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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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CIBERSORT Resource Report Resource Website 1000+ mentions |
CIBERSORT (RRID:SCR_016955) | data analytics software, software application, software resource | Software tool to provide an estimation of the abundances of member cell types in a mixed cell population, using gene expression data. Used for characterizing cell composition of complex tissues from their gene expression profiles, large scale analysis of RNA mixtures for cellular biomarkers and therapeutic targets. | estimation, abundance, cell, type, mixed, population, gene, expression, data, tissue, complex, analysis, RNA, biomarker, therapeutic, target, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Stanford University; Stanford; California |
B&J Cardan Oncology Research Fund ; Damon Runyon Cancer Research Foundation ; Doris Duke Charitable Foundation ; Ludwig Institute for Cancer Research ; NCI T32 CA09302; NCI U01 CA154969; NIAID U19 AI090019; Siebel Stem Cell Institute ; Thomas and Stacey Siebel Foundation ; US Department of Defense |
PMID:25822800 | Not freely available for download or distribution, Available for non commercial users, Registration required | biotools:CIbERSORt | https://bio.tools/CIBERSORT | SCR_016955 | 2026-09-12 01:02:54 | 1908 | ||||||
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Tree-Based Pipeline Optimization Tool Resource Report Resource Website 1+ mentions |
Tree-Based Pipeline Optimization Tool (RRID:SCR_017531) | TPOT | software resource, software toolkit | Software Python package to automate building of ML pipelines by combining flexible expression tree representation of pipelines with stochastic search algorithms such as genetic programming. | Automated, machine, learning, optimize, pipeline, genetic, programming | NIAID R01 AI117694 | Free, Available for download, Freely available | SCR_017532 | https://epistasislab.github.io/tpot/, https://github.com/EpistasisLab/tpot | SCR_017531 | Tree based Pipeline Optimization Tool | 2026-09-12 01:02:55 | 3 | ||||||
|
BEI Resource Repository Resource Report Resource Website 100+ mentions |
BEI Resource Repository (RRID:SCR_013698) | biobank, material storage repository, service resource, storage service resource | Central data repository that supplies organisms and reagents to the broad community of microbiology and infectious diseases researchers. | biomaterial, material, reagent, microbiology, infectious diseases |
is listed by: NIH Data Sharing Repositories is related to: ATCC is related to: NIH Data Sharing Repositories |
infectious disease | NIAID | SCR_013698 | BEI Resource | 2026-09-12 01:03:47 | 258 | ||||||||
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University of California at San Francisco Division of Experimental Medicine Flow Core Facility Resource Report Resource Website |
University of California at San Francisco Division of Experimental Medicine Flow Core Facility (RRID:SCR_017903) | access service resource, core facility, service resource | Flow cytometry facility offering training and services including:Access to two, 17-color BD LSR II analytical instruments with High Throughput Sampler (HTS) module,Configurations:LSRII 1,LSRII 2;Help with Flow Cytometry Panel Design;Fluorofinder (access our cytometers under CFAR Immunology Core);BD Panel designer;SFGH LSRII Flow Core Protocols;LSRII Startup and Shutdown;How to run the CST calibration assay;Access to a 17-color BD FACSAria II for fluorescence-activated cell sorting (FACS);4-way tube sorting;96 well plate sorting;Index sorting;SFGH ARIA Flow Core Protocols and configuration;ARIA Startup;Determining Drop Delay;Side Stream Set Up;Clog Procedure;ARIA Shutdown Protocol;ARIA Configuration;DNA analysis with standard dyes;Analysis of CFP, GFP, YFP, mRFP, mTomato, and mCherry gene expression proteins;Calcium flux measurements using Indo-1;Training of users on the operation of instruments and experimental design through the CIL Flow Cytometry Course;Maintaining and Upgrading Instruments;Research Support Services (study design, assay selection, grant and paper writing support). | Flow, cytometry, support, training, instrumentation, study, design, assay, grant, paper, service, core | NIAID P30 AI027763 | Open | ABRF_778 | SCR_017903 | Flow Cytometry Core | 2026-09-12 01:04:05 | 0 | ||||||||
|
MassQL Resource Report Resource Website 1+ mentions |
MassQL (RRID:SCR_025106) | software resource, source code | Software application for universal searching of Mass Spectrometry data. Open source MS query language for flexible and mass spectrometer manufacturer-independent mining of MS data. Implements common MS terminology to build consensus vocabulary to search for MS patterns in single mass spectrometry run. Enables set of mass spectrometry patterns to be queried directly from raw data. | Mass Spectrometry data searching, mass spectrometry data, mining of MS data, common MS terminology, mass spectrometry patterns, raw data query, | AMED Japan Program for Infectious Diseases Research and Infrastructure ; Betty and Gordon Moore Foundation ; Burroughs Wellcome Fund ; Czech Science Foundation ; German Ministry for Education and Research ; German Research Foundation ; Horizon 2020 programme of the European Union ; Ministry of Innovative Development of the Republic of Uzbekistan ; National Cancer Center Research and Development Fund ; National Research Foundation of Korea ; NIAID R15 AI137996; NIAID R21 AI156669; NIGMS R01 GM107550; NIGMS R01 GM125943; NIGMS R35 GM128690; Novo Nordisk Foundation ; Denmark ; NSF ; Swedish Research Council ; U.S. Department of Energy Joint Genome Institute ; University of Michigan |
DOI:10.1101/2022.08.06.503000 | Free, Available for download, Freely available | https://pypi.org/project/massql/ | SCR_025106 | Mass Spec Query Language | 2026-09-12 01:04:37 | 1 | |||||||
|
IBEX Knowledge Base Resource Report Resource Website 1+ mentions |
IBEX Knowledge Base (RRID:SCR_025296) | knowledge base | Open, global repository as central resource for reagents, protocols, panels, publications, software, and datasets. In addition to IBEX, we support standard, single cycle multiplexed imaging (Multiplexed 2D imaging), volume imaging of cleared tissues with clearing enhanced 3D (Ce3D), highly multiplexed 3D imaging (Ce3D-IBEX), and extension of the IBEX dye inactivation protocol to the Leica Cell DIVE (Cell DIVE-IBEX). Committed to sharing knowledge related to multiplexed imaging. Antibody validation community knowledgebase. | Antibody, validation, multiplexed imaging, | Chan Zuckerberg Initiative ; NCI ; NIAID ; Schroeder Allergy and Immunology Research Institute ; McMaster University ; CA ; Wellcome Trust |
Free, Freely available | https://zenodo.org/records/7693279 | SCR_025296 | Iterative Bleaching Extends Multiplexity (IBEX) Knowledge-Base | 2026-09-12 01:04:41 | 4 | ||||||||
|
drug perturbation Gene Set Enrichment Analysis Resource Report Resource Website 1+ mentions |
drug perturbation Gene Set Enrichment Analysis (RRID:SCR_025351) | dpGSEA | software resource, source code | Software tool to detect phenotypically relevant drug targets through unique transcriptomic enrichment that emphasizes biological directionality of drug-derived gene sets. Exploratory tool to screen for possible drug targeting molecules. | detect phenotypically relevant drug targets, drug-derived gene sets, transcriptomic enrichment, | NHLBI T32HL007567; NIAID P30AI036219 |
DOI:10.1186/s12859-020-03929-0 | Free, Available for download, Freely available | SCR_025351 | 2026-09-12 01:04:42 | 2 | ||||||||
|
Mixed effects association testing for single cells Resource Report Resource Website 1+ mentions |
Mixed effects association testing for single cells (RRID:SCR_025632) | MASC | software resource, source code | Software tool for testing whether specified covariate influences membership of single cells in any of multiple cellular subsets while accounting for technical confounds and biological variation. | specified covariate, influences membership, single cells, multiple cellular subsets, accounting for technical confounds and biological variation, | Doris Duke Charitable Foundation ; NIAID U19AI111224; NIAMSD 1R01AR063759; NIAMSD R01 AR064850; NIAMSD T32 AR007530; NIAMSD UH2AR067677; Rheumatology Research Foundation Tobe and Stephen Malawista ; Ruth L. Kirschstein National Research Service Award ; William Docken Inflammatory Autoimmune Disease Fund |
PMID:30333237 | SCR_025632 | , Mixed-effects modeling of Associations of Single Cells, Mixed-effects Association testing for Single Cells | 2026-09-12 01:04:48 | 4 | ||||||||
|
xCell Resource Report Resource Website 100+ mentions |
xCell (RRID:SCR_026446) | software resource, software toolkit, source code, web application | Software R package for generating cell type scores and R scripts for development of xCell. Web tool that performs cell type enrichment analysis from gene expression data for immune and stroma cell types. Used for Cell types enrichment analysis. | Cell types enrichment analysis, cell type, enrichment analysis, generating cell type scores and R scripts, development of xCell, | Gruss Lipper Postdoctoral Fellowship ; NCI U24 CA195858; NIAID |
PMID:29141660 | Free, Available for download, Freely available | http://xCell.ucsf.edu/ | SCR_026446 | 2026-09-12 01:05:04 | 170 | ||||||||
|
chromvar Resource Report Resource Website 10+ mentions |
chromvar (RRID:SCR_026570) | data analysis software, data processing software, software application, software resource, software toolkit, source code | Software R package for analyzing sparse chromatin-accessibility data by estimating gain or loss of accessibility within peaks sharing the same motif or annotation while controlling for technical biases. Enables accurate clustering of scATAC-seq profiles and characterization of known and de novo sequence motifs associated with variation in chromatin accessibility. Used for analysis of sparse chromatin accessibility data from single cell or bulk ATAC or DNAse-seq data. | analyzing sparse chromatin-accessibility data, analysis of sparse chromatin accessibility data, single cell, bulk ATAC, DNAse-seq data, | is used by: pychromVAR | Broad Institute Fellowship ; Harvard Society of Fellows ; NHGRI P50HG007735; NIAID U19AI057266; Rita Allen Foundation |
PMID:28825706 | Free, Available for download, Freely available | SCR_026570 | chromatin Variability Across Regions | 2026-09-12 01:05:07 | 15 | |||||||
|
CytoML Resource Report Resource Website 1+ mentions |
CytoML (RRID:SCR_027485) | software resource, software toolkit, source code | Software R package that enables cross-platform import, export, and sharing of gated cytometry data. It currently supports Cytobank, FlowJo, Diva, and R, allowing users to import gated cytometry data from commercial platforms into R. | Cross-platform cytometry data sharing, cross-platform import, export, sharing, gated cytometry data, import gated cytometry data, | Bill and Melinda Gates Foundation ; NIAID UM1 AI068635; NIGMS R01 GM118417 |
PMID:30551257 | Free, Available for download, Freely available | https://www.bioconductor.org/packages/release/bioc/html/CytoML.html | SCR_027485 | 2026-09-12 01:05:28 | 6 | ||||||||
|
demuxlet Resource Report Resource Website |
demuxlet (RRID:SCR_027855) | software application, software resource, source code | Software tool that harnesses natural genetic variation to determine the sample identity of each droplet containing a single cell (singlet) and detect droplets containing two cells (doublets). Genetic multiplexing of barcoded single cell RNA-seq. | Genetic multiplexing of barcoded single cell RNA-seq, harnesses natural genetic variation, | NHLBI K25HL121295; NIAID R21AI133337; NIAMSD R01AR071522; NIDCR R03DE025665; NIDDK F30DK115167 |
PMID:29227470 | Free, Available for download, Freely available | SCR_027855 | 2026-09-12 01:05:37 | 0 | |||||||||
|
EpiProfile Resource Report Resource Website |
EpiProfile (RRID:SCR_028224) | software application, software resource, source code | Software tool for processing Epi-Proteomics mass spectrometry data. Discriminates isobaric histone peptides using distinguishing fragment ions in their tandem mass spectra and extracts the chromatographic area under the curve using previous knowledge about peptide retention time. Nanoflow liquid chromatography coupled with high resolution tandem mass spectrometry-based quantification tool for histone peptides, which can also be adapted to analyze nonhistone protein samples. EpiProfile 2.0 is extended version of v1.0 for enhanced quantification of histone peptides based on LC-MS/MS analysis. | LC-MS/MS analysis, peptide, quantification, histone, quantification of histone peptides, quantification of histone peptides based on LC-MS/MS analysis, mass spectrometry data, | NCATS TL1TR001880; NCI CA196539; NIAID AI118891; NIGMS GM110174; NIGMS T32GM008275; UPenn Epigenetics Institute |
PMID:25805797 PMID:29790754 |
Free, Available for download, Freely available | SCR_028224 | EpiProfile 2.0 | 2026-09-12 01:05:46 | 0 | ||||||||
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starCAT Resource Report Resource Website 1+ mentions |
starCAT (RRID:SCR_028475) | software resource, software toolkit, source code | Software pipeline that improves T cell characterization by simultaneously quantifying predefined gene expression programs (scRNA-Seq) capturing activation states and cellular subsets. Used to score cells based on a fixed, multidataset catalog of Gene Expression Programs from any tissues or cell-type. | T cell characterization, simultaneously quantifying predefined gene expression programs, gene expression programs, | NHGRI R56HG013083; NHGRI T32HG002295; NHGRI U01HG012009; NIAID P01AI148102; NIAMS R01AR063759; NIAMS T32AR007530 |
PMID:38746317 | Free, Available for download, Freely available | SCR_028475 | starCellAnnoTator, starCellAnnoTator (starCAT) | 2026-09-12 01:05:52 | 1 | ||||||||
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TryTripDB Resource Report Resource Website 10+ mentions |
TryTripDB (RRID:SCR_028607) | data or information resource, database | Free online resource for data mining of genomic and functional data from these kinetoplastid parasites and is part of the VEuPathDB Bioinformatics Resource Center. Integrates functional genome scale datasets (e.g. transcript expression, protein expression, genetic variation data) and information predicted from automated bioinformatics pipelines and from manual curation. Provides a user friendly web interface and a number of tools and functions for users to conduct in silico experiments to ask questions and generate hypotheses. Researchers can also contribute their expertise via the User Comments form and Apollo annotation platform, and utilize cloud-based workspace to analyze their own data. | data mining, genomic data, functional data, kinetoplastid parasites, | NIAID ; Wellcome Trust |
PMID:36656904 | Free, Freely available | SCR_028607 | 2026-09-12 01:05:55 | 14 | |||||||||
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decontam Resource Report Resource Website |
decontam (RRID:SCR_028857) | software resource, software toolkit, source code | Software R package for the statistical identification and removal of contaminant sequences in marker-gene (e.g. 16S rRNA) and metagenomics sequencing data. Implements frequency- and prevalence-based contaminant identification methods. Used for simple statistical identification and removal of contaminants in marker-gene and metagenomics sequencing data. | Statistical identification and removal of contaminants, marker gene, metagenomics, sequencing data, | NIAID R01 AI112401; NIDCR R01 DE023113; Stanford University |
PMID:30558668 | Free, Available for download, Freely available | SCR_028857 | 2026-09-12 01:06:01 | 0 |
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