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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
CARD Resource Report Resource Website 10+ mentions |
CARD (RRID:SCR_016602) | CARD | data analysis service, analysis service resource, web application, database, software resource, production service resource, service resource, data or information resource | Web application for integrated analysis and interactive visualization of RNA interference (RNAi) screening data. | integrated, analysis, interactive, visualization, RNA, interfernce, screening, data, bio.tools |
is listed by: bio.tools is listed by: Debian |
Australian Cancer Research Foundation ; Victorian Department of Industry ; Innovation and Regional Development ; Australian Government’s Education Investment Fund ; Australasian Genomics Technologies Association ; Brockhoff Foundation ; Peter MacCallum Cancer Centre Foundation |
PMID:26902267 | Free, Freely available | biotools:CARD | https://bio.tools/CARD | SCR_016602 | CARD, Comprehensive Analysis of RNAi-screen Data | 2026-02-16 09:49:04 | 20 | ||||
|
Splicing Express Resource Report Resource Website 1+ mentions |
Splicing Express (RRID:SCR_016498) | software application, data processing software, data visualization software, data analysis software, software resource | Software suite for Alternative Splicing Events (ASEs) analysis from transcriptome sequencing data in any transcriptome. Used for identification, annotation and visualization. Written in Perl and suitable to run only in UNIX-like systems. | alternative, splicing, analysis, next, generation, sequencing, data, transcriptome, identify, annotate, visualize, Perl, UNIX, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:26618088 | Free, Available for download, Freely available | biotools:splicing_express | https://bio.tools/splicing_express | SCR_016498 | 2026-02-16 09:49:02 | 3 | |||||||
|
Agilent MassHunter WorkStation - Qualitative Analysis for GC/MS Resource Report Resource Website 500+ mentions |
Agilent MassHunter WorkStation - Qualitative Analysis for GC/MS (RRID:SCR_016657) | software application, data processing software, software toolkit, data analytics software, data analysis software, software resource, data acquisition software | Software tools for compound-centric data mining and navigation. Used to identify compounds in overlapping and co-eluting peaks with feature extraction and correlation algorithms for chromatographic separation. Used for separating true signals from noise. | compound, centric, data, mining, navigation, chromatic, separation, coeluting, peak, signal, noise, mass, spectrometry, analysis, qualitative |
is listed by: OMICtools is related to: Agilent Masshunter Quantitative Analysis software has parent organization: Agilent Technologies |
SCR_016657 | 2026-02-16 09:49:04 | 733 | |||||||||||
|
SARTools Resource Report Resource Website 100+ mentions |
SARTools (RRID:SCR_016533) | software application, data processing software, software toolkit, data analysis software, software resource | Software package as a DESeq2- and EdgeR-Based R Pipeline for Comprehensive Differential Analysis of RNA-Seq Data. | R package, DESeq2, EdgeR, comprehensive, analysis, RNAseq, data, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: DESeq2 is related to: edgeR has parent organization: Pasteur Institute |
the France Génomique National Infrastructure | PMID:27280887 | Free, Available for download, Freely available | biotools:sartools | https://bio.tools/sartools | SCR_016533 | 2026-02-16 09:49:03 | 136 | ||||||
|
VisR Resource Report Resource Website 1+ mentions |
VisR (RRID:SCR_016658) | VisR | software application, data processing software, software toolkit, data visualization software, data analysis software, software resource | Software as an R-based visual framework for analysis of sequencing datasets. Provides a framework for integrative and interactive analyses. | visual, framework, analysis, sequencing, data, dataset, integrative, interactive, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Bioconductor |
Michael Smith Foundation for Health Research ; Canadian Institutes of Health Research (CIHR) and Genome BC ; NSERC PGS-D |
PMID:26328469 | Free, Available for download, Freely available | biotools:VisR | https://bio.tools/VisR | SCR_016658 | VisRseq, VisR | 2026-02-16 09:49:04 | 5 | ||||
|
IndelGenotyper Resource Report Resource Website 50+ mentions |
IndelGenotyper (RRID:SCR_016663) | GATK | software application, data processing software, sequence analysis software, data analysis software, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 18th,2023. Software package for genome analysis. Used for analysis of next generation genomic data in cancer. | next, generation, analysis, genomic, data, cancer, genome |
is listed by: Debian has parent organization: Broad Institute |
THIS RESOURCE IS NO LONGER IN SERVICE | https://github.com/broadinstitute/gatk/ https://sources.debian.org/src/gatk/ |
SCR_016663 | GATK Indel Genotyper, Genome Analysis Toolkit (GATK) Indel Genotyper, Indel Genotyper, GATK IndelGenotyper | 2026-02-16 09:49:05 | 63 | |||||||
|
Sequenza Resource Report Resource Website 50+ mentions |
Sequenza (RRID:SCR_016662) | software application, data processing software, data visualization software, data analysis software, software resource | Software package for copy number estimation from tumor genome sequencing data.Tools to analyze genomic sequencing data from paired normal-tumor samples, including cellularity and ploidy estimation; mutation and copy number (allele-specific and total copy number) detection, quantification and visualization. | estimate, copy, number, tumor, genome, sequencing, data, cellularity, ploidy, alteration, cancer, mutation, detection, quantification, visualization |
is listed by: CRAN has parent organization: Technical University of Denmark; Lyngby; Denmark |
European Commission 7th Framework Programme ; Danish Council for Independent Research ; Breast Cancer Research Foundation |
PMID:25319062 | https://cran.r-project.org/web/packages/sequenza/ | SCR_016662 | 2026-02-16 09:49:05 | 54 | ||||||||
|
PiGx Resource Report Resource Website 1+ mentions |
PiGx (RRID:SCR_016476) | PiGx | software application, data processing software, software toolkit, sequence analysis software, data analysis software, software resource | Software application as a collection of genomic pipelines used for raw fastq read data of bisulfite experiments, RNAseq samples, single cell dropseq analysis, reads from ChIPseq experiments, analysis of sequence mutations in CRISPR-CAS9 targeted amplicon sequencing data. | collection, genomic, pipeline, bisulfite, sequencing, rnaseq, chipseq, single, cell, reproducibility, sample, analysis, mutation, data | German Federal Ministry of Education and Research (BMBF) 031 A538C RBC (de.NBI); European Union Horizon 2020 No 654248 |
Free, Available for download, Freely available | https://github.com/BIMSBbioinfo/pigx | SCR_016476 | Pipelines in Genomics | 2026-02-16 09:49:02 | 6 | |||||||
|
biobakery Resource Report Resource Website 10+ mentions |
biobakery (RRID:SCR_016596) | software application, data processing software, software toolkit, data analysis software, software resource | Analysis environment and collection of individual software tools to process raw shotgun metagenome or metatranscriptome sequencing data for quantitative microbial community profiling. Used for a metaomics data analysis., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | Huttenhower lab, metaomics, data, analysis, process, raw, shotgun, metagenome, metatranscriptome, sequencing, microbial, profiling, bio.tools |
is used by: Nephele is listed by: Debian is listed by: bio.tools is related to: Human Microbiome Project has parent organization: Harvard University; Cambridge; United States |
NIDDK U54 DE023798; Sloan Foundation 4406J0B; NHGRI R01 HG005220; NSF DBI1053486; NHGRI R01 HG005969; ARO W911NF1110473 |
PMID:29194469 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:biobakery | http://huttenhower.sph.harvard.edu/biobakery https://bio.tools/biobakery |
SCR_016596 | bioBakery, biobakery | 2026-02-16 09:49:04 | 13 | |||||
|
Unpaywall Resource Report Resource Website 10+ mentions |
Unpaywall (RRID:SCR_016471) | web service, data access protocol, data repository, software resource, storage service resource, database, service resource, data or information resource | Database of free scholary articles. Content from over 50,000 publishers and repositories easy to find, track, and use. A website featuring web-based tools created and maintained by Impactstory, Inc. | Impactstory, data, scholary, research, articles, repository, find, track, use, open, reusable, non profit | Open source, Some features require purchase, Unpaywall and Impactstory Privacy Policy, Persons under the age of 13 are not permitted to use the Service | SCR_016471 | 2026-02-16 09:49:02 | 13 | |||||||||||
|
Transcriptome Analysis Console Resource Report Resource Website 10+ mentions |
Transcriptome Analysis Console (RRID:SCR_016519) | TAC | software application, data processing software, sequence analysis software, data analysis software, software resource | Software tool for microarray analysis designed for biologists . Used for identification of differential expression by providing interactive visualizations. | transcriptome, analysis, console, data, array, gene, visualization, identify | Commercially available | SCR_016519 | TAC:Transcriptome Analysis Console | 2026-02-16 09:49:03 | 19 | |||||||||
|
Entrez Resource Report Resource Website 10+ mentions |
Entrez (RRID:SCR_016640) | web service, data access protocol, software resource, portal, data or information resource | Web portal for global query cross database search and retrieval system that provides access to all databases simultaneously with a single query string and user interface. Retrieves nucleotide and protein sequence data, gene centered and genomic mapping information, 3D structures, and references. Covers databases including protein sequence data from PIR-International, PRF, Swiss-Prot, and PDB and nucleotide sequence data from GenBank that includes information from EMBL and DDBJ. | global, query, cross, database, search, retrival, system, database, nucleotide, protein, sequence, data, genomic, mapping, structure, reference |
is affiliated with: PubChem BioAssay is related to: National Library of Medicine has parent organization: NCBI works with: Batch Entrez works with: Biotite |
Free, Freely available | SCR_016640 | 2026-02-16 09:49:04 | 15 | ||||||||||
|
Viewbox4, Cephalometric software Resource Report Resource Website 1+ mentions |
Viewbox4, Cephalometric software (RRID:SCR_016481) | software application, data processing software, data analysis software, image analysis software, software resource | Software for cephalometric analysis. Customizable. Allows rendering, viewing and measuring of 3D data from CT scanners. Used in orthodontic departments for analysis of the dental and skeletal relationships of a human skull. | dHAL Software - The Company, cephalometric, analysis, rendering, viewing, measuring, data, CT scan, orthodontic, dental, skeletal, relationship, human, skull | Commercially available, Tutorial available | SCR_016481 | 2026-02-16 09:49:02 | 5 | |||||||||||
|
PhenoMeNal Resource Report Resource Website 1+ mentions |
PhenoMeNal (RRID:SCR_016605) | phnmnl, PhenoMeNal | web service, organization portal, data access protocol, software resource, consortium, portal, data or information resource | Cloud based standardised European e-infrastructure for metabolomics and phenomics data processing, analysis and information mining on public or private cloud providers. Used for large scale computing for medical metabolomics. | metabolomic, phenomic, data, processing, analysis, information, mining. medical, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: European Molecular Biology Laboratory has parent organization: European Bioinformatics Institute |
European Commission EC654241 | Free, Registration required, Tutorial available | biotools:PhenoMeNal | https://github.com/phnmnl https://bio.tools/PhenoMeNal |
SCR_016605 | Phenome and Metabolome aNalysis | 2026-02-16 09:49:04 | 2 | |||||
|
SPICE Resource Report Resource Website 50+ mentions |
SPICE (RRID:SCR_016603) | SPICE | software application, data processing software, data visualization software, data analysis software, software resource | Software application for data mining and visualization. Used for analyzes of large FLOWJO data sets from polychromatic flow cytometry and organizing the normalized data graphically. | data, mining, visualization, analysis, polychromatic, flow, cytometry, dataset, normalized, graphically, bio.tools |
is listed by: NIAID is listed by: Debian is listed by: bio.tools |
NIAID ; NIH |
PMID:21265010 | Free, Available for download, Freely available | biotools:spice | https://bio.tools/spice | SCR_016603 | Simplified Presentation of Incredibly Complex Evaluations | 2026-02-16 09:49:04 | 66 | ||||
|
National Sleep Research Resource (NSRR) Resource Report Resource Website 50+ mentions |
National Sleep Research Resource (NSRR) (RRID:SCR_016576) | NSRR | data or information resource, organization portal, portal | System for sharing sleep data. Organization portal that aggregates, harmonizes, and organizes sleep and clinical data from individuals studied as part of cohort studies or clinical trials and provides suite of tools to facilitate data exploration and data visualization. National Heart, Lung, and Blood Institute resource designed to provide big data resources to sleep research community. | sleep, clinical, data, cohort, study, trial, dataset, visualization, exploration |
is recommended by: National Library of Medicine lists: Apnea, Bariatric surgery, and CPAP study lists: Sleep Heart Health Study lists: Honolulu-Asia Aging Study of Sleep Apnea lists: Cleveland Family Study lists: Cleveland Children's Sleep and Health Study lists: Best Apnea Interventions for Research (BestAIR) sleep study |
sleep apnea | NHLBI | PMID:29860441 | Free, Freely available, Registration required for membership | https://sleepdata.org/share https://sleepdata.org/datasets |
SCR_016576 | National Sleep Research Resource | 2026-02-16 09:49:03 | 68 | ||||
|
Assemblosis Resource Report Resource Website 1+ mentions |
Assemblosis (RRID:SCR_016571) | software application, data processing software, narrative resource, workflow, training material, software resource, data or information resource | Software tool as a Common Workflow Language (CWL) based automated bioinformatics workflow to assemble haploid/diploid eukaryote genomes of non-model organisms using PacBio long-reads and Illumina short-reads. | common, workflow, language, automated, assemble, haploid, diploid, eukaryote, genome, longread, shortread, data | Free, Available for download, Freely available | SCR_016571 | 2026-02-16 09:49:03 | 1 | |||||||||||
|
NetCirChro Resource Report Resource Website |
NetCirChro (RRID:SCR_016616) | NetCirChro | software application, data processing software, data visualization software, data analysis software, software resource | Software interactive tool for visualizing and analyzing network data in the spatial context of the chromosome. Used to discover the role of gene organization in functional regulatory networks. Plugin enables users of Cytoscape to overlay networks onto a circular chromosomal map. | visualization, analyzing, network, data, gene, spatial, chromosome, circular, map |
is listed by: NIDDK Information Network (dkNET) has parent organization: NIAID works with: Cytoscape |
Free, Available for download, Freely available | SCR_016616 | Networks on Circular Chromosome | 2026-02-16 09:49:04 | 0 | ||||||||
|
Honolulu-Asia Aging Study of Sleep Apnea Resource Report Resource Website |
Honolulu-Asia Aging Study of Sleep Apnea (RRID:SCR_016587) | HAASSA | data or information resource, topical portal, disease-related portal, portal | Portal for sleep-disordered breathing (SDB) in an elderly cohort of Japanese-American men under surveillance for Alzheimer disease (AD) and other dementias. Data to assess relationships between SDB and cognitive performance in late life. | data, polysomnography, aging, sleep, disordered, breathing, elderly, Japanese-American, men, Alzheimer | is listed by: National Sleep Research Resource (NSRR) | sleep disorder | PMID:12938814 | Permission required | SCR_016587 | Honolulu Asia Aging Study of Sleep Apnea | 2026-02-16 09:49:03 | 0 | ||||||
|
Metascape Resource Report Resource Website 1000+ mentions |
Metascape (RRID:SCR_016620) | web service, data analysis service, analysis service resource, data access protocol, software resource, production service resource, service resource | Web service to analyze gene or protein lists. Provides automated meta analysis tools to understand pathways within a group of orthogonal target-discovery studies. | analyze, gene, protein, list, data, annotate, resource, bio.tools |
is listed by: Debian is listed by: bio.tools |
Free, Freely available | biotools:Metascape | https://bio.tools/Metascape | SCR_016620 | 2026-02-16 09:49:04 | 3483 |
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