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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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CAIRN Resource Report Resource Website |
CAIRN (RRID:SCR_019101) | data visualization software, web service, data processing software, software application, data access protocol, software resource | Web tool to graph all copy number alterations present in segment file. Custom data is permitted. Allows to display copy number alterations which overlap user specified region, to quantify number of amplified CNAs and deleted CNAs. Visualization tool to explore copy number alterations discovered in published cancer datasets. Intended to help oncology community observe of relative rates of amplification, deletion, and mutation of interesting genes and regions. | Deleted CNAs quantification, Copy Number Alterations, segment file, data visualization, published cancer datasets CNAs, amplified CNA quantification | Nine Girls Ask Foundation ; NCI CA207729; NIGMS GM132055; NCI CA107263; NCI CA177519; NCI CA102310; NIA AG033082; NCI P30 CA138313 |
PMID:31923184 | Free, Available for download, Freely available | https://github.com/jrdelaney/CAIRN | SCR_019101 | Copy Alterations Intuitive Rendering Navigator | 2026-02-13 10:58:24 | 0 | |||||||
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iTools Resource Report Resource Website 10+ mentions |
iTools (RRID:SCR_009626) | iTools | data repository, storage service resource, web service, software repository, data or information resource, service resource, data access protocol, software resource, database | An infrastructure for managing of diverse computational biology resources - data, software tools and web-services. The iTools design, implementation and meta-data content reflect the broad NCBC needs and expertise (www.NCBCs.org). | computational neuroscience, data, experiment control, hardware, imaging genomics, information specification, java, loni pipeline, model, ontology, os independent, metadata |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: National Centers for Biomedical Computing has parent organization: Laboratory of Neuro Imaging |
NIH Roadmap for Medical Research ; NCRR U54-RR021813; NIDA U54-DA021519; NCI U54-CA121852; NHGRI U54-HG004028; NIGMS U54-GM072970; NIBIB U54-EB005149; NLM U54-LM008748 |
PMID:18509477 | GNU Lesser General Public License | nlx_155852 | http://www.nitrc.org/projects/itools http://www.loni.usc.edu/research/software |
http://itools.loni.ucla.edu/ | SCR_009626 | ITools Resourceome, NCBC iTools | 2026-02-13 10:56:28 | 45 | |||
|
HOMER Resource Report Resource Website 5000+ mentions |
HOMER (RRID:SCR_010881) | HOMER | sequence analysis software, data processing software, data analysis software, software application, software resource | Software tools for Motif Discovery and next-gen sequencing analysis. Used for analyzing ChIP-Seq, GRO-Seq, RNA-Seq, DNase-Seq, Hi-C and numerous other types of functional genomics sequencing data sets. Collection of command line programs for unix style operating systems written in Perl and C++. | motif, discovery, next, generation, sequencing, analysis, genomic, data |
is listed by: OMICtools is related to: findMotif.pl has parent organization: University of California at San Diego; California; USA |
NURSA consortium grant ; NIH HC088093; NIDDK DK063491; NCI CA52599; NIGMS P50 GM081892; Foundation Leducq Transatlantic Network Grant |
PMID:20513432 | OMICS_00483 | http://biowhat.ucsd.edu/homer/index.html | SCR_010881 | HOMER, Hypergeometric Optimization of Motif EnRichment, Homer, Homer v4.5 | 2026-02-13 10:56:42 | 5370 | |||||
|
SnapATAC Resource Report Resource Website 10+ mentions |
SnapATAC (RRID:SCR_020981) | data processing software, data analysis software, software toolkit, software application, software resource | Software package for analyzing scATAC-seq datasets.Used to dissects cellular heterogeneity in unbiased manner and map trajectories of cellular states. Can process data from up to million cells. Incorporates existing tools into comprehensive package for analyzing single cell ATAC-seq dataset. | scATAC-seq datasets analysis, dissects cellular heterogeneity, cellular states, map trajectories | NCI K99 CA252020; UCSD School of Medicine ; NIMH U19 MH114831 |
PMID:33637727 | Free, Available for download, Freely available | https://github.com/r3fang/SnapATAC | SCR_020981 | Single Nucleus Analysis Pipeline for ATAC-seq | 2026-02-13 10:58:26 | 22 | |||||||
|
Exemplar Microscopy Images of Tissues Resource Report Resource Website 1+ mentions |
Exemplar Microscopy Images of Tissues (RRID:SCR_021052) | EMIT | immuno detection protocol, experimental protocol, data repository, storage service resource, 2d spatial image, image collection, data set, data or information resource, immunofluorescence, service resource, image, image repository, narrative resource | Reference dataset of multiplexed immunofluorescence microscopy images collected at HMS Laboratory of Systems Pharmacology. Includes set of images of different types for development and benchmarking of computational methods for image processing. As of 4/2/2021, EMIT comprises tissue microarray containing cores from 34 cancer, non-neoplastic diseases, and normal tissue collected from clinical discards under IRB supervised protocol. TMA was imaged using cyclic immunofluorescence method. Additional extensions of EMIT are currently in the planning stages. Long term goal is to compose ImageNet like resource for highly multiplexed images of tissues and tumors by consolidating high quality curated datasets. | Reference dataset, multiplexed immunofluorescence microscopy images, tissue microarray, cyclic immunofluorescence, tissues images, tumors images |
is related to: Synapse is related to: Harvard Medical School; Massachusetts; USA |
glioblastoma, lung adenocarcinoma, prostate adenocarcinoma, seminoma, meningioma, mesothelioma, GI stromal tumor, liver cirrhosis, leiomyosarcoma, high-grade serous ovarian cancer, diverticulitis, acute appendicitis, metastatic melanoma, dedifferentiated liposarcoma | NIH U54 CA225088; NCI U2C CA233262; NCI U2C CA233280; Ludwig Center at Harvard Medical School and the Ludwig Cancer Research Foundation |
DOI:10.1101/2021.03.15.435473 | Restricted | SCR_021052 | Exemplar Microscopy Images of Tissues ( and Tumors) | 2026-02-13 10:58:27 | 3 | |||||
|
CNVpytor Resource Report Resource Website 10+ mentions |
CNVpytor (RRID:SCR_021627) | sequence analysis software, data processing software, data analysis software, software application, software resource | Software Python package and command line tool for CNV/CNA analysis from depth of coverage by mapped reads. Software tool for CNV/CNA detection and analysis from read depth and allele imbalance in whole genome sequencing. | Copy number variations, copy number alternations, whole genome sequencing, Python | has parent organization: Mayo Clinic | NCI U24 CA220242 | DOI:10.1101/2021.01.27.428472 | Free, Available for download, Freely available | SCR_021627 | 2026-02-13 10:58:36 | 19 | ||||||||
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VAMPIRE Resource Report Resource Website 1+ mentions |
VAMPIRE (RRID:SCR_021721) | data processing software, data analysis software, software application, software resource, image analysis software | Software tool for analysis of cell and nuclear morphology from fluorescence or bright field images. Enables profiling and classification of cells into shape modes based on equidistant points along cell and nuclear contours. Robust method to quantify cell morphological heterogeneity. | cell morphology analysis, nuclear morphology analysis, fluorescence images, bright field images | NCI U54 CA143868; NCI R01 CA174388; NIA P30 AG021334; NIA U01 AG060903 |
DOI:10.1038/s41596-020-00432-x | Free, Available for download, Freely available | SCR_021721 | Visually Aided Morpho-Phenotyping Image Recognition | 2026-02-13 10:58:34 | 2 | ||||||||
|
Cumulus Resource Report Resource Website 1+ mentions |
Cumulus (RRID:SCR_021644) | data analysis software, software resource, data processing software, software application | Software tool as cloud based single cell genomics and spatial transcriptomics data analysis framework that is scalable to massive amounts of data and able to process variety of data types. Consists of cloud analysis workflow, Python analysis package and visualization application. Supports analysis of single-cell RNA-seq, CITE-seq, Perturb-seq, single-cell ATAC-seq, single-cell immune repertoire and spatial transcriptomics data. | Single cell genomics, spatial transcriptomics, single-cell RNA-seq, CITE-seq, Perturb-seq, single-cell ATAC-seq, single-cell immune repertoire, data |
uses: Pegasus uses: Cirrocumulus uses: Pegasus-fus is listed by: Terra is related to: BICCN has parent organization: Broad Institute |
Klarman Cell Observatory ; Manton Foundation ; HHMI ; Ludwig Center at MIT ; Leidos Biomedical Research ; Frederick National Laboratory for Cancer Research ; NCI |
DOI:10.1038/s41592-020-0905-x | Free, Available for download, Freely available | https://app.terra.bio/#workspaces/kco-tech/Cumulus https://github.com/klarman-cell-observatory/cumulus/blob/91336094646217564a4f8e7b31c03c3c6bf2e84b/docs/index.rst |
SCR_021644 | 2026-02-13 10:58:34 | 2 | |||||||
|
Motif Mutation Analysis for Regulatory Genomic Elements Resource Report Resource Website 500+ mentions |
Motif Mutation Analysis for Regulatory Genomic Elements (RRID:SCR_021902) | MMARGE | data processing software, data analysis software, software toolkit, software application, software resource | Software package that integrates genome wide genetic variation with epigenetic data to identify collaborative transcription factor pairs. Optimized to work with chromatin accessibility assays such as ATAC-seq or DNase I hypersensitivity, as well as transcription factor binding data collected by ChIP-seq. Used to identify combinations of cell type specific transcription factors while simultaneously interpreting functional effects of non-coding genetic variation. | genome wide genetic variation, epigenetic data, identify collaborative transcription factor pairs, interpreting functional effects, non-coding genetic variation | NCI CA173903; NIGMS GM085764; NIDDK DK091183; NHLBI R00 123485 |
PMID:29893919 | Free, Available for download, Freely available | SCR_021902 | 2026-02-13 10:58:40 | 608 | ||||||||
|
tximport Resource Report Resource Website 50+ mentions |
tximport (RRID:SCR_016752) | data analysis software, software resource, data processing software, software application | Software R package for importing pseudoaligned reads into R for use with downstream differential expression analysis. Used for import and summarize transcript level estimates for transcript and gene level analysis. | pseudoaligned, reads, R, differential, expression, analysis, gene, transcript, bio.tools |
is listed by: Bioconductor is listed by: Debian is listed by: bio.tools works with: edgeR works with: DESeq2 |
SNSF 143883; European Commission ; NCI T32 CA009337 |
DOI:10.12688/f1000research.7563.1 | Free, Available for download, Freely available | biotools:tximport | https://bioconductor.org/packages/tximport/ https://bioconductor.org/packages/devel/bioc/vignettes/tximport/inst/doc/tximport.html https://github.com/F1000Research/tximport https://bio.tools/tximport |
https://zenodo.org/record/35123#.W_w3behKiM8 | SCR_016752 | tximport v1.4.0 | 2026-02-13 10:57:50 | 91 | ||||
|
Polysolver Resource Report Resource Website 10+ mentions |
Polysolver (RRID:SCR_022278) | data analysis software, software resource, data processing software, software application | Software tool for HLA typing based on whole exome sequencing data and infers alleles for three major MHC class I genes. Enables accurate inference of germline alleles of class I HLA-A, B and C genes and subsequent detection of mutations in these genes using inferred alleles as reference. | HLA typing, whole exome sequencing data, accurate inference of germline alleles, high precision HLA-typing, alleles of class I HLA-A, B and C genes, detection of mutations, inferred alleles | has parent organization: Broad Institute | Blavatnik Family Foundation ; NHLBI 1RO1HL103532; NCI 1R01CA155010; AACR |
PMID:26372948 | Free, Available for download, Freely available | SCR_022278 | POLYmorphic loci reSOLVER, POLYSOLVER | 2026-02-13 10:58:40 | 30 | |||||||
|
CytoTRACE Resource Report Resource Website 100+ mentions |
CytoTRACE (RRID:SCR_022828) | software resource, simulation software, software application | Software tool that predicts differentiation state of cells from single cell RNA sequencing data. Used for predicting differentiation states from scRNA-seq data. | differentiation state of cells, single cell RNA sequencing data, predicting differentiation states, scRNA-seq data | NCI R00CA187192; NCI R01CA100225; Stinehart Reed foundation ; Stanford Bio-X Interdisciplinary Initiatives Seed Grants Program ; Virginia and D.K. Ludwig Fund for Cancer Research ; U.S. Department of Defense ; National Science Foundation Graduate Research Fellowship ; Stanford Bio-X Bowes Graduate Student Fellowship ; Stanford Medical Science Training Program |
PMID:31974247 | Free, Freely available | SCR_022828 | Cellular (Cyto) Trajectory Reconstruction Analysis using gene Counts and Expression | 2026-02-13 10:58:49 | 132 | ||||||||
|
SvABA Resource Report Resource Website 10+ mentions |
SvABA (RRID:SCR_022998) | sequence analysis software, data processing software, data analysis software, software application, software resource | Software tool for detecting structural variants in sequencing data using genome wide local assembly. Genome wide detection of structural variants and indels by local assembly. Used for detecting SVs from short read sequencing data using genome wide local assembly with low memory and computing requirements. | genome wide detection, structural variants, indels, local assembly | NHGRI T32 HG002295; NCI U54CA143798; NCI R01CA188228; DFCI-Novartis Drug Discovery Program ; Voices Against Brain Cancer ; Pediatric Low-Grade Astrocytoma Foundation ; Broad Institute ; Wellcome Fund Career Award for Medical Scientists |
PMID:29535149 | Free, Available for download, Freely available | SCR_022998 | 2026-02-13 10:58:58 | 14 | |||||||||
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Adenoma Polyp Tissue Bank Resource Report Resource Website |
Adenoma Polyp Tissue Bank (RRID:SCR_005366) | APTB | biomaterial supply resource, material resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 29, 2016. The Adenoma Polyp Tissue Bank (APTB) receives whole blood from patients enrolled in the Prevention of Sporadic Colorectal Adenomas with Celecoxib clinical trial. We have reached our accrual on blood submissions, so we will no longer be receiving blood specimens The objectives of this trial are as follows: A. To determine the efficacy and safety of celecoxib versus placebo in preventing the occurrence of newly detected colorectal adenomas in subjects at increased risk for colorectal carcinoma. In addition to incidence, other established risk factors will be evaluated for their association with occurrence of new colorectal adenomas, including cancer family history and adenoma size, histopathologic grade, multiplicity and location. Primary assessment of treatment efficacy will be the reduction in the number of subjects with adenomas at colonoscopy after Year 1 and Year 3 of study drug use. Secondary assessments of treatment efficacy will be 1) the number of adenomas 2) the histopathologic grade of adenomas and 3) the size of adenomas, also measured after one year and three years of study drug use. These factors will be incorporated into a risk model for predicting adenoma occurrence and response to celecoxib. B. To determine the efficacy of celecoxib versus placebo in modulating one or more of a panel of biomarkers for colorectal cancer at the cellular and molecular level sampled in a subset of subjects at selective sites at baseline and after Year 1 and Year 3 of study drug use. These biomarkers will include measurements of aberrant crypt foci (ACF), proliferation (index and crypt distribution), apoptosis (index and crypt distribution), COX expression and activity. If modulation of one or more mucosal biomarkers occur, we will explore whether it correlates with the development of incident colorectal neoplasia (adenomas/carcinomas), thereby attempting to validate the surrogacy of that biomarker. C. To develop a specimen bank. Serum and white blood cells are isolated from whole blood and adenoma tissue blocks and slides are banked. Banked specimens will become available for use in correlative science studies at a later point. This project began in 1999 and will be extended through 2006. The lead principal investigator is Monica M. Bertagnolli, MD, Brigham and Women''s Hospital, Boston, MA, and the APTB Director is Scott Jewell, Ph.D., Department of Pathology, The Ohio State University. The APTB is supported by the NIH, NCI Division of Cancer Prevention, in connection with the Strang Cancer Prevention Center, Cornell University, New York., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | blood, serum, white blood cell, adenoma tissue, tissue, whole blood, block, slide, colorectal adenoma, celecoxib, adenoma, cancer, colorectal cancer, clinical trial, polyp, risk factor |
is listed by: One Mind Biospecimen Bank Listing has parent organization: Human Tissue Resource Network has parent organization: Human Tissue Resource Network |
Increased risk for colorectal carcinoma | NCI | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_144435 | SCR_005366 | APTB Specimen Bank | 2026-02-13 10:55:37 | 0 | |||||
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North Carolina University at Chapel Hill School of Medicine High Throughput Peptide Synthesis and Array Core Facility Resource Report Resource Website 1+ mentions |
North Carolina University at Chapel Hill School of Medicine High Throughput Peptide Synthesis and Array Core Facility (RRID:SCR_017837) | core facility, access service resource, service resource | Core offers services for: High quality synthetic peptides, stable isotope labeled peptides, peptides with PTM and fluorescent and affinity tags, synthesis of peptide libraries. Analysis of synthetic peptides. Purification, lyophilization and aliquoting of synthetic peptides. | Synthetic, peptide, stable, isotope, labeled, library, analysis, purification, lyophilization, aliquoting, service, core, ABRF | is listed by: ABRF CoreMarketplace | NCI P30 CA016086 | Open | ABRF_626 | SCR_017837 | UNC High-Throughput Peptide Synthesis and Array Facility | 2026-02-13 10:58:05 | 6 | |||||||
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North Carolina University at Chapel Hill School of Medicine Macromolecular X-Ray Crystallography Core Facility Resource Report Resource Website |
North Carolina University at Chapel Hill School of Medicine Macromolecular X-Ray Crystallography Core Facility (RRID:SCR_017839) | MX Facility | core facility, access service resource, service resource | Core provides support and infrastructure necessary to initiate and successfully complete structural biology or structural chemistry project. Offers services in Crystallization,X-Ray DiffractionData Collection,Structure Determination and Refinement. | Structural, biology, chemistry, X-ray, crystallography, diffraction, data, collection, refinement, service, core, ABRF | is listed by: ABRF CoreMarketplace | NCI P30 CA016086 | Open | ABRF_629 | SCR_017839 | Macromolecular X-Ray Crystallography | 2026-02-13 10:58:03 | 0 | ||||||
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New York University School of Medicine Langone Cytometry and Cell Sorting Core Facility Resource Report Resource Website |
New York University School of Medicine Langone Cytometry and Cell Sorting Core Facility (RRID:SCR_018827) | core facility, access service resource, service resource | Facility provides cytometry and cell sorting services. Services include immunophenotyping, cell cycle analysis, and intracellular fluorophore detection. Services can be tailored to research needs, certified cytometrists are available to help plan experiments. Offers online and hands-on training in use of cell analyzers and analysis software. | USEDit, flow cytometry service, cell sorting service, immunophenotyping, cell cycle analysis, intracellular fluorophore detection, , ABRF, ABRF |
is listed by: ABRF CoreMarketplace is related to: USEDit has parent organization: New York University; New York; USA |
NCI P30 CA016087 | Open | ABRF_762 | https://coremarketplace.org/?FacilityID=762 | SCR_018827 | New York University Cytometry and Cell Sorting Laboratory, Cytometry and Cell Sorting Laboratory | 2026-02-13 10:58:18 | 0 | ||||||
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Northwestern University Developmental Therapeutics Core Facility Resource Report Resource Website 1+ mentions |
Northwestern University Developmental Therapeutics Core Facility (RRID:SCR_017948) | DTC | core facility, access service resource, service resource | Core evaluates therapeutic agents and diagnostics, as well as existing therapeutics being considered for novel uses, through continued development and deployment of relevant animal models and in vitro cell lines and tissue models. Provides services to investigators to suit many needs, including those who may lack laboratory facilities and/or expertise for conducting experiments associated with preclinical therapeutic hypothesis testing.Services include Proliferation and Apoptosis Assays, Therapy-Response Experiments, Exploratory PK and Tox, Device Implantation and Monitoring,PDX Models,Immunization. | Evaluate, therapeutic, agent, diagnostic, novel, animal, model, development, in vitro, cell, line, tissue, testing, proliferation, apoptosis, assay, therapy, response, immunization, service, core, ABRF |
is listed by: ABRF CoreMarketplace has parent organization: Northwestern University; Illinois; USA |
NCI CA060553 | Open | ABRF_947 | https://coremarketplace.org/?FacilityID=947&citation=1 | https://cdt.northwestern.edu/core-services/ | SCR_017948 | Developmental Therapeutics Core | 2026-02-13 10:58:05 | 3 | ||||
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Northwestern University Proteomics Core Facility Resource Report Resource Website 1+ mentions |
Northwestern University Proteomics Core Facility (RRID:SCR_017945) | core facility, access service resource, service resource | Core offers multiple types of experiments from simple protein identification to protein quantitation. Performs traditional bottom-up proteomics, where proteins are digested with enzyme prior to analysis and intact, top-down proteomics analyses. Services include proteins identification after in-gel or in-solution digestion, top-down mass spectrometry to preserve post-translationally modified forms of proteins present in vivo by measuring them intact, IP-MS Pulldown,BioID service to identify target of biotin ligase that has been tagged onto their protein via traditional cloning methods,Untargeted Quantitative Peptide Proteomics,Targeted Quantitative Peptide Proteomics,Epiproteomic Histone Modification Panel A,Epiproteomic Histone Modification Panel B,Untargeted Metabolomics,Phosphoproteomics,PTM Scan,ChIP-MS. | Protein, indentification, quantitation, proteomics, analysis, enzyme, digestion, mass, spectrometry, peptide, targeted, epiproteomic, histone, modification, untargeted, phosphoproteomics, PTM Scan, ChIP-MS, service, core, ABRF |
is listed by: ABRF CoreMarketplace is related to: USEDit has parent organization: Northwestern University; Illinois; USA |
NCI P30 CA060553; NIH Office of the Director S10 OD025194; NIGMS P41 GM108569 |
Open | SCR_017880, ABRF_944 | https://coremarketplace.org/?FacilityID=944 | https://coremarketplace.org/?FacilityID=738 | SCR_017945 | Northwestern Proteomics, Northwestern University Proteomics Center of Excellence Core Facility | 2026-02-13 10:58:05 | 5 | |||||
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University of Wisconsin-Madison Advanced Genome Editing Laboratory Resource Report Resource Website 1+ mentions |
University of Wisconsin-Madison Advanced Genome Editing Laboratory (RRID:SCR_021070) | AGEL | core facility, access service resource, service resource | Provides services and expertise to unlock genome editing tools to advance your research. Routinely generates new genome edited models, particularly mouse, rats, swine, and cell lines, as well as supports in vivo editing, novel preclinical therapeutic strategies, pooled lentiCRISPR screening, and other applications. | USEDit, generating genome edited models, mouse, rats, swine, ABRF, ABRF, CRISPR, gene editing, genome editing, lentiCRISPR |
is listed by: ABRF CoreMarketplace has parent organization: University of Wisconsin-Madison; Wisconsin; USA |
NCI P30 CA014520 | ABRF_1148 | https://coremarketplace.org/?FacilityID=1148 | SCR_021070 | University of Wisconsin Madison UW-Genome Editing & Animal Models, UW-Genome Editing & Animal Models, University of Wisconsin Madison Advanced Genome Editing Laboratory, UW Biotechnology Center Advanced Genome Editing Laboratory, Genome Editing and Animal Models Core, University of Wisconsin Madison Genome Editing Core Facility, Transgenic Animal Facility | 2026-02-13 10:58:27 | 9 |
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