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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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SWIPE Resource Report Resource Website 1+ mentions |
SWIPE (RRID:SCR_012771) | SWIPE | software resource | A software tool for performing rapid local alignment searches in amino acid or nucleotide sequence databases. | is listed by: OMICtools | PMID:21631914 | OMICS_00998 | SCR_012771 | Smith-Waterman database searches with inter-sequence SIMD parallelisation | 2026-08-08 12:00:16 | 3 | ||||||||
|
SIFT Resource Report Resource Website 10000+ mentions |
SIFT (RRID:SCR_012813) | SIFT | production service resource, web service, software resource, data access protocol, data analysis service, source code, analysis service resource, service resource | Data analysis service to predict whether an amino acid substitution affects protein function based on sequence homology and the physical properties of amino acids. SIFT can be applied to naturally occurring nonsynonymous polymorphisms and laboratory-induced missense mutations. (entry from Genetic Analysis Software) Web service is also available. | gene, genetic, genomic, amino acid, substitution, protein function, coding region, single nucleotide variant, coding indel, deletion, insertion, sequence, protein, bio.tools |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: SIFT 4G has parent organization: Genome Institute of Singapore; Singapore; Singapore has parent organization: J. Craig Venter Institute |
Agency for Science Technology and Research ; NIGMS GM29009 |
PMID:19561590 PMID:12824425 PMID:11337480 DOI:10.1038/nprot.2009.86 |
Non-commercial | biotools:sift, OMICS_00137, nlx_154618 | http://sift.jcvi.org/, https://bio.tools/sift, https://sources.debian.org/src/sift/ | http://sift.bii.a-star.edu.sg/SIFT.html | SCR_012813 | Sorting Intolerant From Tolerant | 2026-08-08 12:00:16 | 10996 | |||
|
lumi Resource Report Resource Website 100+ mentions |
lumi (RRID:SCR_012781) | lumi | software resource | Software that provides an integrated solution for the Illumina microarray data analysis. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite has parent organization: Bioconductor |
biotools:lumi, OMICS_00770 | https://bio.tools/lumi | SCR_012781 | 2026-08-08 11:59:46 | 319 | ||||||||
|
Ngs backbone Resource Report Resource Website 1+ mentions |
Ngs backbone (RRID:SCR_012907) | Ngs_backbone | software resource | A bioinformatic application created to work on sequence analysis by using NGS (Next Generation Sequencing) and sanger sequences. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
biotools:ngs_backbone, OMICS_01132 | https://bio.tools/ngs_backbone | SCR_012907 | 2026-08-08 12:00:04 | 1 | ||||||||
|
rqubic Resource Report Resource Website |
rqubic (RRID:SCR_012869) | rqubic | software resource | This software package implements the QUBIC algorithm for the qualitative biclustering with gene expression data. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
PMID:19509312 | Free | biotools:rqubic, OMICS_01799 | https://bio.tools/rqubic | SCR_012869 | rqubic - Qualitative biclustering algorithm for expression data analysis in R | 2026-08-08 12:00:04 | 0 | |||||
|
European Medicines Agency Resource Report Resource Website 100+ mentions |
European Medicines Agency (RRID:SCR_011215) | EMA | nonprofit organization | An agency responsible for the evaluation and supervision of medicines developed by pharmaceutical companies for use in the European Union. Its main responsibility is the protection and promotion of public and animal health through the evaluation and supervision of medicines for human and veterinary use. The Agency also plays a role in stimulating innovation and research in the pharmaceutical sector. The Agency gives scientific advice and other assistance to companies for the development of new medicines. It publishes guidelines on quality-, safety- and efficacy-testing requirements. A dedicated SME Office provides special assistance to small and medium-sized enterprises. |
is listed by: OMICtools is related to: Predictive Safety Testing Consortium is related to: GetReal is related to: PharmaCog has parent organization: European Union is parent organization of: EU Clinical Trials Register |
grid.452397.e, Wikidata: Q130146, nif-0000-30532 | https://ror.org/01z0wsw92 | SCR_011215 | EU Medicines Agency | 2026-08-08 11:59:28 | 388 | ||||||||
|
MAxEntScan Resource Report Resource Website 50+ mentions |
MAxEntScan (RRID:SCR_016707) | MAxEntScan | simulation software, software resource, software application, service resource | Software tool as a framework for modeling the sequences of short sequence motifs based on the maximum entropy principle (MEP). Used for sequence motifs such as those involved in RNA splicing. | modeling, sequence, short, motif, maximum, entropy, principle, MEP, RNA, splicing |
is listed by: OMICtools has parent organization: Massachusetts Institute of Technology; Massachusetts; USA; |
NSF Grant 0218506; NIH ; Lee Kuan Yew Scholarship for the goverment of Singapore |
PMID:15285897 | Free, Available for download, Freely available | SCR_016707 | Maximum Entropy Scan, MAxEntScan, MAximumEntropyScan | 2026-08-08 12:00:34 | 70 | ||||||
|
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 toolkit, data acquisition software, software resource, software application, data analysis software, data analytics software, data processing 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 | 2026-08-08 12:00:34 | 740 | |||||||||||
|
OmicsNet Resource Report Resource Website 50+ mentions |
OmicsNet (RRID:SCR_016724) | production service resource, web service, software resource, data access protocol, analysis service resource, service resource | Web based tool to create different types of molecular interaction networks and visually explore them in a three-dimensional (3D) space (genes/proteins, microRNAs, transcription factors or metabolites). | create, molecular, interaction, network, visually, 3D, gene, protein, microRNA, transcription factor, metabolite, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
Natural Sciences and Engineering Research Council of Canada ; Genome Canada ; Canada Research Chairs Program |
PMID:29878180 | Free, Freely available | biotools:omicsnet | https://bio.tools/omicsnet | SCR_016724 | 2026-08-08 12:00:35 | 52 | ||||||
|
VecScreen Resource Report Resource Website 50+ mentions |
VecScreen (RRID:SCR_016577) | sequence analysis software, software resource, software application, data analysis software, service resource, data processing software | Software tool to screen a nucleic acid sequence for vector contamination. Detects foreign DNAs such as vector, linker, adapter, and primer regions involved in nucleotide sequences by using blast search against vector sequence database. The main unit of this tool is vecscreen program obtainable from NCBI. | screen, sequence, nucleic acid, segment, vector, contamination | is listed by: OMICtools | Free, Available for download, Freely available | https://www.ddbj.nig.ac.jp/vecscreen-help-e.html | SCR_016577 | 2026-08-08 12:00:59 | 69 | |||||||||
|
ConsensusClusterPlus Resource Report Resource Website 100+ mentions |
ConsensusClusterPlus (RRID:SCR_016954) | software resource, software application, data analysis software, data processing software | Software written in R for determining cluster count and membership by stability evidence in unsupervised analysis. Provides quantitative and visual stability evidence for estimating the number of unsupervised classes in a dataset with item tracking, item consensus and cluster consensus plots. | cluster, count, stability, evidence, unsupervised, analysis, , bio.tools |
is listed by: Bioconductor is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
NCI F32CA142039; Thomas G. Labrecque Foundation ; NCI U24 CA126554 |
PMID:20427518 | Free, Available for download, Freely available | biotools:consensusclusterplus | https://bio.tools/consensusclusterplus | SCR_016954 | 2026-08-08 12:01:02 | 196 | ||||||
|
Ligprep Resource Report Resource Website 50+ mentions |
Ligprep (RRID:SCR_016746) | Ligprep | software resource, software application, simulation software | Software tool to correct and optimize the ligands by generating different protonation states, stereochemistry, tautomers, and ring conformations. Used to generate accurate, energy minimized 3D molecular structures. | correct, optimize, ligand, protonation, stereochemistry, tautomer, conformation, energy, minimized, 3D, moleular, structure |
is listed by: OMICtools is listed by: SoftCite has parent organization: Schrodinger works with: Glide works with: Phase |
Commercially available | SCR_016746 | LigPrep, LigandPreparation, Ligand preparation | 2026-08-08 12:01:01 | 50 | ||||||||
|
Supernova assembler Resource Report Resource Website 10+ mentions |
Supernova assembler (RRID:SCR_016756) | sequence analysis software, software resource, software application, data analysis software, data processing software | Software to generate phased, whole genome de novo assemblies from a Chromium prepared library. Used to create true diploid de novo assemblies and can separate homologous chromosomes over long distances. | generate, phased, whole, genome, de novo, assembly, Chromium, prepared, library | is listed by: OMICtools | Free, Available for download, Freely available | https://support.10xgenomics.com/de-novo-assembly/software/pipelines/latest/installation | SCR_016756 | 2026-08-08 12:00:35 | 34 | |||||||||
|
Discovar assembler Resource Report Resource Website 10+ mentions |
Discovar assembler (RRID:SCR_016755) | Discovar | sequence analysis software, software resource, software application, data analysis software, data processing software | Software tool for variant calling with reference and de novo assembly of genomes. The heart of DISCOVAR is a de novo genome assembler which can generate de novo assemblies for both large and small genomes. | variant, calling, reference, de novo, assembly, genome, genetic, human, sequence, analysis |
is listed by: OMICtools has parent organization: Broad Institute |
NHGRI R01 HG003474; NHGRI U54 HG003067; NIAID HHSN272200900018C |
PMID:25326702 | Free, Available for download, Freely available | SCR_016755 | Discovar de novo, Discovar | 2026-08-08 12:01:01 | 20 | ||||||
|
PathwayMatcher Resource Report Resource Website 1+ mentions |
PathwayMatcher (RRID:SCR_016759) | software resource, network analysis software, software application, data analysis software, data processing software | Software tool for multi omics pathway mapping and proteoform network generation. Open source software writen in Java to search for pathways related to a list of proteins in Reactome. | mapping, omics, data, pathways, network, analysis, proteoform, generate, Reactome, database, match, bio.tools |
is listed by: Galaxy is listed by: OMICtools is listed by: Debian is listed by: bio.tools works with: Reactome |
European Research Council ; Research Council of Norway ; Bergen Research Foundation ; NIGMS U54 GM114833; NHGRI U41 HG003751 |
DOI:10.1101/375097 | Free, Available for download, Freely available | BioTools:PathwayMatcher, biotools:PathwayMatcher | https://anaconda.org/bioconda/pathwaymatcher, https://toolshed.g2.bx.psu.edu/repository?repository_id=6d75f02b86acc421, https://bio.tools/PathwayMatcher, https://bio.tools/PathwayMatcher, https://bio.tools/PathwayMatcher | SCR_016759 | 2026-08-08 12:00:35 | 1 | ||||||
|
Epik Resource Report Resource Website 1+ mentions |
Epik (RRID:SCR_016745) | software resource, software application, simulation software | Software program for pKa prediction and protonation state generation for drug like molecules. | predict, pKa, value, chemical, structure, drug, profile, protonation, state, molecule, Schrodinger |
is listed by: OMICtools is listed by: SoftCite has parent organization: Schrodinger |
PMID:17899391 | Commercially available | SCR_016745 | 2026-08-08 12:00:35 | 6 | |||||||||
|
mzStudio Resource Report Resource Website 1+ mentions |
mzStudio (RRID:SCR_017088) | software resource, software application, data analysis software, data visualization software, data processing software | Software tool for proteomics data analysis, visualization, and notebook application. Dynamic digital canvas for user driven interrogation of mass spectrometry data. Operating system Unix/Linux, Windows. | proteomic, data, analysis, visualization, notebooking, mass, spectrometry, modification, gas, phase, fragmentation, behavior |
is listed by: OMICtools is related to: Python Programming Language |
NCI CA188881; NCI CA178860; NCI CA042368; Dana-Farber Strategic Research Initiative ; Barr Program in Basic Research ; Honorable Tina Brozman Foundation for Ovarian Cancer Research ; Michael J. Fox Foundation |
PMID:28763045 | Free, Available for download, Freely available | OMICS_26946 | https://omictools.com/mzstudio-tool | SCR_017088 | 2026-08-08 12:00:43 | 1 | ||||||
|
Metacell Resource Report Resource Website 10+ mentions |
Metacell (RRID:SCR_017013) | MetaCell | software resource, software application, data analysis software, data processing software | Software package for single cell RNA-seq data analysis using k-NN graph partitions. Used to analyze group of scRNA profiles that are highly similar and provides features for deriving them. Can be used with large datasets., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. |
is listed by: OMICtools is related to: NWB Explorer |
DOI:10.1101/437665 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_32475 | https://bitbucket.org/tanaylab/metacell/src/default/ | SCR_017013 | 2026-08-08 12:00:41 | 31 | |||||||
|
OmicsSIMLA Resource Report Resource Website 1+ mentions |
OmicsSIMLA (RRID:SCR_017011) | software toolkit, software resource, software application, simulation software | Software tool for generating multi omics data with disease status. Simulates genomics (SNPs and copy number variations), epigenomics ( whole genome bisulphite sequencing), transcriptomics ( RNA seq), and proteomics (normalized reverse phase protein array) data at the whole genome level. Available as desktop and web application version. | multi, omics, data, simulator, disease, genomic, epigenomic, transcriptomic, proteomic, genome, sequencing, protein, RNA | is listed by: OMICtools | Ministry of Science and Technology in Taiwan | DOI:10.1101/426510 | Freely available, Available to download, Free | OMICS_31363 | SCR_017011 | 2026-08-08 12:00:41 | 1 | |||||||
|
cwl-metrics Resource Report Resource Website 1+ mentions |
cwl-metrics (RRID:SCR_017076) | CWL-metrics | software library, software resource, software toolkit | Software framework to collect and analyze computational resource usage of workflow runs based on common workflow language CWL. Used to share set of tools packaged in containers. Enables users to choose proper cloud instance for workflow runs based on run time metrics data. Operating system Unix/Linux. | collect, analyze, computational, resource, usage, workflow, common, language, container, cloud, data, analysis | is listed by: OMICtools | Japan Science and Technology Agency | DOI:10.1101/456756 | Free, Available for download, Freely available | OMICS_32746 | SCR_017076 | Common Workflow Language-metrics, common workflow language metrix | 2026-08-08 12:00:43 | 1 |
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