initiative builds on resources already developed by the NCI, including the Biospecimen Research Network and the NCI Best Practices for Biospecimen Resources, both of which were developed to address challenges around standardization of the collection and dissemination of quality biospecimens. caHUB will develop the infrastructure for collaborative biospecimen research and the production of evidence-based biospecimen standard operating procedures. | biospecimen, clinical, biomaterial supply resource, tissue |
is listed by: NIDDK Information Network (dkNET) is related to: Biorepositories and Biospecimens Research Branch has parent organization: National Cancer Institute |
Cancer | NCI ; ARRA |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_156094 | SCR_009657 | The Cancer Human Biobank, cancer Human Biobank | 2026-09-03 04:58:49 | 0 | |||||
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ChIP-X Enrichment Analysis 3 Resource Report Resource Website 100+ mentions |
ChIP-X Enrichment Analysis 3 (RRID:SCR_023159) | ChEA3 | software resource, web application | Web based transcription factor enrichment analysis. Web server ranks TFs associated with user-submitted gene sets. ChEA3 background database contains collection of gene set libraries generated from multiple sources including TF-gene co-expression from RNA-seq studies, TF-target associations from ChIP-seq experiments, and TF-gene co-occurrence computed from crowd-submitted gene lists. Enrichment results from these distinct sources are integrated to generate composite rank that improves prediction of correct upstream TF compared to ranks produced by individual libraries. | Transcription Factor, gene sets, transcription factor enrichment analysis, TF-gene co-expression from RNA-seq studies, TF-target associations from ChIP-seq experiments, TF-gene co-occurrence, prediction of correct upstream, | NCI U24CA224260; NHLBI U54HL127624; NIGMS T32GM062754; NIH Office of the Director OT3OD025467 |
PMID:31114921 | Free, Freely available | SCR_023159 | ChIP-X Enrichment Analysis Version 3 (ChEA3) | 2026-09-03 04:58:58 | 193 | |||||||
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SPRING Resource Report Resource Website 10+ mentions |
SPRING (RRID:SCR_023578) | data access protocol, software resource, web service | Interactive web tool to visualize single cell data using force directed graph layouts. Kinetic interface for visualizing high dimensional single cell expression data. Collection of pre-processing scripts and web browser based tool for visualizing and interacting with high dimensional data. | visualizing high dimensional single cell expression data, single cell expression data visualization, high dimensional data, | has parent organization: Harvard University; Cambridge; United States | Burroughs-Wellcome Career Award at the Scientific Interface ; Edward J Mallinckrodt Foundation Fellowship ; NCI 1R33CA212697; NIGMS 5T32GM080177 |
PMID:29228172 | Free, Available for download, Freely available | https://github.com/AllonKleinLab/SPRING/, https://github.com/AllonKleinLab/SPRING_dev | SCR_023578 | 2026-09-03 04:59:36 | 26 | |||||||
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HemOnc Knowledgebase Resource Report Resource Website 1+ mentions |
HemOnc Knowledgebase (RRID:SCR_023436) | data or information resource, disease-related portal, portal, topical portal | Medical wiki of interventions, regimens, and general information relevant to fields of hematology and oncology. Knowledge base for hematology and oncology providers, containing details about hematology/oncology drugs and treatment regimens. Any healthcare professional can sign up to contribute. Acuracy and completeness of content is overseen by Editorial Board. | Hematology and oncology knowledge base, hematology providers, oncology providers, hematology reference, oncology reference, hematology, oncology, drug interventions, treatment regimens, reference, healthcare professional, | cancer | NCI U24 CA265879 | Free, Freely available | https://hemonc.org/wiki/ | SCR_023436 | , HemOnc, Free Hematology/Oncology Reference, HemOnc.org | 2026-09-03 04:59:10 | 7 | |||||||
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DESeq2 Resource Report Resource Website 10000+ mentions |
DESeq2 (RRID:SCR_015687) | data analysis software, data processing software, software application, software resource, software tool | Software package for differential gene expression analysis based on the negative binomial distribution. Used for analyzing RNA-seq data for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates. | differential, gene, expression, analysis, binominal, distribution, RNA-seq data, Bioconductor, bio.tools |
is used by: Glimma is used by: TEtranscripts is listed by: Bioconductor is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: SARTools works with: tximport |
European Union’s 7th Framework Programme ; International Max Planck Research School for Computational Biology and Scientific Computing ; NCI T32 CA009337 |
Free, Available for download, Freely available | biotools:deseq2 | https://github.com/mikelove/DESeq2, https://bio.tools/deseq2 | SCR_015687 | 2026-09-03 04:58:06 | 50789 | |||||||
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Northwestern University Proteomics Core Facility Resource Report Resource Website |
Northwestern University Proteomics Core Facility (RRID:SCR_017880) | core facility, access service resource, service resource | Core offers multiple types of experiments from simple protein identification to protein quantitation (both relative and absolute), performs both traditional bottom-up proteomics, where proteins are digested with enzyme prior to analysis and intact, top-down proteomics analyses. Core proteomics specialists help guide your project to completion. | Protein, identification, quantitation, proteomics, enzyme, digestion, analysis, service, core | NCI P30 CA060553; NIH Office of the Director S10 OD025194; NIGMS P41 GM108569 |
Open | ABRF_738 | SCR_017880 | Northwestern Proteomics | 2026-09-03 04:58:28 | 0 | ||||||||
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StringTie Resource Report Resource Website 1000+ mentions |
StringTie (RRID:SCR_016323) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software application for assembling of RNA-Seq alignments into potential transcripts. It enables improved reconstruction of a transcriptome from RNA-seq reads. This transcript assembling and quantification program is implemented in C++ . | assembling, RNA, sequence, transcript, gene, alignment, reconstruction, read, analysis, process, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools |
NCI R01 CA120185; NCI R01 CA134292; NHGRI R01 HG006102; NHGRI R01 HG006677; NIGMS R01 GM105705; the Cancer Prevention and Research Institute of Texas |
PMID:25690850 DOI:10.1038/nbt.3122 |
Open source, Free, Freely available, Available for download | biotools:stringtie, OMICS_07226 | https://github.com/gpertea/stringtie, https://bio.tools/stringtie, https://sources.debian.org/src/stringtie/ | SCR_016323 | 2026-09-03 04:58:23 | 4976 | ||||||
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Differential Gene Correlation Analysis Resource Report Resource Website 1+ mentions |
Differential Gene Correlation Analysis (RRID:SCR_020964) | DGCA | data analysis software, data processing software, software application, software resource | Software R package to perform differential gene correlation analysis. Performs differential correlation analysis on input matrices, with multiple conditions specified by design matrix. | Differential gene, gene, gene correlation, correlation analysis, input matrices, differential correlations, identifier pairs, gene expression data, calculate differential correlations | is listed by: CRAN | NCI R01 CA163772; NIAID U01 AI111598; NIA F30 AG052261; NIA R01 AG046170 |
PMID:27846853 | Free, Available for download, Freely available | https://github.com/andymckenzie/DGCA | SCR_020964 | 2026-09-03 04:58:32 | 1 | ||||||
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Skyline Resource Report Resource Website 1000+ mentions |
Skyline (RRID:SCR_014080) | data analysis software, data processing software, software application, software resource | Software tool as Windows client application for targeted proteomics method creation and quantitative data analysis. Open source document editor for creating and analyzing targeted proteomics experiments. Used for large scale quantitative mass spectrometry studies in life sciences. | Proteomics, SRM, MRM, DDA, DIA, shotgun, mass, spectrometry, data, analysis, quantitative |
uses: MSstats is related to: ProteoWizard has parent organization: University of Washington; Seattle; USA works with: PanoramaWeb |
NCI U24 CA126479; NCRR P41 RR011823; NHLBI R01 HL082747; NIA P30 AG013280; NIDDK R01 DK069386 |
PMID:20147306 | Free, Available for download, Freely available | SCR_014080 | 2026-09-03 04:52:33 | 3040 | ||||||||
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Tscratch Resource Report Resource Website 10+ mentions |
Tscratch (RRID:SCR_014282) | data analysis software, data processing software, image analysis software, software application, software resource, standalone software | Software tool for automated analysis of monolayer wound healing assays. Available as a stand alone application for Macintosh and Windows and as a source code. Offers a graphical user interface for inspection of analysis results and manual modification of analysis parameters., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | analyze, wound, scratch, healing, assay, cell, migration, monolayer |
uses: MATLAB has parent organization: ETH Zurich; Zurich; Switzerland |
Austrian Science Foundation ; Cancer League Zurich ; Commission of the European Communities ; NCCR CO-ME ; NCI CA69184; Swiss National Fund |
PMID:19450233 | THIS RESOURCE IS NO LONGER IN SERVICE | https://github.com/cselab/TScratch | SCR_014282 | 2026-09-03 04:52:29 | 48 | |||||||
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National Longitudinal Mortality Study Resource Report Resource Website 10+ mentions |
National Longitudinal Mortality Study (RRID:SCR_008946) | NLMS | data or information resource, data set | A database based on a random sample of the noninstitutionalized population of the United States, developed for the purpose of studying the effects of demographic and socio-economic characteristics on differentials in mortality rates. It consists of data from 26 U.S. Current Population Surveys (CPS) cohorts, annual Social and Economic Supplements, and the 1980 Census cohort, combined with death certificate information to identify mortality status and cause of death covering the time interval, 1979 to 1998. The Current Population Surveys are March Supplements selected from the time period from March 1973 to March 1998. The NLMS routinely links geographical and demographic information from Census Bureau surveys and censuses to the NLMS database, and other available sources upon request. The Census Bureau and CMS have approved the linkage protocol and data acquisition is currently underway. The plan for the NLMS is to link information on mortality to the NLMS every two years from 1998 through 2006 with research on the resulting database to continue, at least, through 2009. The NLMS will continue to incorporate data from the yearly Annual Social and Economic Supplement into the study as the data become available. Based on the expected size of the Annual Social and Economic Supplements to be conducted, the expected number of deaths to be added to the NLMS through the updating process will increase the mortality content of the study to nearly 500,000 cases out of a total number of approximately 3.3 million records. This effort would also include expanding the NLMS population base by incorporating new March Supplement Current Population Survey data into the study as they become available. Linkages to the SEER and CMS datasets are also available. Data Availability: Due to the confidential nature of the data used in the NLMS, the public use dataset consists of a reduced number of CPS cohorts with a fixed follow-up period of five years. NIA does not make the data available directly. Research access to the entire NLMS database can be obtained through the NIA program contact listed. Interested investigators should email the NIA contact and send in a one page prospectus of the proposed project. NIA will approve projects based on their relevance to NIA/BSR''s areas of emphasis. Approved projects are then assigned to NLMS statisticians at the Census Bureau who work directly with the researcher to interface with the database. A modified version of the public use data files is available also through the Census restricted Data Centers. However, since the database is quite complex, many investigators have found that the most efficient way to access it is through the Census programmers. * Dates of Study: 1973-2009 * Study Features: Longitudinal * Sample Size: ~3.3 Million Link: *ICPSR: http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/00134 | national, longitudinal, mortality, demographic, socio-economic, age, cause of death, death, death record, ethnicity, mortality rate, gender, marital status, race, late adult human, FASEB list |
is listed by: Inter-university Consortium for Political and Social Research (ICPSR) has parent organization: U.S. Census Bureau |
Aging | NCI ; NHLBI ; NIA ; National Center for Health Statistics ; U.S. Census Bureau |
Public | nlx_151861 | SCR_008946 | National Longitudinal Mortality Study (NLMS) | 2026-09-03 05:06:33 | 32 | |||||
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Chernobyl Tissue Bank Resource Report Resource Website 1+ mentions |
Chernobyl Tissue Bank (RRID:SCR_010662) | CTB | biomaterial supply resource, material resource | The CTB (Chernobyl Tissue Bank) is an international cooperation that collects, stores and disseminates biological samples from tumors and normal tissues from patients for whom the aetiology of their disease is known - exposure to radioiodine in childhood following the accident at the Chernobyl power plant. The main objective of this project is to provide a research resource for both ongoing and future studies of the health consequences of the Chernobyl accident. It seeks to maximize the amount of information obtained from small pieces of tumor by providing multiple aliquots of RNA and DNA extracted from well documented pathological specimens to a number of researchers world-wide and to conserve this valuable material for future generations of scientists. It exists to promote collaborative, rather than competitive, research on a limited biological resource. Tissue is collected to an approved standard operating procedure (SOP) and is snap frozen; the presence or absence of tumor is verified by frozen section. A representative paraffin block is also obtained for each case. Where appropriate, we also collect fresh and paraffin-embedded tissue from loco-regional metastases. Currently we do not issue tissue but provide extracted nucleic acid, paraffin sections and sections from tissue microarrays from this material. The project is coordinated from Imperial College, London and works with Institutes in the Russian Federation (the Medical Radiological Research Centre in Obninsk) and Ukraine (the Institute of Endocrinology and Metabolism in Kiev) to support local scientists and clinicians to manage and run a tissue bank for those patients who have developed thyroid tumors following exposure to radiation from the Chernobyl accident. Belarus was also initially included in the project, but is currently suspended for political reasons. |
is listed by: One Mind Biospecimen Bank Listing has parent organization: Imperial College London; London; United Kingdom |
Tumor, Normal, Exposure to radioiodine in childhood following the accident at the Chernobyl power plant | European Union ; Sasakawa Memorial Health Foundation ; NCI |
nlx_70828 | SCR_010662 | 2026-09-03 05:04:20 | 9 |
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