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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) | software application, data analytics software, 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 |
Doris Duke Charitable Foundation ; Damon Runyon Cancer Research Foundation ; B&J Cardan Oncology Research Fund ; Ludwig Institute for Cancer Research ; NCI U01 CA154969; NIAID U19 AI090019; NCI T32 CA09302; US Department of Defense ; Siebel Stem Cell Institute ; Thomas and Stacey Siebel Foundation |
PMID:25822800 | Not freely available for download or distribution, Available for non commercial users, Registration required | biotools:CIbERSORt | https://bio.tools/CIBERSORT | SCR_016955 | 2026-02-15 09:21:12 | 1239 | ||||||
|
Tree-Based Pipeline Optimization Tool Resource Report Resource Website 1+ mentions |
Tree-Based Pipeline Optimization Tool (RRID:SCR_017531) | TPOT | software toolkit, software resource | 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 | 2026-02-15 09:22:04 | 1 | ||||||
|
Sparse Inverse Covariance Estimation for Ecological Association Inference Resource Report Resource Website 10+ mentions |
Sparse Inverse Covariance Estimation for Ecological Association Inference (RRID:SCR_022646) | SPIEC-EASI | software toolkit, software resource | Software R package estimates inverse covariance matrix from sequencing data.Statistical method for inference of microbial ecological networks from amplicon sequencing datasets. | inverse covariance matrix estimation, sequencing data, microbial ecological networks inference, amplicon sequencing datasets microbial ecological networks, | NIAID T32AI007180; NIDDK R01 DK103358; NIGMS RO1 GM63270; Simons Foundation |
PMID:25950956 | Free, Available for download, Freely available | SCR_022646 | SParse InversE Covariance Estimation for Ecological Association Inference | 2026-02-15 09:22:50 | 12 | |||||||
|
BEI Resource Repository Resource Report Resource Website 100+ mentions |
BEI Resource Repository (RRID:SCR_013698) | material storage repository, biobank, 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 | 2026-02-15 09:20:51 | 216 | ||||||||
|
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 | 2026-02-15 09:21:29 | 0 | ||||||||
|
MassQL Resource Report Resource Website 1+ mentions |
MassQL (RRID:SCR_025106) | source code, software resource | 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, | NIGMS R01 GM125943; NIGMS R01 GM107550; NIGMS R35 GM128690; NIAID R21 AI156669; NIAID R15 AI137996; NSF ; Burroughs Wellcome Fund ; University of Michigan ; National Research Foundation of Korea ; German Research Foundation ; Swedish Research Council ; Ministry of Innovative Development of the Republic of Uzbekistan ; German Ministry for Education and Research ; Horizon 2020 programme of the European Union ; Czech Science Foundation ; U.S. Department of Energy Joint Genome Institute ; National Cancer Center Research and Development Fund ; AMED Japan Program for Infectious Diseases Research and Infrastructure ; Novo Nordisk Foundation ; Denmark ; Betty and Gordon Moore Foundation |
DOI:10.1101/2022.08.06.503000 | Free, Available for download, Freely available | https://pypi.org/project/massql/ | SCR_025106 | Mass Spec Query Language | 2026-02-15 09:23:53 | 1 | |||||||
|
drug perturbation Gene Set Enrichment Analysis Resource Report Resource Website 1+ mentions |
drug perturbation Gene Set Enrichment Analysis (RRID:SCR_025351) | dpGSEA | source code, software resource | 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 | 2026-02-15 09:23:55 | 1 | ||||||||
|
Mixed effects association testing for single cells Resource Report Resource Website 1+ mentions |
Mixed effects association testing for single cells (RRID:SCR_025632) | MASC | source code, software resource | 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, | NIAMSD UH2AR067677; NIAID U19AI111224; NIAMSD 1R01AR063759; NIAMSD R01 AR064850; Doris Duke Charitable Foundation ; NIAMSD T32 AR007530; William Docken Inflammatory Autoimmune Disease Fund ; Ruth L. Kirschstein National Research Service Award ; Rheumatology Research Foundation Tobe and Stephen Malawista |
PMID:30333237 | SCR_025632 | , Mixed-effects modeling of Associations of Single Cells, Mixed-effects Association testing for Single Cells | 2026-02-15 09:23:57 | 2 | ||||||||
|
xCell Resource Report Resource Website 50+ mentions |
xCell (RRID:SCR_026446) | web application, source code, software toolkit, software resource | 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 | 2026-02-15 09:24:12 | 62 | ||||||||
|
chromvar Resource Report Resource Website 10+ mentions |
chromvar (RRID:SCR_026570) | software application, source code, data processing software, software resource, software toolkit, data analysis software | 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 | NHGRI P50HG007735; NIAID U19AI057266; Rita Allen Foundation ; Harvard Society of Fellows ; Broad Institute Fellowship |
PMID:28825706 | Free, Available for download, Freely available | SCR_026570 | chromatin Variability Across Regions | 2026-02-15 09:23:19 | 11 | |||||||
|
CytoML Resource Report Resource Website 1+ mentions |
CytoML (RRID:SCR_027485) | source code, software toolkit, software resource | 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, | NIGMS R01 GM118417; Bill and Melinda Gates Foundation ; NIAID UM1 AI068635 |
PMID:30551257 | Free, Available for download, Freely available | https://www.bioconductor.org/packages/release/bioc/html/CytoML.html | SCR_027485 | 2026-02-15 09:24:13 | 5 | ||||||||
|
demuxlet Resource Report Resource Website |
demuxlet (RRID:SCR_027855) | software application, source code, software resource | 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, | NIAMSD R01AR071522; NIAID R21AI133337; NIDDK F30DK115167; NHLBI K25HL121295; NIDCR R03DE025665 |
PMID:29227470 | Free, Available for download, Freely available | SCR_027855 | 2026-02-15 09:23:37 | 0 |
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