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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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VAMPS Resource Report Resource Website 10+ mentions |
VAMPS (RRID:SCR_004483) | VAMPS | analysis service resource, data analysis service, data or information resource, data repository, database, production service resource, service resource, storage service resource | A publicly-accessible website to measure and visualize similarities and differences between molecular profiles of complex microbial communities. The project includes visualization tools such as heat maps that simultaneously compare the taxonomic distributions of multiple datasets and 3-D charts of the frequency distributions of 16S rRNA tags. Analytical tools include Chao diversity estimates and rarefaction curves. As a service to the community, researchers have the opportunity to upload their own data to the site for private viewing with the full range of data and analysis tools. Public data can be downloaded for further analysis locally. |
is listed by: OMICtools has parent organization: Marine Biological Laboratory |
Alfred P. Sloan Foundation ; NSF ; NASA Astrobiology Institute |
PMID:24499292 | Public, The community can contribute to this resource | OMICS_01501 | SCR_004483 | SciCrunch Registry | VAMPS Project, Visualization and Analysis of Microbial Population Structure | 2026-09-26 02:13:42 | 28 | ||||||
|
Mercury Resource Report Resource Website 500+ mentions |
Mercury (RRID:SCR_004231) | Mercury | software resource | An automated, flexible, and extensible analysis workflow that provides accurate and reproducible genomic results at scales ranging from individuals to large cohorts. The analysis pipeline is deployed in local hardware and the Amazon Web Services cloud via the DNAnexus platform. | next-generation sequencing, genome, cloud, exome, cloud computing, illumina, bam, variant call file |
is listed by: OMICtools is related to: Amazon Web Services has parent organization: Baylor College of Medicine Human Genome Sequencing Center |
PMID:24475911 | OMICS_02290 | SCR_004231 | SciCrunch Registry | Illumina Mercury pipeline | 2026-09-26 02:13:40 | 989 | |||||||
|
CB-Commander Resource Report Resource Website |
CB-Commander (RRID:SCR_004237) | CB-Commander | software resource | A plugin based software tool that tries to integrate high throughput sequencing algorithms. It allows researchers to design and execute their experiments through a user friendly interface, enabling users to integrate di erent components of an experiment, e.g. algorithms and converters, into one graphically interfaced application that is very easy to use when working on remote servers as well as local computers. The graphical user interface facilitates a visual design of experiments by using a block diagram to represent the components (algorithms, converters, etc.) of an experiment as a pipeline. The users can easily modify this pipeline. | java, java swing, high throughput sequencing |
is listed by: OMICtools has parent organization: SourceForge has parent organization: Simon Fraser University; British Columbia; Canada |
GNU General Public License, v2 | OMICS_01534 | http://sourceforge.net/projects/cb-commander/ | SCR_004237 | SciCrunch Registry | 2026-09-26 02:13:40 | 0 | |||||||
|
Artemis: Genome Browser and Annotation Tool Resource Report Resource Website 100+ mentions |
Artemis: Genome Browser and Annotation Tool (RRID:SCR_004267) | Artemis | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Free genome browser and annotation tool that allows visualization of sequence features, next generation data and the results of analyses within the context of the sequence, and also its six-frame translation. Artemis is free software and is distributed under the terms of the GNU General Public License. Artemis is written in Java, and is available for UNIX, Macintosh and Windows systems. It can read EMBL and GENBANK database entries or sequence in FASTA, indexed FASTA or raw format. Other sequence features can be in EMBL, GENBANK or GFF format. | training tool, genome browser, gene annotation, java, bio.tools |
is listed by: OMICtools is listed by: 3DVC is listed by: Debian is listed by: bio.tools is related to: DNAPlotter has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom works with: Alien-hunter |
Wellcome Trust | PMID:11120685 DOI:10.1093/bioinformatics/btr703 |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_28554, OMICS_00903, biotools:artemis | https://bio.tools/artemis, https://sources.debian.org/src/art-nextgen-simulation-tools/ | SCR_004267 | SciCrunch Registry | 2026-09-26 02:13:41 | 422 | |||||
|
PeaKDEck Resource Report Resource Website 10+ mentions |
PeaKDEck (RRID:SCR_004268) | PeaKDEck | software resource | A peak-calling software program for DNAseI-seq data. | perl, command line, gui |
is listed by: OMICtools has parent organization: University of Oxford; Oxford; United Kingdom |
PMID:24407222 | OMICS_02207 | SCR_004268 | SciCrunch Registry | 2026-09-26 02:13:40 | 10 | ||||||||
|
Tree and reticulogram REConstruction Resource Report Resource Website 10+ mentions |
Tree and reticulogram REConstruction (RRID:SCR_004497) | T-REX | analysis service resource, data analysis service, production service resource, service resource, software resource | A web server dedicated to the reconstruction of phylogenetic trees, reticulation networks and to the inference of horizontal gene transfer (HGT) events. | phylogenetic tree, analysis, visualization, network, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University of Quebec in Montreal; Quebec; Canada |
PMID:22675075 | biotools:t-rex, OMICS_04264 | https://bio.tools/t-rex | SCR_004497 | SciCrunch Registry | Trex-online | 2026-09-26 02:13:42 | 33 | ||||||
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Velvet-SC Resource Report Resource Website 1+ mentions |
Velvet-SC (RRID:SCR_004377) | Velvet SC | data analysis software, data processing software, sequence analysis software, software application, software resource | Software package for short read data from single cells that improves assembly through use of progressively increasing coverage cutoff. Used for single cell Illumina sequences, allows variable coverage datasets to be utilized with assembly of E. coli and S. aureus single cell reads. Assembles single cell genome of uncultivated SAR324 clade of Deltaproteobacteria. | genome, single, cell, short, read, assembly |
is listed by: OMICtools is related to: Velvet has parent organization: University of California at San Diego; California; USA |
NCRR P41 RR024851; NHGRI R01 HG003647; Sloan Foundation |
PMID:21926975 | Free, Available for download, Freely available | OMICS_01504 | SCR_004377 | SciCrunch Registry | Velvet Single Cell | 2026-09-26 02:13:42 | 5 | |||||
|
DER Finder Resource Report Resource Website 1+ mentions |
DER Finder (RRID:SCR_004250) | DER Finder | data processing software, software application, software library, software resource, software toolkit | R package for differential expression analysis of RNA-seq data. | differential expression, rna-seq, false discovery rate, genomics, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:24398039 | Free, Public | biotools:derfinder, OMICS_02208 | https://bio.tools/derfinder | SCR_004250 | SciCrunch Registry | derfinder | 2026-09-26 02:13:40 | 5 | |||||
|
PubMed Central Resource Report Resource Website 100+ mentions |
PubMed Central (RRID:SCR_004166) | PMC | data or information resource, database, service resource, storage service resource | Collection of full text archive of biomedical and life sciences journal literature at U.S. National Institutes of Health National Library of Medicine (NIH/NLM). With PubMed Central, NCBI is taking lead in preserving and maintaining open access to electronic literature. Value of PubMed Central, in addition to its role as an archive, lies in what can be done when data from diverse sources is stored in common format in single repository. All articles in PMC are free (sometimes on a delayed basis). Some journals go beyond free, to Open Access. | literature, biomedical, life, science, journal, repository, electronic, literature, gold standard |
uses: PubReader is used by: NIH Heal Project is listed by: OMICtools is related to: PubMed is related to: JISC Open Citations is related to: Biotea is related to: NIF Registry Automated Crawl Data is related to: NIF Literature is related to: Europe PubMed Central is related to: PubReader has parent organization: NCBI |
NIH | Free, Some open access - authors retain copyright, | nlx_18862, OMICS_01193 | SCR_004166 | SciCrunch Registry | 2026-09-26 02:13:39 | 253 | |||||||
|
PubChem Resource Report Resource Website 10000+ mentions |
PubChem (RRID:SCR_004284) | data or information resource, data repository, database, service resource, storage service resource | Collection of information about chemical structures and biological properties of small molecules and siRNA reagents hosted by the National Center for Biotechnology Information (NCBI). | collection, information, data, chemical, structure, biological, property, small, molecule, siRNA reagent, bio.tools |
uses: ChEMBL is used by: NIF Data Federation is used by: Pathway Analysis Tool for Integration and Knowledge Acquisition is used by: GEROprotectors is listed by: OMICtools is listed by: re3data.org is listed by: NIH Data Sharing Repositories is listed by: bio.tools is listed by: Debian is related to: NCBI Structure is related to: Molecular Libraries Program is related to: NIH Data Sharing Repositories is related to: PubChem BioAssay has parent organization: NCBI is parent organization of: PubChem Substance works with: MiMeDB |
NLM | PMID:21418625 PMID:21272340 PMID:20970519 PMID:20298522 PMID:19825798 |
Free, Freely Available | biotools:pubchem, nlx_42691, nlx_29861, r3d100010538, OMICS_01587 | https://bio.tools/pubchem, https://doi.org/10.17616/R3GW37 | SCR_004284 | SciCrunch Registry | 2026-09-26 02:13:40 | 15598 | ||||||
|
InsertionMapper Resource Report Resource Website |
InsertionMapper (RRID:SCR_004163) | InsertionMapper | software resource | A pipeline tool for the identification of targeted sequences from multidimensional high throughput sequencing data. It consists of four independently working modules: Data Preprocessing, Database Modeling, Dimension Deconvolution and Element Mapping. This pipeline tool is applicable to scenarios requiring analysis of the tremendous output of short reads produced in NGS sequencing experiments of targeted genome sequences. | high throughput sequencing, dna sequence, next generation sequencing, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge has parent organization: Montclair State University; New Jersey; USA |
PMID:24090499 | Acknowledgement requested, GNU General Public License | OMICS_01547, biotools:insertionmapper | https://bio.tools/insertionmapper | SCR_004163 | SciCrunch Registry | 2026-09-26 02:13:39 | 0 | ||||||
|
TagDust Resource Report Resource Website 50+ mentions |
TagDust (RRID:SCR_004175) | TagDust | software resource | A program to eliminate artifactual reads from next-generation sequencing data sets. | unix/linux, bio.tools, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:19737799 | biotools:tagdust, OMICS_01095, biotools:nexalign | https://bio.tools/tagdust, https://bio.tools/nexalign | SCR_004175 | SciCrunch Registry | 2026-09-26 02:13:39 | 55 | |||||||
|
Kdetrees Resource Report Resource Website |
Kdetrees (RRID:SCR_004522) | software resource | R package using a non-parametric method for estimating distributions of phylogenetic trees, with the goal of identifying trees that are significantly different from the rest of the trees in the sample. | applet, mac os x, unix/linux, windows, r, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: CRAN |
PMID:24764459 | GNU General Public License, v2 | biotools:kdetrees, OMICS_04172 | https://github.com/grady/kdetrees, https://bio.tools/kdetrees | SCR_004522 | SciCrunch Registry | kdetrees: Nonparametric method for identifying discordant phylogenetic trees | 2026-09-26 02:13:43 | 0 | ||||||
|
SnoopCGH Resource Report Resource Website 1+ mentions |
SnoopCGH (RRID:SCR_004420) | SnoopCGH | software resource | A java desktop application for visualising and exploring comparative genomic hybridization (CGH) data. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:19687029 | biotools:snoopcgh, OMICS_00736 | https://bio.tools/snoopcgh | SCR_004420 | SciCrunch Registry | 2026-09-26 02:13:41 | 2 | |||||||
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SCPD - Saccharomyces cerevisiae promoter database Resource Report Resource Website 10+ mentions |
SCPD - Saccharomyces cerevisiae promoter database (RRID:SCR_004412) | SCPD | analysis service resource, data analysis service, data or information resource, data repository, database, production service resource, service resource, storage service resource | A promoter database of Saccharomyces cerevisiae. Users can explore the promoter regions of ~6000 genes and ORFs in yeast genome, annotate putative regulatory sites of all genes and ORFs, locate intergenic regions, and retrieve sequence of the promoter region. In regards to regulatory elements and transcription factors, users can provide information on transcriptionally related genes, browse matrix and consensus sequences, view the correlation between elements, observe binding affinity and expression, and look at genomewise distribution. SCPD also provides some simple but useful tools for promoter sequence analysis. Gene, consensus and matrix records may be submitted. | promoter, gene, genome, orf, transcription factor binding site, transcriptional start site, transcription factor |
is listed by: OMICtools has parent organization: Cold Spring Harbor Laboratory |
PMID:10487868 | OMICS_01867, nif-0000-03445 | SCR_004412 | SciCrunch Registry | SCPD - The Promoter Database of Saccharomyces cerevisiae | 2026-09-26 02:13:41 | 20 | |||||||
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GASSST Resource Report Resource Website 1+ mentions |
GASSST (RRID:SCR_004413) | GASSST | software resource | Software that finds global alignments of short DNA sequences against large DNA banks. It is able to perform fast gapped alignments and works well for both short and longer reads. It has been tested for reads up to 500bp. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Rennes 1; Rennes; France |
PMID:20739310 | CeCILL license, v2 | biotools:gassst, OMICS_00663 | https://bio.tools/gassst | SCR_004413 | SciCrunch Registry | GASSST : Global Alignment Short Sequence Search Tool, Global Alignment Short Sequence Search Tool | 2026-09-26 02:13:41 | 7 | |||||
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BioDiscovery Nexus Copy Number Resource Report Resource Website 100+ mentions |
BioDiscovery Nexus Copy Number (RRID:SCR_004557) | BioDiscovery | data analysis software, data analytics software, data processing software, software application, software resource | Software package provides statistical tools. Derives copy number and BAF from variety of NGS data including WES, WGS, targeted panel, and shallow sequencing as well as Microarray data. Multifaceted desktop software for rapid discovery of genomic alterations. Accepts data from various manufacturers and technologies including Infinium GSA and CytoScan XON. | Derives copy number, BAF, NGS data, WES, WGS, targeted panel, shallow sequencing, microarray data | is listed by: OMICtools | Commercially available | OMICS_01122 | http://www.biodiscovery.com/software/nexus-expression/ | SCR_004557 | SciCrunch Registry | Nexus Copy Number | 2026-09-26 02:13:43 | 168 | ||||||
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MetaPhlAn Resource Report Resource Website 500+ mentions |
MetaPhlAn (RRID:SCR_004915) | data analysis resource, data analysis software, data processing software, sequence analysis software, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data. It relies on unique clade-specific marker genes identified from reference genomes. | microbial community, microbial composition, microbial genome, microbial sequence |
is listed by: OMICtools is listed by: Human Microbiome Project is listed by: Debian has parent organization: Bitbucket has parent organization: Harvard T.H. Chan School of Public Health |
PMID:22688413 DOI:10.1038/nmeth.3589 |
OMICS_02286 | http://huttenhower.sph.harvard.edu/metaphlan https://bitbucket.org/nsegata/metaphlan/, https://sources.debian.org/src/metaphlan2/ | SCR_004915 | SciCrunch Registry | MetaPhlAn, Metagenomic Phylogenetic Analysis, MetaPhlAn version 2, MetaPhlAn - Metagenomic Phylogenetic Analysis, MetaPhlAn v2 | 2026-09-26 02:13:46 | 645 | |||||||
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MetaCluster-TA Resource Report Resource Website 1+ mentions |
MetaCluster-TA (RRID:SCR_004599) | MetaCluster-TA | software resource | A software for binning and annotating short paired-end reads. | binning, annotation, metagenomics | is listed by: OMICtools | PMID:24564377 | OMICS_01473 | SCR_004599 | SciCrunch Registry | 2026-09-26 02:13:43 | 4 | ||||||||
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PRISM - Pair Read Informed Split Mapper Resource Report Resource Website 1+ mentions |
PRISM - Pair Read Informed Split Mapper (RRID:SCR_004812) | PRISM (Pair Read Informed Split Mapper) | software resource | Software for split read (reads which span across a structrual variant -- SV ) mapping and SV calling from the mapping result. It is able to detect small insertions and abitrary size deletions, inversions and tandom duplications with the direction of discordant read pairs. PRISM_CTX is a tool for detecting inter-chromosome trans-location events. | structural variant, split read mapping, insertion, deletion, inversion, tandom duplication, discordant read pair, chromosome, trans-location event, duplication, breakpoint, genome |
is listed by: OMICtools has parent organization: University of Toronto; Ontario; Canada |
PMID:22851530 | Free, Public | OMICS_02288 | SCR_004812 | SciCrunch Registry | PRISM (Pair Read Informed Split Mapper), Pair Read Informed Split Mapper | 2026-09-26 02:13:45 | 7 |
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
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