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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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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 | 2026-09-12 01:00:17 | 50789 | |||||||
|
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 | 2026-09-12 01:00:18 | 4976 | ||||||
|
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 | 2026-09-12 01:00:22 | 1 | ||||||
|
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 | 2026-09-12 01:00:26 | 86 | ||||||||
|
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 | 2026-09-12 01:00:28 | 4 | |||||||||
|
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 | 2026-09-12 01:00:30 | 0 | ||||||
|
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 | 2026-09-12 01:00:32 | 0 | |||||
|
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) | 2026-09-12 01:00:36 | 193 | |||||||
|
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 | 2026-09-12 01:00:40 | 26 | |||||||
|
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 | 2026-09-12 01:00:39 | 7 | |||||||
|
Hetnet Connectivity Search Resource Report Resource Website 1+ mentions |
Hetnet Connectivity Search (RRID:SCR_023630) | Hetnet | data access protocol, software resource, web service | Web app that allows users to search for the most important paths connecting any two nodes in Hetionet. | Hetionet, paths connection, paths search, paths connecting any two nodes in Hetionet, | Gordon and Betty Moore Foundation ; NCI R01 CA237170; NHGRI R01 HG010067; NHGRI T32 HG000046; Pfizer Inc |
PMID:36711546 | Free, Freely available | SCR_023630 | , Heterogeneous network Connectivity Search, heterogeneous network | 2026-09-12 01:00:41 | 2 | |||||||
|
Kinase Enrichment Analysis 3 Resource Report Resource Website 10+ mentions |
Kinase Enrichment Analysis 3 (RRID:SCR_023623) | KEA3 | data access protocol, software resource, web service | Web server application that infers overrepresentation of upstream kinases whose putative substrates are in user inputted list of proteins. Used to analyze data from phosphoproteomics and proteomics studies to predict upstream kinases responsible for observed differential phosphorylations. | overrepresentation of upstream kinases, upstream kinases, upstream kinases substrates, user inputted list of proteins, | has parent organization: Icahn School of Medicine at Mount Sinai; New York; USA | NCI U24 CA224260; NHLBI U54 HL127624; NIGMS T32 GM062754; NIH Office of the Director OT3 OD025467 |
PMID:34019655 | Free, Freely available | SCR_023623 | 2026-09-12 01:00:40 | 16 | |||||||
|
GeneRanger Resource Report Resource Website |
GeneRanger (RRID:SCR_023622) | data access protocol, software resource, web service | Web server application that provides access to processed data about expression of human genes and proteins across human cell types, tissues, and cell lines from several atlases. Used to explore single gene expression across tissues and cell types. | explore single gene expression, gene expression across tissues and cell types, gene expression, |
is related to: TargetRanger has parent organization: Icahn School of Medicine at Mount Sinai; New York; USA |
NCI U24CA224260; NCI U24CA264250; NCI U24CA271114; NIDDK R01DK131525; NIDDK RC2DK131995; NIH Office of the Director OT2OD030160 |
PMID:37166966 | Free, Freely available | SCR_023622 | 2026-09-12 01:00:40 | 0 | ||||||||
|
TargetRanger Resource Report Resource Website 1+ mentions |
TargetRanger (RRID:SCR_023621) | data access protocol, software resource, web service | Web server application that identifies targets from user inputted RNA-seq samples collected from cells we wish to target. By comparing inputted samples with processed RNA-seq and proteomics data from several atlases, TargetRanger identifies genes that are highly expressed in target cells while lowly expressed across normal human cell types, tissues, and cell lines. | identify targets, identify genes, user inputted RNA-seq samples, target cells, proteomics data, human cells, |
is related to: GeneRanger has parent organization: Icahn School of Medicine at Mount Sinai; New York; USA |
NCI U24CA224260; NCI U24CA264250; NCI U24CA271114; NIDDK R01DK131525; NIDDK RC2DK131995; NIH Office of the Director OT2OD030160 |
PMID:37166966 | Free, Freely available | https://maayanlab.github.io/Workshop.io/generanger | SCR_023621 | 2026-09-12 01:00:40 | 2 | |||||||
|
Interactive Line Graph Resource Report Resource Website 1+ mentions |
Interactive Line Graph (RRID:SCR_018334) | analysis service resource, data access protocol, data analysis service, production service resource, service resource, software resource, web service | Interactive web based tool for creating line graphs for scientific publications. Users can view different summary statistics, examine lines for any individual in data, focus on time points or groups of interest, and view changes between any two time points and conditions. | Line graph, scientific publication, summary statistics, examine lines, time point, changes between time points, data, statistic, plot | NCI P50 AG44170; Office of Research on Women Health |
PMID:27332507 | Free, Freely available | SCR_018334 | 2026-09-12 12:59:00 | 1 | |||||||||
|
Combined Annotation Dependent Depletion Resource Report Resource Website 500+ mentions |
Combined Annotation Dependent Depletion (RRID:SCR_018393) | CADD | data access protocol, data analysis software, data processing software, sequence analysis software, service resource, software application, software resource, web service | Web tool for predicting deleteriousness of variants throughout human genome. Software tool for scoring deleteriousness of single nucleotide variants as well as insertion and deletions variants in human genome. | Human genome, disease, prediction, injurious variant, single nucleotide variant, insertion variant, deletion variant, deleteriousness scoring | has parent organization: University of Washington; Seattle; USA | Berlin Institute of Health ; Brotman Baty Institute for Precision Medicine ; Charite University Medicine Berlin ; German Research Foundation ; Howard Hughes Medical Institute ; NCI R01 CA197139; NHGRI U54 HG006493 |
PMID:30371827 PMID:24487276 |
Restricted | SCR_018393 | Combined Annotation Dependent Depletion | 2026-09-12 12:59:00 | 784 | ||||||
|
GeoDa Resource Report Resource Website 100+ mentions |
GeoDa (RRID:SCR_018559) | data analysis software, data processing software, data visualization software, software application, software resource | Software program for spatial analysis for non geographic information systems specialists. Includes functionality ranging from simple mapping to exploratory data analysis, visualization of global and local spatial autocorrelation, and spatial regression. | Spatial analysis, data analysis, spatial autocorrelation visualization, spatial regression, mapping | NCI R01 CA95949; NSF BCS 9978058 |
DOI:10.1111/j.0016-7363.2005.00671.x | Free, Freely available | SCR_018559 | 2026-09-12 12:59:02 | 232 | |||||||||
|
FairSubset Resource Report Resource Website |
FairSubset (RRID:SCR_019102) | data access protocol, software resource, web service | Web tool to choose representative subsets of data for use with replicates or groups of different sample sizes. Used to retain distribution information at single datum level and may be considered for standardized use in fair publishing practices. | Representative data subsets, different sample sizes groups, different sample sizes replicates, retaining distribution information, fair publishing | NCI CA207729; Polish government grant |
PMID:31583263 | Free, Freely available | SCR_019102 | 2026-09-12 12:59:10 | 0 | |||||||||
|
Stitchr Resource Report Resource Website 1+ mentions |
Stitchr (RRID:SCR_022139) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software Python tool for stitching coding T cell receptors nucleotide sequences from V,J,CDR3 information. Produces complete coding sequences representing fully spliced TCR cDNA given minimal V,J,CDR3 information. | Stitch together coding TCR nucleotide sequences, Python, T cell receptors nucleotide, V and J gene symbols, hypervariable CDR3 amino acid sequence, fully spliced TCR cDNA | Emily Venanzi Fund ; NCI R01 CA164273; NCI R43 CA232942; NIAID R43 AI120313 |
PMID:35325179 | Free, Available for download, Freely available | SCR_022139 | 2026-09-12 01:00:05 | 3 | |||||||||
|
Drug Target Ontology Resource Report Resource Website 1+ mentions |
Drug Target Ontology (RRID:SCR_015581) | DTO | controlled vocabulary, data or information resource, ontology | Ontology of drug targets to be used as a reference for drug targets, with the longer-term goal of creating a community standard that will facilitate the integration of diverse drug discovery information from numerous heterogeneous resources. The project itself aims to develop a novel semantic framework to formalize knowledge about drug targets with a focus on the current IDG protein families. | drug ontology, drug target ontology, protein family | has parent organization: University of Miami; Florida; USA | NCI U54CA189205; NHLBI U54HL127624 |
Available for download | https://github.com/DrugTargetOntology/DTO http://bioportal.bioontology.org/ontologies/DTO | SCR_015581 | Drug Target Ontology (DTO) | 2026-09-12 12:58:28 | 2 |
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
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