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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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AbMining ToolBox Resource Report Resource Website |
AbMining ToolBox (RRID:SCR_000090) | software resource | Python scripts to analyze antibody libraries sequenced by next generation sequencing methods (454, Ion Torrent, MiSeq). | standalone software, illumina, roche, life technologies, python |
is listed by: OMICtools has parent organization: SourceForge |
PMID:24423623 | Free, Available for download, Freely available | OMICS_04063 | SCR_000090 | SciCrunch Registry | 2026-10-10 12:35:28 | 0 | ||||||||
|
SNAVI Resource Report Resource Website |
SNAVI (RRID:SCR_000091) | software resource | Desktop application for analysis and visualization of large-scale cell signaling networks. | standalone software, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Google Code |
PMID:19154595 | Free, Available for download, Freely available | biotools:snavi, OMICS_04122 | https://bio.tools/snavi | SCR_000091 | SciCrunch Registry | Signaling Networks Analysis and Visualization | 2026-10-10 12:35:29 | 0 | ||||||
|
CovalentDock Cloud Resource Report Resource Website |
CovalentDock Cloud (RRID:SCR_000126) | CovalentDock Cloud | data access protocol, software resource, web service | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 30,2023. Web service that is used by researchers and scientists to perform protein-ligand covalent docking. This form allows for the formation of covalent linkages between the ligand and the receptor. | protein ligand covalent docking, ligand, receptor, covalent linkage, data analysis service, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:23034731 | THIS RESOURCE IS NO LONGER IN SERVICE | covalentdock_cloud, OMICS_01597 | https://bio.tools/covalentdock_cloud | SCR_000126 | SciCrunch Registry | 2026-10-10 12:35:30 | 0 | ||||||
|
SP-Designer Resource Report Resource Website |
SP-Designer (RRID:SCR_000031) | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. An open source software program for the design of specific PCR primer pairs from a DNA sequence alignment containing sequences from various taxa. | standalone software, windows |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23634845 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_03932 | SCR_000031 | SciCrunch Registry | 2026-10-10 12:35:27 | 0 | ||||||||
|
SNPSVM Resource Report Resource Website |
SNPSVM (RRID:SCR_000028) | software resource | A support vector machine for calling variants from next-gen sequencing data. It takes as input a BAM-formatted alignment of sequencing reads, and emits a VCF formatted file describing where all the SNPs (single nucleotide polymorphisms) are. | standalone software | is listed by: OMICtools | PMID:23620357 | Free, Available for download, Freely available | OMICS_03838 | SCR_000028 | SciCrunch Registry | 2026-10-10 12:35:27 | 0 | ||||||||
|
GHOSTM Resource Report Resource Website |
GHOSTM (RRID:SCR_000062) | data analysis software, data processing software, software application, software resource | Software homology search tool for huge short reads generated by next-generation sequencers.Can detect remote homologs like BLAST and is about 40 times more efficient than BLAST by using a GPU-computing technique. | homology search, next-generation sequencers short reads, detect remote homologs, |
is listed by: OMICtools is listed by: Google Code |
PMID:22574135 | Free, Available for download, Freely available, | OMICS_02563 | SCR_000062 | SciCrunch Registry | GPU-based HOmology Search Tool for Metagenomics, ghostm: GPU-based HOmology Search Tool for Metagenomics | 2026-10-10 12:35:28 | 0 | |||||||
|
PD5 Resource Report Resource Website |
PD5 (RRID:SCR_000068) | software library, software resource, software toolkit | An open-source C++ software library of classes for the design and analysis of primers suitable for a wide range of PCR applications. | c++, primer design, primer, pcr, software repository, library |
is listed by: OMICtools is listed by: Google Code has parent organization: Aberystwyth University; Wales; United Kingdom |
PMID:24278254 | Free, Available for download, Freely available | OMICS_02366 | SCR_000068 | SciCrunch Registry | PD5: A Software Library for the Development of Primer Design Applications | 2026-10-10 12:35:28 | 0 | |||||||
|
MysiRNA-designer Resource Report Resource Website |
MysiRNA-designer (RRID:SCR_000102) | software resource | Software that integrates several factors in an automated work-flow considering mRNA transcripts variations, siRNA and mRNA target accessibility, and both near-perfect and partial off-target matches. | standalone software |
is listed by: OMICtools has parent organization: SourceForge |
PMID:22046244 | Free, Available for download, Freely available | OMICS_04748 | SCR_000102 | SciCrunch Registry | 2026-10-10 12:35:29 | 0 | ||||||||
|
Fusion Analyser Resource Report Resource Website |
Fusion Analyser (RRID:SCR_000059) | data analysis software, data processing software, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 16, 2023. Software used to detect gene fusions from paired-end RNA-Seq data. | gene fusion, rna-seq, paired-end rna-seq data, fusion event, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:22570408 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01347, biotools:fusionanalyser | https://bio.tools/fusionanalyser | SCR_000059 | SciCrunch Registry | FusionAnalyser | 2026-10-10 12:35:28 | 0 | ||||||
|
CorMut Resource Report Resource Website |
CorMut (RRID:SCR_000053) | data analysis software, data processing software, sequence analysis software, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 16,2023. Software package for computing correlated mutations based on selection pressure. Three methods are provided for detecting correlated mutations, including conditional selection pressure, mutual information and Jaccard index. The computation consists of two steps: First, the positive selection sites are detected; second, the mutation correlations are computed among the positive selection sites. Note that the first step is optional. Meanwhile, CorMut facilitates the comparison of the correlated mutations between two conditions by the means of correlated mutation network. | sequencing, correlated mutation, selection pressure, r, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: CRAN has parent organization: Bioconductor |
PMID:24681904 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_03636, biotools:cormut | https://bio.tools/cormut | SCR_000053 | SciCrunch Registry | CorMut - Detect the correlated mutations based on selection pressure | 2026-10-10 12:35:27 | 0 | ||||||
|
metaSeq Resource Report Resource Website |
metaSeq (RRID:SCR_000056) | metaSeq | data analysis software, data processing software, software application, software resource | Software package for meta-analysis of RNA-Seq count data in multiple studies. The probabilities by one-sided NOISeq are combined by Fisher's method or Stouffer's method. | differential expression, rna-seq, sequencing |
is listed by: OMICtools has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_02123 | SCR_000056 | SciCrunch Registry | 2026-10-10 12:35:28 | 0 | ||||||||
|
pairheatmap Resource Report Resource Website |
pairheatmap (RRID:SCR_003109) | software resource | A software tool to compare two heatmaps and discover patterns within and across groups. In the context of biology, group can be defined based on gene ontology. | standalone software, r, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: CRAN |
PMID:24016862 | Free, Available for download, Freely available | biotools:pairheatmap, OMICS_04853 | https://www.rdocumentation.org/packages/pairheatmap/versions/1.0.1/topics/pairheatmap | SCR_003109 | SciCrunch Registry | pairheatmap: A tool for comparing heatmaps | 2026-10-10 12:36:32 | 0 | ||||||
|
MFEprimer Resource Report Resource Website 10+ mentions |
MFEprimer (RRID:SCR_003066) | software resource | A fast thermodynamics-based software program for checking PCR primer specificity against genomic DNA and mRNA/cDNA sequence databases. | standalone software, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:22689644 | Free, Available for download, Freely available | biotools:mfeprimer-2.0, OMICS_02355 | https://www.mfeprimer.com/ | SCR_003066 | SciCrunch Registry | MFEprimer-2.0 | 2026-10-10 12:36:21 | 21 | ||||||
|
MIPE Resource Report Resource Website 10+ mentions |
MIPE (RRID:SCR_003065) | data or information resource, interchange format, narrative resource, software resource, standard specification | A XML format that enables genomics researchers to store critical information on PCR experiments. Accompagnying perl scripts are written to read from (dbSTS) or write to a MIPE XML file. | standalone software, pcr, xml, data storage, data exchange |
is listed by: OMICtools is listed by: Debian has parent organization: SourceForge |
Free, Available for download, Freely available | OMICS_02358 | http://mipe.sourceforge.net/, https://sources.debian.org/src/mipe/ | SCR_003065 | SciCrunch Registry | Minimal Information for PCR Experiments | 2026-10-10 12:36:46 | 32 | |||||||
|
eQtlBma Resource Report Resource Website 1+ mentions |
eQtlBma (RRID:SCR_003102) | software resource | Software package that implements Bayesian statistical methods to detect eQTLs jointly in multiple subgroups (e.g. tissues). Key features are to borrow information across subgroups, to explicitly model heterogeneity (qualitatively and quantitatively), and to borrow information across genes to estimate hyper-parameters from the data (empirical Bayes). | standalone software, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Chicago; Illinois; USA |
PMID:23671422 | Free, Available for download, Freely available | biotools:eqtlbma, OMICS_04875 | https://bio.tools/eqtlbma | SCR_003102 | SciCrunch Registry | 2026-10-10 12:36:46 | 6 | |||||||
|
MPprimer Resource Report Resource Website 10+ mentions |
MPprimer (RRID:SCR_003063) | analysis service resource, data analysis service, production service resource, service resource, software resource | A software program for reliable multiplex PCR primer design. It employs the widely used primer design program Primer3 and the primer specificity evaluation program MFEprimer to design and evaluate the candidate primers based on genomic or transcript DNA database, followed by careful examination to avoid primer dimerization. The graph-expanding algorithm derived from the greedy algorithm was used to determine the optimal primer set combinations (PSCs) for multiplex PCR. In addition, it provides a virtual electrophotogram to help users choose the best PSC. It is a valuable tool for designing specific, no dimer formation and amplicons size constrained PSCs to improve the multiplex PCR experiments. | standalone software, pcr, multiplexpcr, mfeprimer, primer3, specificity, dimer, primer design |
is listed by: OMICtools has parent organization: Google Code |
PMID:20298595 | GNU General Public License, v3 | OMICS_02364 | http://biocompute.bmi.ac.cn/MPprimer/ | SCR_003063 | SciCrunch Registry | MPprimer: a program for reliable multiplex PCR primer design | 2026-10-10 12:36:22 | 14 | ||||||
|
Triplex Resource Report Resource Website 10+ mentions |
Triplex (RRID:SCR_003061) | software resource | Software package that provides functions for identification and visualization of potential intramolecular triplex patterns in DNA sequence. The main functionality is to detect the positions of subsequences capable of folding into an intramolecular triplex (H-DNA) in a much larger sequence. The potential H-DNA (triplexes) should be made of as many canonical nucleotide triplets as possible. The package includes visualization showing the exact base-pairing in 1D, 2D or 3D. | software package, mac os x, unix/linux, windows, r, gene regulation, sequence matching, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
PMID:23709494 | Free, Available for download, Freely available | OMICS_06259, biotools:triplex | http://www.fi.muni.cz/~lexa/triplex/, https://bio.tools/triplex | SCR_003061 | SciCrunch Registry | triplex - Search and visualize intramolecular triplex-forming sequences in DNA | 2026-10-10 12:36:21 | 10 | ||||||
|
WormBase Resource Report Resource Website 1000+ mentions |
WormBase (RRID:SCR_003098) | WB, WB REF, WP | data or information resource, data repository, database, service resource, storage service resource | Central data repository for nematode biology including complete genomic sequence, gene predictions and orthology assignments from range of related nematodes.Data concerning genetics, genomics and biology of C. elegans and related nematodes. Derived from initial ACeDB database of C. elegans genetic and sequence information, WormBase includes genomic, anatomical and functional information of C. elegans, other Caenorhabditis species and other nematodes. Maintains public FTP site where researchers can find many commonly requested files and datasets, WormBase software and prepackaged databases. | RIN, Resource Information Network, catalog, database, blast, genomic sequence, gene prediction, orthology assignment, gene function, ortholog, roundworm, geneotype, phenotype, gene mapping, genomics, gene expression, transposon family, c elegans, wormmart, FASEB list, RRID Community Authority |
uses: InterMOD is used by: NIF Data Federation is used by: Resource Identification Portal is used by: PhenoGO is used by: Integrated Animals is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: OMICtools is listed by: re3data.org is listed by: InterMOD is listed by: Resource Information Network is affiliated with: InterMOD is related to: AmiGO is related to: GBrowse is related to: Textpresso is related to: Expression Patterns for C. elegans promoter GFP fusions is related to: C. elegans Gene Knockout Consortium is related to: NIH Data Sharing Repositories is related to: UniParc at the EBI is related to: UniParc is related to: Integrated Manually Extracted Annotation is related to: PhenoGO has parent organization: Cold Spring Harbor Laboratory has parent organization: Washington University in St. Louis; Missouri; USA has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom is parent organization of: C. elegans Development Vocabulary is parent organization of: C. elegans Gross Anatomy Vocabulary is parent organization of: C. elegans Phenotype Vocabulary is parent organization of: OpenWorm works with: A plasmid Editor is organization facet of: Alliance of Genome Resources |
BBSRC ; MRC ; NHGRI ; NHGRI U41 HG002223; NIH Blueprint for Neuroscience Research ; NIHGRI P41 HG02223 |
PMID:24194605 PMID:19910365 PMID:17991679 PMID:15608221 |
nif-0000-00053, OMICS_01664, r3d100010424 | http://www.wormbase.org/#01-23-6, https://doi.org/10.17616/R3089Z | SCR_003098 | SciCrunch Registry | , WB, Worm Base, WB REF, WP | 2026-10-10 12:36:22 | 1911 | |||||
|
mrsFAST Resource Report Resource Website 10+ mentions |
mrsFAST (RRID:SCR_003128) | mrsFAST | software resource | A cache-oblivious algorithm designed to map short reads to reference genome assemblies in a fast and memory-efficient manner. It optimizes cache usage to get higher performance. Currently Supported Features: * Mistmatches, No indels * Paired-end Mapping Mode * Discordant Paired-end Mapping Mode (to be used in conjuction with Variation Hunter) | next-generation sequencing, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: SPLITREAD has parent organization: SourceForge |
PMID:20676076 | Free, Available for download, Freely available | biotools:mrsfast, nlx_156780 | https://bio.tools/mrsfast | SCR_003128 | SciCrunch Registry | mrsFAST: micro-read substitution-only Fast Alignment Search Tool, micro-read substitution-only Fast Alignment Search Tool | 2026-10-10 12:36:23 | 22 | |||||
|
NOISeq Resource Report Resource Website 500+ mentions |
NOISeq (RRID:SCR_003002) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software used for the identification of differentially expressed genes from count data or previously normalized count data. It empirically models the noise distribution of count changes by contrasting fold-change differences (M) and absolute expression differences (D) for all the features in samples within the same condition. This reference distribution is then used to assess whether the M-D values computed between two conditions for a given gene is likely to be part of the noise or represent a true differential expression. | differentially expressed genes, gene identification |
is listed by: OMICtools is hosted by: Bioconductor |
DOI:10.1101/gr.124321.111 | Available for download, Acknowledgement requested | OMICS_01311 | SCR_003002 | SciCrunch Registry | 2026-10-10 12:36:29 | 695 |
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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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