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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Mfuzz Resource Report Resource Website 10+ mentions |
Mfuzz (RRID:SCR_000523) | software resource | Software package for noise-robust soft clustering of gene expression time-series data (including a graphical user interface)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | r, time series, gene expression, clustering, microarray, preprocessing, time course, visualization, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Humboldt University of Berlin; Berlin; Germany has parent organization: Bioconductor |
PMID:18084642 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:mfuzz, OMICS_02012 | https://bio.tools/mfuzz | http://itb.biologie.hu-berlin.de/~futschik/software/R/Mfuzz/ | SCR_000523 | Mfuzz - Soft clustering of time series gene expression data | 2026-09-05 06:24:21 | 16 | |||||
|
Pindel Resource Report Resource Website 10+ mentions |
Pindel (RRID:SCR_000560) | Pindel | software resource | Software to detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data. It uses a pattern growth approach to identify the breakpoints of these variants from paired-end short reads., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | deletion, insertion, nucleotide, genome, read, inversion, tandem duplication, structural variant, next-generation sequencing, pattern growth, indel, breakpoint, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Washington University School of Medicine in St. Louis; Missouri; USA works with: cgpPindel |
PMID:19561018 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:pindel, OMICS_00321 | https://bio.tools/pindel | SCR_000560 | 2026-09-05 06:24:21 | 25 | ||||||
|
OntoMorph Tab Resource Report Resource Website |
OntoMorph Tab (RRID:SCR_000443) | data analysis software, data processing software, software application, software resource | OntoMorph is a tab plugin for Protege-OWL 3 that allows a user to mark-up portions of a Neurolucida neuron morphology with OWL instances. A user loads a Neurolucida morphology file, either from their hard drive or from an arbitrary URL, into an interface that allows them to zoom, rotate, and translate the morphology. The interface allows them to select points on the morphology to indicate points, segments, or subtrees of the morphology they wish to assign to an OWL instance. After this selection has been made, OntoMorph saves the selection to the currently active OWL instance in the ontology that is currently loaded into Protege. No modifications are made to the Neurolucida file itself. As a result, an association is created between that portion of the morphology and the OWL instance, such that selecting the OWL instance allows retrieval of the portion. Upon retrieval, the morphology portion can be highlighted, so the user can keep track of what pieces each instance refer to. | annotation, java, morphology, neurolucida, neuron, neuroscience, plugin, protege, software, ontology, owl | has parent organization: University of California at San Diego; California; USA | Free, Available for download, Freely available | nif-0000-24916 | SCR_000443 | OntoMorph | 2026-09-05 06:24:19 | 0 | ||||||||
|
SiPhy Resource Report Resource Website 1+ mentions |
SiPhy (RRID:SCR_000564) | SiPhy | sequence analysis resource | Software that implements rigorous statistical tests to detect bases under selection from a multiple alignment data. It takes full advantage of deeply sequenced phylogenies to estimate both unlikely substitution patterns as well as slowdowns or accelerations in mutation rates. It can be applied as an Hidden Markov Model (HMM), in sliding windows, or to specific regions. | java, mutation, phylogeny, substitution pattern, mutation rate |
is listed by: OMICtools has parent organization: Broad Institute |
NHGRI ; NSF |
PMID:19478016 | Free, Available for download, Freely available, | OMICS_00183 | SCR_000564 | 2026-09-05 06:24:23 | 6 | ||||||
|
Scaffold builder Resource Report Resource Website |
Scaffold builder (RRID:SCR_000556) | scaffold_builder | analysis service resource, data analysis service, production service resource, service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 6,2023. Tool designed to generate scaffolds (super contigs of sequences joined by N-bases) using the homology provided by a closely related reference sequence. Scaffold_builder is an advanced wrapper for Nucmer, written in Python that resolves several situations that may arise when mapping contigs to the reference genome. | scaffolding |
is listed by: OMICtools has parent organization: San Diego Supercomputer Center |
PMID:24267787 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00046 | SCR_000556 | 2026-09-05 06:24:23 | 0 | |||||||
|
SNPiR Resource Report Resource Website 1+ mentions |
SNPiR (RRID:SCR_000557) | SNPiR | software resource | Software for reliable Identification of Genomic Variants Using RNA-seq Data. | genomic variant, rna-seq |
is listed by: OMICtools has parent organization: Stanford University; Stanford; California |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01362 | SCR_000557 | SNPiR: Reliable Identification of Genomic Variants Using RNA-seq Data | 2026-09-05 06:24:21 | 1 | |||||||
|
FPSAC Resource Report Resource Website 1+ mentions |
FPSAC (RRID:SCR_000555) | FPSAC | software resource | Sogftware for fast Phylogenetic Scaffolding of Ancient Contigs. | genome, scaffolding, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Simon Fraser University; British Columbia; Canada |
PMID:24068034 | biotools:fpsac, OMICS_00041 | https://bio.tools/fpsac | SCR_000555 | Fast Phylogenetic Scaffolding of Ancient Contigs (FPSAC) and application to the medieval Black Death agent, Fast Phylogenetic Scaffolding of Ancient Contigs, FPSAC: fast phylogenetic scaffolding of ancient contigs | 2026-09-05 06:24:21 | 1 | ||||||
|
ACCUSA2 Resource Report Resource Website |
ACCUSA2 (RRID:SCR_000558) | ACCUSA2 | software resource | Multi-purpose SNV calling software enhanced by probabilistic integration of quality scores. | snv | is listed by: OMICtools | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01360 | SCR_000558 | 2026-09-05 06:24:21 | 0 | ||||||||
|
DySC Resource Report Resource Website |
DySC (RRID:SCR_000553) | DySC | software resource | Software for Greedy Clustering of 16S rRNA Reads which uses a dynamic seeding strategy. | cluster, 16s rrna, read |
is listed by: OMICtools has parent organization: Google Code |
PMID:22730435 | Free, Available for download, Freely available, | OMICS_01443 | SCR_000553 | DySC: Software for Greedy Clustering of 16S rRNA Reads | 2026-09-05 06:24:21 | 0 | ||||||
|
NEI Clinical Studies Resource Report Resource Website |
NEI Clinical Studies (RRID:SCR_000546) | clinical trial, data or information resource, portal, topical portal | An archived portal of clinical studies, both ongoing and completed, that have been conducted and supported by the National Eye Institute (NEI) since 1970. The portal covers corneal diseases, glaucoma, epidemiology, lens and cataract, retinal diseases, strabismus, amblyopia and visual processing. | eye, clinical, corneal disease, glaucoma, epidemiology, lens, cataract, retinal disease, strabismus, amblyopia, visual processing, clinical trial, research, vision | has parent organization: National Eye Institute (NEI) Commons | Corneal disease, Glaucoma, Cataract, Retinal disease, Strabismus, Amblyopia | NEI | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-00237 | http://www.nei.nih.gov/neitrials/index.asp | SCR_000546 | National Eye Institute Clinical Studies | 2026-09-05 06:24:23 | 0 | |||||
|
POPBAM Resource Report Resource Website |
POPBAM (RRID:SCR_000464) | POPBAM | data analysis software, data processing software, software application, software resource | A tool to perform evolutionary or population-based analyses of next-generation sequencing data. POPBAM takes a BAM file as its input and can compute many widely used evolutionary genetics measures in sliding windows across a genome. | next-generation sequencing, evolution, population, bam, genome, evolutionary genetics, c++, short read, sequence alignment, sliding window, command-line, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge has parent organization: University of Rochester; New York; USA |
PMID:24027417 | Free, Available for download, Freely available | biotools:popbam, OMICS_01559 | https://bio.tools/popbam | http://popbam.sourceforge.net/ | SCR_000464 | 2026-09-05 06:24:21 | 0 | |||||
|
drFAST Resource Report Resource Website 1+ mentions |
drFAST (RRID:SCR_000586) | drFAST | software resource | A software which maps di-base reads (SOLiD color space reads) to reference genome assemblies in a fast and memory-efficient manner. | di-base, solid color space, genome assemblies, memory-efficient, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: SPLITREAD has parent organization: SourceForge |
PMID:21586516 | Free, Available for download, Freely available | biotools:drfast, OMICS_00661 | https://bio.tools/drfast | SCR_000586 | di-base read Fast Alignment Search Tool, drFAST: di-base read Fast Alignment Search Tool | 2026-09-05 06:24:22 | 1 | |||||
|
Genome BioInformatics Research Lab - gff2ps Resource Report Resource Website 1+ mentions |
Genome BioInformatics Research Lab - gff2ps (RRID:SCR_000462) | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software program for visualizing annotations of genomic sequences. The program has features such as the ability to create comprehensive plots, customizable parameters, and flexibility in file format. | genome, sequence, visualization, parameters, bioinformatics, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
PMID:11099262 DOI:10.1093/bioinformatics/16.8.743 |
Free, Available for download, Freely available | OMICS_17140, biotools:gff2ps, nif-0000-30611 | https://bio.tools/gff2ps, https://sources.debian.org/src/gff2ps/ | SCR_000462 | gff2ps | 2026-09-05 06:24:20 | 1 | ||||||
|
NGSmethPipe Resource Report Resource Website 1+ mentions |
NGSmethPipe (RRID:SCR_000583) | NGSmethPipe | software resource | A software tool which generates high-quality methylation maps. | computation, genomics, bioinformatics, methylation maps, visualization |
is listed by: OMICtools has parent organization: University of Granada; Granada; Spain |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00611 | SCR_000583 | NGSmethPipe - A tool to generate high-quality methylation maps | 2026-09-05 06:24:22 | 3 | |||||||
|
sybil - Efficient Constrained Based Modelling in R Resource Report Resource Website |
sybil - Efficient Constrained Based Modelling in R (RRID:SCR_000457) | sybil | software resource | A Systems Biology Library for R, implementing algorithms for constraint based analyses of metabolic networks (e.g. flux-balance analysis (FBA), minimization of metabolic adjustment (MOMA), regulatory on/off minimization (ROOM), robustness analysis and flux variability analysis). This is an implementation of COBRA toolbox in R language. | unix/linux, windows, r |
is listed by: OMICtools is related to: SBML is related to: CRAN |
PMID:24224957 | Free, Available for download, Freely available | OMICS_06008 | http://www.cs.hhu.de/en/research-groups/bioinformatics/software/sybil.html | http://cran.r-project.org/web/packages/sybil/index.html | SCR_000457 | sybil: sybil - Efficient Constrained Based Modelling in R | 2026-09-05 06:24:20 | 0 | ||||
|
msbwt Resource Report Resource Website |
msbwt (RRID:SCR_000458) | software resource | A software package for creating, merging, and querying multi-string BWTs. | standalone software, python |
is listed by: OMICtools has parent organization: Google Code |
PMID:25172922 | Free, Available for download, Freely available | OMICS_05976 | https://code.google.com/p/msbwt/ | SCR_000458 | multi-string BWT | 2026-09-05 06:24:21 | 0 | ||||||
|
MAXCHELATOR Resource Report Resource Website 50+ mentions |
MAXCHELATOR (RRID:SCR_000459) | MAXC | software resource | A series of programs for determining the free metal concentration in the presence of chelators or total metal given a desired free concentration. | metal, concentration, chelator |
is related to: WEBMAXC STANDARD is related to: WEBMAXC EXTENDED has parent organization: Stanford University; Stanford; California |
PMID:8201981 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_156862 | SCR_000459 | 2026-09-05 06:24:20 | 74 | |||||||
|
Rdisop Resource Report Resource Website |
Rdisop (RRID:SCR_000453) | software resource | Software for identification of metabolites using high precision mass spectrometry. MS Peaks are used to derive a ranked list of sum formulae, alternatively for a given sum formula the theoretical isotope distribution can be calculated to search in MS peak lists. | standalone software, mac os x, unix/linux, windows, r, mass spectrometry, metabolomics, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_02416, biotools:rdisop | https://github.com/sneumann/Rdisop, https://bio.tools/rdisop | SCR_000453 | Rdisop - Decomposition of Isotopic Patterns, Rdisop: Decomposition of Isotopic Patterns, Decomposition of Isotopic Patterns | 2026-09-05 06:24:19 | 0 | |||||||
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AdaptiveCrawler Resource Report Resource Website |
AdaptiveCrawler (RRID:SCR_000573) | AdaptiveCrawler | software resource, web application | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 9,2022. A web crawler that can intelligently acquire social media content on the Internet to meet the specific online data source acquisition needs of cancer researchers. | web crawler, acquire social media content on Internet, cancer research, |
is listed by: OMICtools has parent organization: Oak Ridge National Laboratory |
Cancer, Breast cancer, Lung cancer | PMID:24078710 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01170 | SCR_000573 | Adaptive Crawler, Smart Web Crawler | 2026-09-05 06:24:22 | 0 | |||||
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National Spasmodic Dysphonia Association Resource Report Resource Website 1+ mentions |
National Spasmodic Dysphonia Association (RRID:SCR_000447) | data or information resource, portal, topical portal | The mission of the National Spasmodic Dysphonia Association is to advance medical research into the causes of and treatments for spasmodic dysphonia, promote physician and public awareness of the disorder, and provide support to those affected by spasmodic dysphonia. | patient support | nif-0000-00490 | SCR_000447 | NSDA | 2026-09-05 06:24:19 | 1 |
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The data sets included in this resource are published in Kravitz et al, 2012. Distinct roles for direct and indirect pathway striatal neurons in reinforcement (Nat. Neurosci).
