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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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MirSNP Resource Report Resource Website 50+ mentions |
MirSNP (RRID:SCR_001629) | MirSNP | data or information resource, database | Database of human SNPs in predicted miRNA-mRNA binding sites, based on information from dbSNP135 and mirBASE18. MirSNP is highly sensitive and covers most experiments confirmed SNPs that affect miRNA function. MirSNP may be combined with researchers' own GWAS or eQTL positive data sets to identify the putative miRNA-related SNPs from traits/diseases associated variants. They aim to update the MirSNP database as new versions of mirBASE and dbSNP database become available. | single nucleotide polymorphism, mirna, genome-wide association study, expression quantitative trait locus, mirna-mrna binding site, trait, disease, variant, gene, mrna, FASEB list | has parent organization: Peking University; Beijing; China | National Natural Science Foundation of China 81071087; National Natural Science Foundation of China 81071088; International Science and Technology Cooperation Program of China 2010DFB30820; National High Technology Research and Development Program of China 2009AA022702 |
PMID:23173617 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_153896 | http://202.38.126.151/hmdd/mirsnp/search/ | SCR_001629 | 2026-02-11 10:56:16 | 73 | |||||
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AnimalTFDB Resource Report Resource Website 100+ mentions |
AnimalTFDB (RRID:SCR_001624) | AnimalTFDB | data or information resource, database | A comprehensive transcription factor (TF) database in which they identified and classified all the genome-wide TFs in 50 sequenced animal genomes (Ensembl release version 60). In addition to TFs, it also collects transcription co-factors and chromatin remodeling factors of those genomes, which play regulatory roles in transcription. Here they defined the TFs as proteins containing a sequence-specific DNA-binding domain (DBD) and regulating target gene expression. Currently, the AnimalTFDB classifies all the animal TFs into 72 families according to their conserved DBDs. Gene lists of transcription factors, transcription co-factors and chromatin remodeling factors of each species are available for downloading., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | transcription factor, dna-binding domain, transcription co-factor, chromatin remodeling factor, gene structure, functional domain, go annotation, protein interaction, ortholog, paralog, 3d structure, pathway, protein-protein interaction, binding site, target, data set, image collection, 3d spatial image, bio.tools, FASEB list |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: Gene Ontology is related to: Ensembl has parent organization: Huazhong University of Science and Technology; Wuhan; China |
Huazhong University of Science and Technology; Wuhan; China ; Fundamental Research Funds for the Central Universities 2010MS045; National Natural Science Foundation of China 31171271 |
PMID:22080564 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_153892, OMICS_01856, biotools:animal_tfdb | https://bio.tools/animal_tfdb | SCR_001624 | Animal Transcription Factor Database | 2026-02-11 10:56:16 | 289 | ||||
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IndelFR - Indel Flanking Region Database Resource Report Resource Website 1+ mentions |
IndelFR - Indel Flanking Region Database (RRID:SCR_006050) | IndelFR | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. Indel Flanking Region Database is an online resource for indels and the flanking regions of proteins in SCOP superfamilies, including amino acid sequences, lengths, locations, secondary structure constitutions, hydrophilicity / hydrophobicity, domain information, 3D structures and so on. It aims at providing a comprehensive dataset for analyzing the qualities of amino acid insertion/deletions(indels), substitutions and the relationship between them. The indels were obtained through the pairwise alignment of homologous structures in SCOP superfamilies. The IndelFR database contains 2,925,017 indels with flanking regions extracted from 373,402 structural alignment pairs of 12,573 non-redundant domains from 1053 superfamilies. IndelFR has already been used for molecular evolution studies and may help to promote future functional studies of indels and their flanking regions. | indel, flanking region, protein, structural domain, domain, protein superfamily, protein structure, insertion/deletion, insertion, deletion, protein sequence, sequence, structure, protein domain, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: SCOP: Structural Classification of Proteins is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) has parent organization: Shandong University; Shandong; China |
Independent Innovation Foundation of Shandong University 2009JC006; National Natural Science Foundation of China 30970092; National Natural Science Foundation of China 61070017; Scientific Research Reward Fund for excellent Young and Middle-Aged scientists in Shandong Province 20090451326 |
PMID:22127860 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:indelfr, nlx_151448 | https://bio.tools/indelfr | SCR_006050 | IndelFR: Indel Flanking Region Database, Indel Flanking Region Database | 2026-02-11 10:57:18 | 2 | ||||
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Dr.VIS - Human Disease-Related Viral Integration Sites Resource Report Resource Website 1+ mentions |
Dr.VIS - Human Disease-Related Viral Integration Sites (RRID:SCR_005965) | Dr.VIS, Dr. VIS | data or information resource, database | Dr.VIS collects and locates human disease-related viral integration sites. So far, about 600 sites covering 5 virus organisms and 11 human diseases are available. Integration sites in Dr.VIS are located against chromosome, cytoband, gene and refseq position as specific as possible. Viral-cellular junction sequences are extracted from papers and nucleotide databases, and linked to corresponding integration sites Graphic views summarizing distribution of viral integration sites are generated according to chromosome maps. Dr.VIS is built with a hope to facilitate research of human diseases and viruses. Dr.VIS provides curated knowledge of integration sites from chromosome region narrow to genomic position, as well as junction sequences if available. Dr.VIS is an open resource for free. | disease, virus, viral integration, viral integration site, integration site, malignant disease, chromosome region, genomic position, viral-host junction sequence, junction sequence, oncogene, chromosome, catalog, graphic interface, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Tongji University; Shanghai; China |
State Key Basic Research Program 973 2011CB910204; National Natural Science Foundation of China ; Major State Basic Research Development Program ; 863 Hi-Tech Program of China ; National Key Technology R&D Program in the 11th Five Year Plan of China ; Major State Basic Research Development Program of China |
PMID:22135288 | Open - Free to browse and download data in Dr.VIS. | nlx_151323, biotools:dr.vis | http://www.scbit.org/dbmi/drvis https://bio.tools/dr.vis |
SCR_005965 | Dr. VIS - Database of Human Disease-related Viral Integration Sites, Database of Human Disease-related Viral Integration Sites | 2026-02-11 10:57:12 | 1 | ||||
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Beijing: Short TR Study Resource Report Resource Website 1+ mentions |
Beijing: Short TR Study (RRID:SCR_003502) | Beijing Short TR | data or information resource, data set | Dataset of resting state fMRI scans obtained using two different TR's in healthy college-aged volunteers. Specifically, for each participant, data is being obtained with a short TR (0.4 seconds) and a long TR (2.0 seconds). In addition this dataset contains a 64-direction DTI scan for every participant. The following data are released for every participant: * 8-minute resting-state fMRI scan (TR = 2 seconds, # repetitions = 240) * 8-minute resting-state fMRI scans (TR = 0.4 seconds, # repetitions = 1200) * MPRAGE anatomical scan, defaced to protect patient confidentiality * 64-direction diffusion tensor imaging scan (2mm isotropic) * Demographic information | nifti, fmri, resting-state fmri, image collection, early adult human, mprage, diffusion tensor imaging, neuroimaging, brain, demographic |
has parent organization: Beijing Normal University; Beijing; China has parent organization: 1000 Functional Connectomes Project |
Healthy | National Natural Science Foundation of China 30770594; National High Technology Program of China 2008AA02Z405 |
Creative Commons Attribution-NonCommercial License | nlx_157642 | SCR_003502 | Beijing Normal University State Key Laboratory of Cognitive Neuroscience and Learning Short TR Sample, BNU Short TR Sample | 2026-02-11 10:56:45 | 6 | |||||
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EVmiRNA Resource Report Resource Website 1+ mentions |
EVmiRNA (RRID:SCR_018795) | data or information resource, database | Collection of comprehensive miRNA expression profiles in extracellular vesicles from tissues. Includes miRNA expression profiles, miRNA regulated pathways, miRNA function, miRNA related drugs and publications to support miRNA biomarker discovery. | miRNA, miRNA expression profile, extracellular vesicle, tissue, miRNA regulated pathway, miRNA function, drug, publication, miRNA biomarker, data | National Key Research and Development Program of China ; National Natural Science Foundation of China ; China Postdoctoral Science Foundation |
PMID:30335161 | Free, Freely available | SCR_018795 | Extracellular Vesicles miRNA Database | 2026-02-11 10:59:51 | 1 | ||||||||
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Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform Resource Report Resource Website 100+ mentions |
Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (RRID:SCR_023757) | TCMSP | data or information resource, database | Pharmacology platform of Chinese herbal medicines that captures relationships between drugs, targets and diseases. Database includes chemicals, targets and drug-target networks, and associated drug-target-disease networks, as well as pharmacokinetic properties for natural compounds involving oral bioavailability, drug-likeness, intestinal epithelial permeability, blood-brain-barrier, aqueous solubility. | Pharmacology platform, Chinese herbal medicines, drugs, targets and diseases, drug-target networks, natural compounds, pharmacokinetic properties, | National Natural Science Foundation of China | PMID:24735618 | Free, Freely available | https://tcmsp-e.com/ | SCR_023757 | TCMSP database | 2026-02-11 11:00:44 | 195 | ||||||
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NeuroPep Resource Report Resource Website 10+ mentions |
NeuroPep (RRID:SCR_023102) | data or information resource, database | Comprehensive resource of neuropeptides, which holds non-redundant neuropeptide entries. Data collected from resources including MEDLINE abstracts, full papers, UniProt,database at www.neuropeptides.nl and Neuropedia. Contains detailed annotations for each entry, including source organisms, tissue specificity, families, names, post-translational modifications, 3D structures and literature references. Amino acid compositions, isoelectric points, molecular weight and other physicochemical properties of peptides are also provided. Search database with keywords such as sequence, name, family, etc.,User friendly web tools like browsing, sequence alignment and mapping are also integrated.Users can submit new entries online. Each new entry is validated before incorporating it. | neuropeptide database, neuropeptide, non-redundant neuropeptide, | National Natural Science Foundation of China ; Fundamental Research Funds for the Central Universities of China |
PMID:25931458 | Free, Freely available | SCR_023102 | 2026-02-11 11:00:32 | 10 | |||||||||
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OncoboxPD Resource Report Resource Website 1+ mentions |
OncoboxPD (RRID:SCR_023723) | data or information resource, database | Structured curated collection of protein based and of metabolic human molecular pathways. Human molecular pathways database with tools for activity calculating and visualization.All pathways are functionally classified according to GO terms enrichment patterns. All pathway participants, their interactions and reactions are uniformly processed and annotated, and are ready for numeric analysis of experimental expression data.For every comparison graph is generated summarizing top up and down regulated pathways. | Gene Ontology terms enrichment patterns, human molecular pathways, curated collection, GO terms enrichment patterns, experimental expression data analysis, |
is related to: oncoboxlib is related to: Gene Ontology |
Russian Science Foundation ; National Natural Science Foundation of China ; Qingdao Key Research Project ; Qingdao Key Health Discipline Development Fund |
PMID:35615022 | Free, Freely available | SCR_023723 | Oncobox Pathway Databank | 2026-02-11 11:00:44 | 3 | |||||||
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Brassicaceae Database Resource Report Resource Website 100+ mentions |
Brassicaceae Database (RRID:SCR_023019) | BRAD | data or information resource, database | Database includes newly released genome sequences of Brassiceae species and published genomic data of most other Brassicaceae species.Data can be browsed in JBrowse or searched in BLAST. Offers service of searching for syntenic genes, which are generated based on their syntenic relationships to genes in Arabidopsis thaliana. Regularly updated with newly released reference genomes. | genome sequences, Brassiceae species, published genomic data, syntenic genes, | National Programon Key Research Project ; National Natural Science Foundation of China |
DOI:10.1093/nar/gkab1057 | Free, Freely available | SCR_023019 | 2026-02-11 11:00:31 | 291 | ||||||||
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DaTo Resource Report Resource Website 1+ mentions |
DaTo (RRID:SCR_010280) | DaTo | data or information resource, database | A biological database and software tool catalog based on text mined and human annotated url mentions in PubMed abstracts. Data are annotated as to the author''''s country of origin and url status is checked. | metadata, catalog, text mining |
is related to: Cytoscape is related to: PubMed has parent organization: Zhejiang University; Zhejiang; China |
National Natural Science Foundation of China 30971743; National Natural Science Foundation of China 31371328 |
nlx_157296 | SCR_010280 | DA&TO - The Atlas of biology databases and tools, DAandTO, Da&To | 2026-02-11 10:58:15 | 8 | |||||||
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NONCODE Resource Report Resource Website 100+ mentions |
NONCODE (RRID:SCR_007822) | data or information resource, database | Collection of non-coding RNAs (excluding tRNAs and rRNAs) as an integrated knowledge database. Used to get text information such as class,name,location,related publication,mechanism through which it exerts its function, view figures which show their location in the genome or in a specific DNA fragment, and the regulation elements flanking the ncRNA gene sequences. | collection, long, non, coding, RNA, integrated, database, FASEB list |
has parent organization: Chinese Academy of Sciences; Beijing; China works with: Genotate |
National High Technology Research and Development Program of China ; Training Program of the Major Research Plan of the National Natural Science Foundation of China ; National Natural Science Foundation of China ; Chinese Academy of Science Strategic Project of Leading Science and Technology |
PMID:26586799 | nif-0000-03195, r3d100012169 | http://www.bioinfo.org/noncode/ https://doi.org/10.17616/R3194Q https://doi.org/10.17616/R3194Q |
http://bioinfo.ibp.ac.cn/NONCODE/index.htm, http://www.noncode.org/NONCODERv3/ | SCR_007822 | NONCODE 2016 | 2026-02-11 10:57:42 | 475 | |||||
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DiseaseMeth Resource Report Resource Website 10+ mentions |
DiseaseMeth (RRID:SCR_005942) | data repository, service resource, storage service resource, database, data or information resource | Human disease methylation database. DiseaseMeth version 2.0 is focused on aberrant methylomes of human diseases. Used for understanding of DNA methylation driven human diseases. | disease, methylation, dna methylation, genome, gene, epigenetics, epigenomics, methylome, bio.tools |
is listed by: 3DVC is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Harbin Medical University; Heilongjiang; China |
National Natural Science Foundation of China ; Natural Science Foundation of Heilongjiang Province ; State Key Laboratory of Urban Water Resource and Environment ; Scientific Research Fund of Heilongjiang Provincial Education Department |
PMID:22135302 PMID:27899673 |
Free,Freely available | OMICS_01838, nlx_151289, biotools:diseasemeth, SCR_017488 | http://bioinfo.hrbmu.edu.cn/diseasemeth https://bio.tools/diseasemeth |
http://202.97.205.78/diseasemeth/ | SCR_005942 | , Disease Meth-The Human Disease Methylation Database, DiseaseMeth database, DiseaseMeth version 2.0 | 2026-02-12 09:44:13 | 34 | ||||
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SpliceDisease Resource Report Resource Website 1+ mentions |
SpliceDisease (RRID:SCR_006130) | SpliceDisease | data repository, service resource, storage service resource, database, data or information resource | Curated database of experimentally supported data of RNA Splicing mutation and disease. The RNA Splicing mutations include cis-acting mutations that disrupt splicing and trans-acting mutations that affecting RNA-dependent functions that cause disease. Information such as EntrezGeneID, gene genomic sequence, mutation (nucleotide substitutions, deletions and insertions), mutation location within the gene, organism, detailed description of the splicing mutation and references are also given. Users are able to submit new entries to the database. This database integrating RNA splicing and disease associations would be helpful for understanding not only the RNA splicing but also its contribution to disease. In SpliceDisease database, they manually curated 2337 splicing mutation disease entries involving 303 genes and 370 diseases, which have been supported experimentally in 898 publications. The SpliceDisease database provides information including the change of the nucleotide in the sequence, the location of the mutation on the gene, the reference PubMed ID and detailed description for the relationship among gene mutations, splicing defects and diseases. They standardized the names of the diseases and genes and provided links for these genes to NCBI and UCSC genome browser for further annotation and genomic sequences. For the location of the mutation, they give direct links of the entry to the respective position/region in the genome browser. | rna splicing, mutation, disease, gene, genomic sequence, nucleotide substitution, deletion, insertion, mutation location, splicing mutation, nucleotide, disease association, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Peking University; Beijing; China |
National Natural Science Foundation of China 81001481 | PMID:22139928 | The community can contribute to this resource | biotools:splicedisease_db, nlx_151614 | https://bio.tools/splicedisease_db | SCR_006130 | Splice Disease, SpliceDisease Database Site, Splice Disease Database, SpliceDisease Database | 2026-02-12 09:44:17 | 2 | ||||
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REST: a toolkit for resting-state fMRI Resource Report Resource Website 500+ mentions |
REST: a toolkit for resting-state fMRI (RRID:SCR_009641) | REST | software toolkit, software resource, software application, data processing software, image processing software, image analysis software | A user-friendly convenient toolkit to calculate Functional Connectivity (FC), Regional Homogeneity (ReHo), Amplitude of Low-Frequency Fluctuation (ALFF), Fractional ALFF (fALFF), Gragner causality and perform statistical analysis. You also can use REST to view your data, perform Monte Carlo simulation similar to AlphaSim in AFNI, calculate your images, regress out covariates, extract Region of Interest (ROI) time courses, reslice images, and sort DICOM files. | correlation, cross-correlation, fourier time-domain analysis, gnome, kde, linux, macos, matlab, microsoft, modeling, magnetic resonance, nifti, posix/unix-like, spatial transformation, spectral analysis, statistical operation, temporal transformation, time domain analysis, two dimensional display, visualization, windows, resting-state functional magnetic resonance imaging, resting-state fmri |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Beijing Normal University; Beijing; China |
National High Technology Program of China ; National Natural Science Foundation of China ; Program for Changjiang Scholars and Innovative Research Team in University |
PMID:21949842 | Academic Free License | nlx_155936 | http://www.nitrc.org/projects/rest | SCR_009641 | Resting-State fMRI Data Analysis Toolkit, REsting State fMRI Data analysis Toolkit | 2026-02-12 09:45:08 | 866 | ||||
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m6ASNP: Annotation of genetic variants by m6A function Resource Report Resource Website 1+ mentions |
m6ASNP: Annotation of genetic variants by m6A function (RRID:SCR_016048) | software resource, data access protocol, web service, software application, data analysis software, data processing software, data visualization software | Web server implemented in JAVA and PHP for annotating genetic variants by m6A function. It predicts and annotates N6-methyladenosine (m6A) alterations from genetic variants data such as germline SNPs or cancer somatic mutations. It employs two accurate prediction models for human and mouse using Random Forest algorithm. It conducts a statistical analysis for all the predicted m6A alterations. Provides statistical diagrams and a genome browser to visualize the topology characteristics of predicted m6A alterations. | N6-methyladenosine (m6A), variant annotation, effect prediction, random forest, miclip, m6a, mutant | National Key Research and Development Program 2017YFA0106700; National Natural Science Foundation of China 31771462; China Postdoctoral Science Foundation 2017M622864; Fundamental Research Funds for the Central Universities No. 17lgpy106; Guangdong Natural Science Foundation 2014TQ01R387 |
PMID:29617790 DOI:10.1093/gigascience/giy035 |
Free, Available for download, Freely available | https://github.com/RenLabBioinformatics/m6ASNP | SCR_016048 | m6ASNP | 2026-02-12 09:46:23 | 3 | |||||||
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clusterProfiler Resource Report Resource Website 10000+ mentions |
clusterProfiler (RRID:SCR_016884) | software resource, software application, data analysis software, data processing software, data visualization software | Software R package for statistical analysis and visualization of functional profiles for genes and gene clusters. | data, statistical, analysis, visualization, gene, cluster, bio.tools |
is listed by: Bioconductor is listed by: Debian is listed by: bio.tools is related to: R Project for Statistical Computing |
National 973 Projects of China ; 2007 Chang-Jiang Scholars Program ; National Natural Science Foundation of China ; Guangdong Natural Science Research Grant ; Fundamental Research Funds for the Central Universities |
PMID:22455463 | Free, Available for download, Freely available | biotools:clusterprofiler | https://github.com/GuangchuangYu/clusterProfiler https://guangchuangyu.github.io/software/clusterProfiler/ https://bio.tools/clusterprofiler |
SCR_016884 | Cluster Profiler | 2026-02-12 09:46:57 | 10762 | |||||
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BinPacker Resource Report Resource Website 10+ mentions |
BinPacker (RRID:SCR_017038) | software resource, software application, data analysis software, data processing software | Software tool as de novo trascriptome assembler for RNA-Seq data. Used to assemble full length transcripts by remodeling problem as tracking set of trajectories of items over splicing graph. Input RNA-Seq reads in fasta or fastq format, and ouput all assembled candidate transcripts in fasta format. Operating system Unix/Linux. | de novo, transcriptome, assembler, RNAseq, data, full, length, transcript, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
National Natural Science Foundation of China ; NSF 1553680; NCRR P20 RR01 6460; NIGMS P20 GM103429 |
PMID:26894997 | Free, Available for download, Freely available | OMICS_11199, biotools:binpacker | http://sourceforge.net/projects/transcriptomeassembly/files/BinPacker_1.0.tar.gz/download http://sourceforge.net/projects/transcriptomeassembly/files/BinPacker_binary.tar.gz/download https://bio.tools/binpacker |
SCR_017038 | 2026-02-12 09:46:28 | 10 | ||||||
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funRiceGenes Resource Report Resource Website 10+ mentions |
funRiceGenes (RRID:SCR_015778) | data or information resource, database, data set | Dataset of functionally characterized rice genes and members of different gene families. The dataset was created by integrating data from available databases and reviewing publications of rice functional genomic studies. | rice, functional genomics, interaction network, genetic improvement, gene, data integration | National Key Research and Development Program of China 2016YFD0100903; National Natural Science Foundation of China 31771873 and National Natural Science Foundation of China; Outstanding Young Talents Program |
Freely available, Public, Available for download, Free | https://github.com/venyao/RICENCODE http://funricegenes.ncpgr.cn/ |
SCR_015778 | RICENCODE | 2026-02-12 09:46:37 | 44 | ||||||||
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PhaSeDis Resource Report Resource Website 1+ mentions |
PhaSeDis (RRID:SCR_024963) | data or information resource, database | Manually curated database of relations between phase separation and diseases. | Manually curated database, relations between phase separation and diseases, | National Key Research and Development Program of China ; National Natural Science Foundation of China |
PMID:33126250 | Free, Freely available | SCR_024963 | MloDisDB | 2026-02-11 11:00:52 | 4 |
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