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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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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, | 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 | 2026-02-13 10:59:28 | 1 | |||||||
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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 | 2026-02-13 10:59:26 | 1 | ||||||||
|
xCell Resource Report Resource Website 50+ mentions |
xCell (RRID:SCR_026446) | software resource, source code, software toolkit, 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 | 2026-02-13 10:59:45 | 62 | ||||||||
|
chromvar Resource Report Resource Website 10+ mentions |
chromvar (RRID:SCR_026570) | data processing software, data analysis software, source code, software toolkit, software application, software resource | 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 | 2026-02-13 10:59:43 | 11 | |||||||
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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, | 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 | 2026-02-13 10:59:30 | 2 | ||||||||
|
CytoML Resource Report Resource Website 1+ mentions |
CytoML (RRID:SCR_027485) | software resource, source code, software toolkit | 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 | 2026-02-13 10:59:47 | 5 | ||||||||
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SingleR Resource Report Resource Website 100+ mentions |
SingleR (RRID:SCR_023120) | software resource, software toolkit | Software R package for unbiased cell type recognition of scRNA-seq data. Performs unbiased cell type recognition from single-cell RNA sequencing data, by leveraging reference transcriptomic datasets of pure cell types to infer cell of origin of each single cell independently. | unbiased cell type recognition, scRNA-seq data, reference transcriptomic datasets, pure cell types, infer cell of origin | UCSF Marcus Award ; NHLBI HL131560; UCSF Nina Ireland Program award ; NHLBI HL139897; NIAID |
PMID:30643263 | Free, Available for download, Freely available | https://github.com/dviraran/SingleR https://github.com/LTLA/SingleR |
SCR_023120 | Single-cell RNA-seq cell types Recognition | 2026-02-13 10:58:53 | 321 | |||||||
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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 resource, software toolkit | 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 | 2026-02-13 10:58:46 | 12 | |||||||
|
DADA2 Resource Report Resource Website 500+ mentions |
DADA2 (RRID:SCR_023519) | software resource, software toolkit | Open source software R package for modeling and correcting Illumina sequenced amplicon errors. Fast and accurate sample inference from amplicon data with single nucleotide resolution. | modeling and correcting amplicon errors, Illumina sequenced amplicon errors, amplicon errors, sample inference, amplicon data, single nucleotide resolution |
is used by: ImmuMicrobiome is related to: dadasnake has parent organization: Stanford University; Stanford; California |
NSF ; NIAID R01AI112401; Samarth Foundation |
PMID:27214047 | Free, Available for download, Freely available | https://bioconductor.org/packages/dada2/ | SCR_023519 | 2026-02-13 10:58:58 | 960 | |||||||
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ATHLATES Resource Report Resource Website 1+ mentions |
ATHLATES (RRID:SCR_023689) | software resource, software toolkit | Software package for determining HLA genotypes for individuals from Illumina exome sequencing data. Program applies assembly, allele identification and allelic pair inference to short read sequences, and applies it to data from Illumina platforms. | Illumina, HLA genotypes determination, Illumina exome sequencing data, allele identification, allelic pair inference, short read sequence, | Washington University School of Medicine ; NIAID ; National Institutes of Health ; Department of Health and Human Services |
PMID:23748956 | Free, Available for download, Freely available | SCR_023689 | 2026-02-13 10:59:01 | 3 | |||||||||
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demuxlet Resource Report Resource Website |
demuxlet (RRID:SCR_027855) | software resource, source code, software application | 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 | 2026-02-13 10:59:52 | 0 | |||||||||
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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) | core facility, access service resource, 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 | 2026-02-13 10:58:04 | 0 |
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