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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Physician Data Query Resource Report Resource Website 1+ mentions |
Physician Data Query (RRID:SCR_006833) | PDQ | clinical trial, database, ontology, people resource, registry, data or information resource, controlled vocabulary | NCI''s comprehensive cancer database that contains summaries on a wide range of cancer topics; a registry of 8,000+ open and 19,000+ closed cancer clinical trials from around the world; a directory of professionals who provide genetics services; the NCI Dictionary of Cancer Terms, with definitions for 6,800+ cancer and medical terms; and the NCI Drug Dictionary, which has information on 2,300+ agents used in the treatment of cancer or cancer-related conditions. The PDQ cancer information summaries are peer reviewed and updated monthly by six editorial boards comprised of specialists in adult treatment, pediatric treatment, supportive care, screening and prevention, genetics, and complementary and alternative medicine. The Boards review current literature from more than 70 biomedical journals, evaluate its relevance, and synthesize it into clear summaries. Many of the summaries are also available in Spanish. | adult, pediatric, child, alternative, breast, clinical trial, colorectal, hypercalcemia, legal, lung, medicine, medullary, nausea, ovarian, pain, pathophysiology, pediatric, pharmaceutical, physician, prevention, prognosis, prostate, psychosocial, query, risk factor, screening, social, syndrome, thyroid, treatment, umls, genetics, medical, drug, peer review |
is listed by: BioPortal has parent organization: National Cancer Institute |
Cancer, Cancer-related condition | NCI | nif-0000-21318 | SCR_006833 | PDQ - NCI''s Comprehensive Cancer Database | 2026-02-15 09:19:20 | 2 | ||||||
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Synapse Resource Report Resource Website 1000+ mentions |
Synapse (RRID:SCR_006307) | Synapse | database, service resource, storage service resource, data repository, data or information resource | A cloud-based collaborative platform which co-locates data, code, and computing resources for analyzing genome-scale data and seamlessly integrates these services allowing scientists to share and analyze data together. Synapse consists of a web portal integrated with the R/Bioconductor statistical package and will be integrated with additional tools. The web portal is organized around the concept of a Project which is an environment where you can interact, share data, and analysis methods with a specific group of users or broadly across open collaborations. Projects provide an organizational structure to interact with data, code and analyses, and to track data provenance. A project can be created by anyone with a Synapse account and can be shared among all Synapse users or restricted to a specific team. Public data projects include the Synapse Commons Repository (SCR) (syn150935) and the metaGenomics project (syn275039). The SCR provides access to raw data and phenotypic information for publicly available genomic data sets, such as GEO and TCGA. The metaGenomics project provides standardized preprocessed data and precomputed analysis of the public SCR data. | data sharing, collaboration, data management, analysis, genome, phenotype, crowd sourcing, open data, provenance, resource management, annotation, authoring, markup, r, python, java, command-line, cloud, FASEB list |
is used by: NF Data Portal is listed by: FORCE11 is listed by: DataCite is listed by: re3data.org is related to: clearScience is related to: Exemplar Microscopy Images of Tissues has parent organization: Sage Bionetworks |
Cancer, Normal, Cardiovascular disease, Floppy hat syndrome | Life Sciences Discovery Fund ; NCI ; NHLBI ; Alfred P. Sloan Foundation |
The community can contribute to this resource | nlx_151983, DOI:10.17616/R3B934, r3d100011894, DOI:10.7303 | https://doi.org/10.17616/R3B934 https://doi.org/10.48550/arxiv.1506.00272 https://doi.org/10.7303/ https://dx.doi.org/10.7303 https://doi.org/10.17616/R3B934 |
SCR_006307 | 2026-02-15 09:19:12 | 1002 | |||||
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StringTie Resource Report Resource Website 1000+ mentions |
StringTie (RRID:SCR_016323) | software application, sequence analysis software, data processing software, software resource, data analysis software | 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 |
the Cancer Prevention and Research Institute of Texas ; NHGRI R01 HG006677; NIGMS R01 GM105705; NHGRI R01 HG006102; NCI R01 CA120185; NCI R01 CA134292 |
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 | 2026-02-15 09:21:38 | 4072 | ||||||
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DESeq2 Resource Report Resource Website 10000+ mentions |
DESeq2 (RRID:SCR_015687) | software tool, software application, data processing software, software resource, data analysis software | 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 |
International Max Planck Research School for Computational Biology and Scientific Computing ; NCI T32 CA009337; European Union’s 7th Framework Programme |
Free, Available for download, Freely available | biotools:deseq2 | https://github.com/mikelove/DESeq2 https://bio.tools/deseq2 |
SCR_015687 | 2026-02-15 09:21:36 | 43994 | |||||||
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Cooperative Human Tissue Network Resource Report Resource Website 10+ mentions |
Cooperative Human Tissue Network (RRID:SCR_004446) | CHTN | material resource, tissue bank, biomaterial supply resource | The Cancer Diagnosis Program of the National Cancer Institute (NCI) initiated the Cooperative Human Tissue Network (CHTN) in 1987 to provide increased access to human tissue for basic and applied scientists from academia and industry to accelerate the advancement of discoveries in cancer diagnosis and treatment. This unique resource provides remnant human tissues and fluids from routine procedures to investigators who utilize human biospecimens in their research. Unlike tissue banks, the CHTN works prospectively with each investigator to tailor specimen acquisition and processing to meet their specific project requirements. Because the CHTN is funded by the NCI, the CHTN is able to maintain nominal processing fees for its services. The CHTN is comprised of five adult divisions and one pediatric division. Each of the adult divisions coordinates investigator applications/requests based upon the investigator's geographic location within North America. The Pediatric Division manages all investigators who request pediatric specimens only. The CHTN divisions share coordination for requests from outside North America. The CHTN divisions work both independently with individual investigators and together as a seamless unit to fulfill requests that are difficult to serve by any single division. The CHTN's unique informatics system allows each division to effectively communicate and network the needs of its investigators to all CHTN divisions. The Network as a whole can then help fulfill an investigator's request. Biospecimens from surgeries, autopsies and other routine procedures: Malignant, Benign, Diseased, Normal, Biofluids (urine, serum, plasma, buffy coat) High quality specimens at LOW processing fees: Fresh, Frozen, Floating in fixative, RNAlater, Paraffin embedded or and/or unstained slides, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | biomaterial supply resource, human tissue, network, cancer, NCI |
is listed by: One Mind Biospecimen Bank Listing is related to: UAB SPORE Biorepository Banks is related to: University of Alabama; Alabama; USA is related to: University of Pennsylvania; Philadelphia; USA is related to: University of Virginia; Virginia; USA is related to: Ohio State University College of Medicine; Ohio; USA is related to: Vanderbilt University; Tennessee; USA |
NCI | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_44126 | http://www.chtn.nci.nih.gov/ | SCR_004446 | Cooperative Human Tissue Network | 2026-02-15 09:18:43 | 25 | |||||
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Ohio State Biorepository Resource Report Resource Website |
Ohio State Biorepository (RRID:SCR_004714) | HTRN Biospecimen Bank | material resource, tissue bank, biomaterial supply resource | The HTRN biospecimen bank is comprised of samples for the Ohio State University Cancer and Leukemia Group B Pathology Coordinating Office (CALGB-PCO) and the Ohio State University Midwestern Division of the Cooperative Human Tissue Network (CHTN). The CALGB-PCO banks biospecimens donated by patients enrolled in clinical trials. Samples can include tumor and normal tissue, plasma, serum, whole blood and white blood cells and urine. All of these samples are used later in correlative studies. The Midwestern Division of the CHTN stores a temporary biospecimen bank of tumor and normal tissue, tissue slides and paraffin embedded tissue blocks for research investigators throughout the country and Canada who are trying to find a cure for cancer. As part of the HTRN biospecimen bank, a Rees Scientific equipment monitoring system helps to secure the integrity and quality of samples stored in the biorepository. Scientific research within the HTRN is currently underway to determine the best methods in tissue storage for long term use. The NCI First-Generation Guidelines for NCI-Supported Biorepositories and the NCI Best Practices for Biospecimen Resources are continuously reviewed and adapted by the HTRN. | tumor tissue, normal tissue, plasma, serum, whole blood, white blood cell, urine, blood, tissue, tissue slide, paraffin embedded tissue block, slide, paraffin, cancer, leukemia, research |
is listed by: One Mind Biospecimen Bank Listing has parent organization: Ohio State University College of Medicine; Ohio; USA has parent organization: Human Tissue Resource Network |
Cancer, Leukemia, Tumor | NCI | Private and Public (USA and Canada): Serves the Ohio State University Cancer and Leukemia Group B Pathology Coordinating Office (CALGB-PCO) and the Ohio State University Midwestern Division of the Cooperative Human Tissue Network (CHTN). The Midwestern Division of the CHTN stores a temporary biospecimen bank of tumor and normal tissue, Tissue slides and paraffin embedded tissue blocks for research investigators throughout the country and Canada who are trying to find a cure for cancer. | nlx_71208 | http://www.pathology.med.ohio-state.edu/htrn/Biorepository/default.asp | SCR_004714 | Human Tissue Resource Network Biospecimen Bank, HTRN Biorepository Biospecimen Resource, HTRN Biorepository & Biospecimen Resource, HTRN Biorepository and Biospecimen Resource, HTRN Biorepository | 2026-02-15 09:18:48 | 0 | ||||
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PILGRM Resource Report Resource Website 1+ mentions |
PILGRM (RRID:SCR_004749) | PILGRIM | service resource, analysis service resource, data analysis service, production service resource | PILGRM (the platform for interactive learning by genomics results mining) puts advanced supervised analysis techniques applied to enormous gene expression compendia into the hands of bench biologists. This flexible system empowers its users to answer diverse biological questions that are often outside of the scope of common databases in a data-driven manner. This capability allows domain experts to quickly and easily generate hypotheses about biological processes, tissues or diseases of interest. Specifically PILGRM helps biologists generate these hypotheses by analyzing the expression levels of known relevant genes in large compendia of microarray data. PILGRM is for the biologist with a set of proteins relevant to a disease, biological function or tissue of interest who wants to find additional players in that process. It uses a data driven method that provides added value for literature search results by mining compendia of publicly available gene expression datasets using lists of relevant and irrelevant genes (standards). PILGRM produces publication quality PDFs usable as supplementary material to describe the computational approach, standards and datasets. Each PILGRM analysis starts with an important biological question (e.g. What genes are relevant for breast cancer but not mammary tissue in general?). For PILGRM to discover relevant genes, it needs examples of both genes that you would (positive) and would not (negative) find interesting. Lists of these genes are what we call standards and in PILGRM you can build your own standards or you can use standards from common sources that we pre-load for your convenience. PILGRM lets you build your own literature-documented standards so that processes, disease, and tissues that are not well covered in databases of tissue expression, disease, or function can still be used for an analysis. | data mining, gene expression, user directed data mining, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Princeton University; New Jersey; USA |
NSF DBI-0546275; NIGMS R01 GM071966; NIGMS P50 GM071508; NCI T32 CA005928 |
PMID:21653547 | nlx_75372, biotools:pilgrm | https://bio.tools/pilgrm | SCR_004749 | Platform for Interactive Learning by Genomics Results Mining | 2026-02-15 09:18:54 | 1 | |||||
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Case Comprehensive Cancer Center Biorepository and Tissue Processing Core Facility Resource Report Resource Website |
Case Comprehensive Cancer Center Biorepository and Tissue Processing Core Facility (RRID:SCR_004382) | BTPC | material resource, tissue bank, biomaterial supply resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 11, 2023. The Case Comprehensive Cancer Center''s Biorepository and Tissue Processing Core Facility (BTPC) serves two primary functions: 1. To build an inventory of remnant human tissues, blood and other body fluids (collectively termed biospecimens) targeted towards cancer and other medical research, for later assignment to investigators; and 2. To provide long term, controlled storage of biospecimens for specific researchers. These samples are for research purposes only and may not be used for clinical diagnosis or implantation into humans. Clinical information relating to the samples and donors are collected and maintained in a secure database. Samples and data are de-identified or de-linked before release to the researcher unless he/she has specific IRB approval to gain access to this information. Remnant biospecimens are prospectively collected from surgical procedures, autopsies and clinical laboratories for the BTPC by the Human Tissue Procurement Facility (HTPF), which operates under UH-IRB Protocol 01-02-45. Blood and bone marrow specimens are collected for the BTPC by the Hematopoietic Stem Cell Core Facility (HSCC), which operates under UH-IRB Protocol 09-90-195. The Division of Surgical Pathology at University Hospitals Case Medical Center (UHCMC) has clinical archives of paraffin blocks that can be made available through the BTPC for retrospective research studies under the approval of the Vice Chair for Clinical Affairs at UHCMC. Surgical Pathologists associated with the BTPC are responsible for determining which blocks can be made available and how much material can be removed from the blocks. Types of Tissue Available * Malignant, benign, diseased, normal and normal human tissues * Normal adjacent tissues available paired with tumor specimens in many cases * Tissues are collected from over 50 anatomic sites * Frozen specimens, OCT-embedded and paraffin-embedded tissues * Large array of paraffin-embedded specimens from clinical archives of paraffin blocks and QC research blocks maintained by the HTPF * Peripheral blood and bone marrow samples from initial visits and follow-up procedures are processed to obtain serum and cell fractions for storage * No samples are collected from individuals with known infectious illnesses * Fetal biospecimens are not collected due to state and local statutes | tissue, blood, body fluid, bone marrow, stem cell, serum, cell fraction, paraffin block, clinical data, malignant tissue, benign tissue, diseased tissue, normal tissue, cancer, control, research, frozen, oct-embedded, paraffin-embedded, tumor, paraffin, oct |
is listed by: One Mind Biospecimen Bank Listing has parent organization: Case Western Reserve University Case Comprehensive Cancer Center |
Cancer, Control, Tumor | NCI P30 CA43703 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_39515 | http://cancer.case.edu/sharedresources/biorepository/ | SCR_004382 | Case Western Biorepository, Case Western Reserve University: Biorepository and Tissue Processing Core Facility, CWRU BTPC, Biorepository and Tissue Processing Core Facility of the Case Comprehensive Cancer Center, Case BTPC, Case Comprehensive Cancer Center Biorepository Tissue Processing Core Facility, Case CCC BTPC, Case Comprehensive Cancer Center Biorepository and Tissue Processing Core Facility, Biorepository Tissue Processing Core Facility, Case Western Biorepository and Tissue Processing Core Facility, CWRU CCC Biorepository Tissue Processing Core Facility, Case CCC Biorepository Tissue Processing Core Facility | 2026-02-15 09:18:42 | 0 | ||||
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AIDS Malignancy Bank Resource Report Resource Website |
AIDS Malignancy Bank (RRID:SCR_004417) | AMB | material resource, tissue bank, biomaterial supply resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on February 27, 2012. The National Cancer Institute established centers in the United States and its territories for the collection and distribution of tissues, blood and secretions from patients with clinically-characterized AIDS related malignancies in 1994. The AIDS Malignancy Bank makes these tissues available to qualified investigators in the United States for research on AIDS malignancies. It is hoped that by providing access to these high-quality specimens, research in AIDS-related malignancies will be encouraged and expanded. The AMB contains formalin-fixed paraffin-embedded tissues, fresh-frozen tissues, malignant-cell suspensions, fine-needle aspirates, and cell lines from AIDS-related malignancies. The bank also contains serum, plasma, urine, bone marrow, cervical secretions, anal swabs, saliva semen and multi-site autopsy tissues from patients with AIDS-related malignancies who have participated in clinical trials. The bank has an associated database that contains prognostic, staging, outcome and treatment data on patients from whom tissues were obtained. Researchers pay for preparation and shipping of specimens. | tissue, blood, bodily fluid, malignant-cell, fine-needle aspirate, cell line, serum, plasma, urine, bone marrow, cervical secretion, anal swab, saliva, semen, autopsy, clinical data, formalin-fixed paraffin-embedded, fresh-frozen, frozen, suspension, aids, aids related malignancy |
is listed by: One Mind Biospecimen Bank Listing has parent organization: David Geffen School of Medicine at UCLA; California; USA |
AIDS, AIDS related malignancy | NCI | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_143727 | SCR_004417 | 2026-02-15 09:18:47 | 0 | ||||||
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NCI Breast and Colon Cancer Family Registries Resource Report Resource Website 1+ mentions |
NCI Breast and Colon Cancer Family Registries (RRID:SCR_006664) | Breast and Colon CFR | material resource, tissue bank, biomaterial supply resource | The Breast Cancer Family Registry (Breast CFR) and the Colon Cancer Family Registry (Colon CFR) were established by the National Cancer Institute (NCI) as a unique resource for investigators to use in conducting studies on the genetics and molecular epidemiology of breast and colon cancer. Known collectively as the CFRs, they share a central goal: the translation of research to the clinical and prevention settings for the benefit of Registry participants and the general public. The CFRs are particularly interested in: * Identifying and characterizing cancer susceptibility genes; * Defining gene-gene and gene-environment interactions in cancer etiology; and * Exploring the translational, preventive, and behavioral implications of research findings. The CFRs do not provide funding for studies; however, researchers can apply to access CFR data and biospecimens contributed by thousands of families from across the spectrum of risk for these cancers and from population-based or relative controls. Special features of the CFRs include: * Population-based and clinic-based ascertainment; * Systematic collection of validated family history; * Epidemiologic risk factor , clinical, and followup data; * Biospecimens (including tumor blocks and Epstein-Barr virus (EBV)-transformed cell lines); * Ongoing molecular characterization of the participating families; and * A combined informatics center. | breast, colon, breast cancer, colon cancer, biospecimen, tumor block, epstein-barr virus-transformed cell line, cell line, cancer, tumor |
is listed by: One Mind Biospecimen Bank Listing has parent organization: National Cancer Institute |
Breast cancer, Colon cancer, Cancer, Tumor | NCI | Public: Researchers can apply to access CFR data and biospecimens contributed by thousands of families from across the spectrum of risk for these cancers and from population-based or relative controls. | nlx_143711 | SCR_006664 | 2026-02-15 09:19:19 | 3 | ||||||
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ESEfinder 3.0 Resource Report Resource Website 100+ mentions |
ESEfinder 3.0 (RRID:SCR_007088) | ESEfinder | service resource, analysis service resource, data analysis service, production service resource | A web-based resource that facilitates rapid analysis of exon sequences to identify putative exonic splicing enhancers (ESEs) responsive to the human SR proteins SF2/ASF, SC35, SRp40 and SRp55, and to predict whether exonic mutations disrupt such elements. | exonic splicing enhancer, sr protein, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Cold Spring Harbor Laboratory |
NIGMS GM42699; NCI CA88351; NHGRI HG01696 |
PMID:12824367 | Free for non-profit use, Non-commercial, Acknowledgement requested, Commercial use with license | biotools:esefinder, nif-0000-30496 | http://rulai.cshl.edu/tools/ESE2/ https://bio.tools/esefinder |
http://exon.cshl.edu/ESE/ | SCR_007088 | 2026-02-15 09:19:27 | 211 | ||||
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cBioPortal Resource Report Resource Website 5000+ mentions |
cBioPortal (RRID:SCR_014555) | data or information resource, database, portal | A portal that provides visualization, analysis and download of large-scale cancer genomics data sets. | cancer, genomics, database, portal, data sets, FASEB list | is used by: NaviCom | NCI U24CA143840; NCRR RR031228-02 |
PMID:23550210 PMID:22588877 |
Please cite, Software is available via GitHub, Open source | https://github.com/cBioPortal/cbioportal/ https://github.com/cBioPortal/cbioportal/blob/master/docs/README.md | SCR_014555 | cBioPortal for Cancer Genomics | 2026-02-15 09:21:04 | 8539 | ||||||
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liftOver Resource Report Resource Website 500+ mentions |
liftOver (RRID:SCR_018160) | software application, service resource, data processing software, software resource | Web tool to convert genome coordinates and genome annotation files between assemblies. Used to translate genomic coordinates from one assembly version into another and retrieves putative orthologous regions in other species using UCSC chained and netted alignments. | Convert genome coordinate, genome annotation file, translate genomic coordinate, assembly version, retrieve orthologous region |
is related to: UCSC Genome Browser has parent organization: University of California at Santa Cruz; California; USA |
NHGRI ; Howard Hughes Medical Institute ; NCI |
DOI:10.1093/nar/gkj144 | Free, Available for download, Freely available | SCR_018160 | 2026-02-15 09:22:11 | 762 | ||||||||
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mosdepth Resource Report Resource Website 10+ mentions |
mosdepth (RRID:SCR_018929) | software application, data processing software, software resource | Software command line tool for rapidly calculating genome wide sequencing coverage. Measures depth from BAM or CRAM files at either each nucleotide position in genome or for sets of genomic regions. Used for fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing quick coverage calculation for genomes and exomes. | Calculating genome, wide sequencing coverage, depth measurement, BAM file, CRAM file, nucleotide position, genome, genomic region set, WGS exom, targeted sequencing, coverage calculation, exom, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
NHGRI R01 HG006693; NHGRI R01 HG009141; NIGMS R01 GM124355; NCI U24 CA209999 |
PMID:29096012 | Free, Available for download, Freely available | OMICS_20873, biotools:mosdepth | https://bio.tools/mosdepth https://sources.debian.org/src/mosdepth/ |
SCR_018929 | 2026-02-15 09:22:17 | 38 | ||||||
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Differential Gene Correlation Analysis Resource Report Resource Website 1+ mentions |
Differential Gene Correlation Analysis (RRID:SCR_020964) | DGCA | software application, data processing software, data analysis software, 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 | NIA F30 AG052261; NIA R01 AG046170; NCI R01 CA163772; NIAID U01 AI111598 |
PMID:27846853 | Free, Available for download, Freely available | https://github.com/andymckenzie/DGCA | SCR_020964 | 2026-02-15 09:22:30 | 1 | ||||||
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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 | software application, data processing software, data analysis software, 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 | NICHD DP1 HD084071; NCI R01 CA164729; NCI P30 CA008748; American Cancer Society ; Simons SFARI grants |
PMID:29961576 | Free, Available for download, Freely available | SCR_022371 | 2026-02-15 09:22:52 | 83 | ||||||||
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Minimum Information about Tissue Imaging Resource Report Resource Website |
Minimum Information about Tissue Imaging (RRID:SCR_022830) | MITI | organization portal, portal, consortium, data or information resource, narrative resource, 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 CA233262; NCI U54 CA225088; NCI U2C CA233280; NCI U2C CA233195; NCI U2C CA233291; NCI U2C CA233311; NCI U2C CA233238; NCI U2C CA233285; NCI U2C CA233303; NCI U2C CA233284; NCI U2C CA233254 |
PMID:35277708 | Free, Freely available | https://github.com/miti-consortium/MITI | SCR_022830 | MITI Consortium | 2026-02-15 09:22:20 | 0 | ||||||
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miQC Resource Report Resource Website 1+ mentions |
miQC (RRID:SCR_022697) | software application, data processing software, data analysis software, 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 | NCI CA237170; NHGRI HG009007; European Union Horizon 2020 research and innovation program ; Academy of Finland ; Cancer Foundation Finland |
PMID:34428202 | Free, Available for download, Freely available | SCR_022697 | 2026-02-15 09:22:56 | 2 | |||||||||
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HemOnc Knowledgebase Resource Report Resource Website 1+ mentions |
HemOnc Knowledgebase (RRID:SCR_023436) | disease-related portal, topical portal, data or information resource, 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 | 2026-02-15 09:23:06 | 4 | |||||||
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ChIP-X Enrichment Analysis 3 Resource Report Resource Website 100+ mentions |
ChIP-X Enrichment Analysis 3 (RRID:SCR_023159) | ChEA3 | web application, software resource | 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, | NHLBI U54HL127624; NCI U24CA224260; NIGMS T32GM062754; NIH Office of the Director OT3OD025467 |
PMID:31114921 | Free, Freely available | SCR_023159 | ChIP-X Enrichment Analysis Version 3 (ChEA3) | 2026-02-15 09:23:11 | 108 |
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