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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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FlyFactorSurvey Resource Report Resource Website 10+ mentions |
FlyFactorSurvey (RRID:SCR_002113) | FlyFactorSurvey | database, data or information resource | Database of Drosophila transcription factor DNA binding specificity using the bacterial one-hybrid method, DNase I or SELEX methods. The database provides community access to recognition motifs and position weight matrices for transcription factors (TFs), including many unpublished motifs. Search tools and flat file downloads are provided to retrieve binding site information (as sequences, matrices and sequence logos) for individual TFs, groups of TFs or for all TFs with characterized binding specificities. Linked analysis tools allow users to identify motifs within the database that share similarity to a query matrix or to view the distribution of occurrences of an individual motif throughout the Drosophila genome. This database and its associated tools provide computational and experimental biologists with resources to predict interactions between Drosophila TFs and target cis-regulatory sequences. | transcription factor, motif, cis-regulatory module, transcription factor binding site, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Massachusetts Medical School; Massachusetts; USA |
NHGRI 1R01HG005287-01A1 | PMID:21097781 | Free, Available for download, Freely available | biotools:flyfactorsurvey, OMICS_01879 | https://bio.tools/flyfactorsurvey | SCR_002113 | 2026-08-08 12:03:39 | 26 | |||||
|
HEXEvent Resource Report Resource Website 1+ mentions |
HEXEvent (RRID:SCR_002106) | HEXEvent | database, data or information resource | A free database that provides a list of human internal exons and reports all their known splice events based on EST information from the UCSC Genome Browser. This list can be restricted by the user to either only a specific region in the genome (by specifying the chromosome, the strand and the start and end position), to a whole chromosome or to a group of genes. Furthermore, exons can be filtered according to their splicing type (constitutive exons, cassette exons and exons with one or more alternative 3' and/or 5' splice sites). In order to extract a customized set of exons, the user-specific definitions of exon types can be fixed. The user needs to specify in what fraction of ESTs an exon is allowed to be alternatively spliced in order to still be called constitutive. Furthermore, the user can restrict the set of requested cassette exons by a certain upper inclusion level, which, for instance, is useful when only looking for low-inclusion exons. | exon, splicing, est, splice event, gene, chromosome, genome, splice |
is listed by: OMICtools is related to: UCSC Genome Browser has parent organization: University of California at Irvine; California; USA |
PMID:23118488 | THIS RESOURCE IS NO LONGER IS SERVICE. | OMICS_01888 | SCR_002106 | HEXEvent - a database of Human EXon splicing Events | 2026-08-08 12:03:39 | 5 | ||||||
|
Bacteriome.org Resource Report Resource Website 1+ mentions |
Bacteriome.org (RRID:SCR_001934) | Bacteriome.org | database, data or information resource | Database integrating physical (protein-protein) and functional interactions within the context of an E. coli knowledgebase. Presently the resource offers access to two types of network: * A network of functional interactions derived through exploiting available functional genomic datasets within a Bayesian framework * Two networks of experimentally derived protein-protein interactions - a "core" network consisting of interactions deemed to be of "high quality"; and an "extended" network which extends the "core" network by including interactions for which experimental evidence is less strong. | functional interaction, genetics, genome, protein, protein-protein interaction, protein interaction, function, evolution, structure, gene, phylogenetic profile, chromosome, blast, phylogenetic, complex, network |
is listed by: OMICtools has parent organization: University of Toronto; Ontario; Canada |
Canadian Institutes of Health Research | PMID:219798435 PMID:17942431 |
nif-0000-02592, OMICS_01899, r3d100012726 | http://128.100.134.188/bacteriome/ | SCR_001934 | Bacteriome.org - Bacterial Protein Interaction Database | 2026-08-08 12:03:38 | 4 | |||||
|
Mpstruct Resource Report Resource Website 10+ mentions |
Mpstruct (RRID:SCR_013284) | Mpstruct | data or information resource, data set | Table providing information about integral membrane proteins whose crystallographic, or sometimes NMR, structures have been determined to a resolution sufficient to identify TM helices of helix-bundle membrane proteins (typically 4 - 4.5 angstroms). It is based upon Preusch et al. (1998) as revised by White & Wimley (1999). Reference is made to all of the protein types whose structures have been determined. They have attempted to make the database as inclusive as possible. | membrane protein, structure, protein, FASEB list |
is listed by: OMICtools has parent organization: University of California at Irvine; California; USA |
OMICS_01610 | SCR_013284 | Membrane Proteins of Known 3D Structure | 2026-08-08 12:06:18 | 46 | ||||||||
|
cnvHiTSeq Resource Report Resource Website 1+ mentions |
cnvHiTSeq (RRID:SCR_013160) | cnvHiTSeq | commercial organization, software resource | A set of Java-based command-line tools for detecting Copy Number Variants (CNVs) using next-generation sequencing data. | matlab |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23259578 | Commercial license | OMICS_00342 | SCR_013160 | cnvHiTSeq - A set of tools for detecting CNVs using sequencing data | 2026-08-08 12:06:18 | 4 | ||||||
|
Amazon Web Services Resource Report Resource Website 50+ mentions |
Amazon Web Services (RRID:SCR_012854) | AWS | computational hosting, service resource | IT infrastructure services for businesses in the form of web services, now commonly known as cloud computing. This highly reliable, scalable, low-cost infrastructure platform in the cloud powers hundreds of thousands of businesses. With data center locations in the U.S., Europe, Singapore, and Japan, customers across all industries are taking advantage of the following benefits: * Low cost * Agility and Instant Elasticity * Open and Flexible * Secure | cloud computing, cloud, web service |
is listed by: OMICtools is related to: Mercury is related to: PathSeq is parent organization of: NITRC Computational Environment is parent organization of: Amazon Web Services Public Data Sets is parent organization of: 1000 Genomes Project and AWS |
OMICS_01201, nlx_144341 | SCR_012854 | 2026-08-08 12:06:17 | 91 | |||||||||
|
dChip Software Resource Report Resource Website 100+ mentions |
dChip Software (RRID:SCR_013504) | dChip | software resource | Software for analysis and visualization of gene expression and SNP microarrays. |
is listed by: OMICtools is related to: OMICtools |
, OMICS_00719, OMICS_00752, SCR_013506 | SCR_013504 | dChip Software, dChip Software: Analysis and visualization of gene expression and SNP microarrays | 2026-08-08 12:06:24 | 456 | |||||||||
|
qBasePLUS Resource Report Resource Website 100+ mentions |
qBasePLUS (RRID:SCR_003370) | qbase+ | commercial organization, software resource | Software program for quantitative PCR (qPCR) data analysis based on geNorm and qBase technology. | real-time quantitative pcr |
is listed by: OMICtools is listed by: SoftCite is related to: geNORM has parent organization: Biogazelle |
PMID:17291332 | Free, Available for download, Freely available | OMICS_02320 | https://biogazelle-qbaseplus.software.informer.com/2.0/ | http://medgen.ugent.be/qbase/ | SCR_003370 | 2026-08-08 12:05:48 | 344 | |||||
|
PANDAseq Resource Report Resource Website 500+ mentions |
PANDAseq (RRID:SCR_002705) | software resource, source code | Software program to align Illumina reads, optionally with PCR primers embedded in the sequence, and reconstruct an overlapping sequence. | standalone software, unix/linux, mac os x, windows, c | is listed by: OMICtools | PMID:22333067 | Free, Available for download, Freely available | OMICS_05255 | SCR_002705 | PAired-eND Assembler for DNA sequences | 2026-08-08 12:05:43 | 720 | |||||||
|
FastPCR Resource Report Resource Website 50+ mentions |
FastPCR (RRID:SCR_003155) | FastPCR | commercial organization, software resource | Software tool for PCR primers or probe design, in silico PCR, oligonucleotide assembly and analyses, alignment and repeat searching. | probe design, probe, windows, pcr primer | is listed by: OMICtools | PMID:24395370 | Free, Available for download, Freely available | OMICS_02336 | SCR_003155 | 2026-08-08 12:05:48 | 93 | |||||||
|
CistromeFinder Resource Report Resource Website 1+ mentions |
CistromeFinder (RRID:SCR_005405) | CistromeFinder | data or information resource, data set | Data portal that can help query, evaluate and visualize publicly available Chromatin immunoprecipitation and DNase I hypersensitivity assays with high-throughput sequencing data in human and mouse. The database currently contains 6378 samples over 4391 datasets, 313 factors and 102 cell lines or cell populations (May 2013). Each dataset has gone through a consistent analysis and quality control pipeline; therefore, users could evaluate the overall quality of each dataset before examining binding sites near their genes of interest. CistromeFinder is integrated with UCSC genome browser for visualization, Primer3Plus for ChIP-qPCR primer design and CistromeMap for submitting newly available datasets. It also allows users to leave comments to facilitate data evaluation and update. | chip-seq, dnase-seq, cell, tissue, disease, histone modification, transcription factor, chromatin regulator, dnase, binding site, gene, transcription regulation |
is listed by: OMICtools is related to: UCSC Genome Browser is related to: CistromeMap has parent organization: Dana-Farber Cancer Institute |
PMID:23508969 | The community can contribute to this resource | OMICS_00528 | SCR_005405 | 2026-08-08 12:05:51 | 2 | |||||||
|
Picard Resource Report Resource Website 10000+ mentions Rating or validation data |
Picard (RRID:SCR_006525) | software resource, software toolkit, source code | Java toolset for working with next generation sequencing data in the BAM format. | next generation sequencing, java, bam |
is listed by: OMICtools is listed by: Debian is listed by: SoftCite has parent organization: SourceForge has parent organization: Broad Institute is required by: SL-quant |
Available for download, Free | OMICS_01066 | http://sourceforge.net/projects/picard/, https://github.com/broadinstitute/picard, https://sources.debian.org/src/picard-tools/ | SCR_006525 | 2026-08-08 12:05:44 | 15653 | ||||||||
|
Biopieces Resource Report Resource Website 10+ mentions |
Biopieces (RRID:SCR_005783) | Biopieces | software resource, software toolkit, source code | A collection of bioinformatics tools that can be pieced together in a very easy and flexible manner to perform both simple and complex tasks. The Biopieces work on a data stream in such a way that the data stream can be passed through several different Biopieces, each performing one specific task: modifying or adding records to the data stream, creating plots, or uploading data to databases and web services. The Biopieces are executed in a command line environment where the data stream is initialized by specific Biopieces which read data from files, databases, or web services, and output records to the data stream that is passed to downstream Biopieces until the data stream is terminated at the end of the analysis. The advantage of the Biopieces is that a user can easily solve simple and complex tasks without having any programming experience. Moreover, since the data format used to pass data between Biopieces is text based, different developers can quickly create new Biopieces in their favorite programming language - and all the Biopieces will maintain compatibility. Finally, templates exist for creating new Biopieces in Perl and Ruby. There are currently ~190 Biopieces (March 2014). | bioinformatics, tool, framework, biopieces, language independent, bio.tools, FASEB list |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Google Project Hosting |
Danish Agency for Science Technology and Innovation 272-06-0325 | GNU General Public License, v2 | nlx_149253, biotools:biopieces, OMICS_01036 | http://code.google.com/p/biopieces/, https://bio.tools/biopieces | SCR_005783 | www.biopieces.org, biopieces - Biopieces is a bioinformatic framework of tools easily used and easily created | 2026-08-08 12:05:51 | 40 | |||||
|
Slidepath Resource Report Resource Website 10+ mentions |
Slidepath (RRID:SCR_005597) | Slidepath | commercial organization, software resource | A high performance, intuitive client viewer with integrated reporting functionality that can be used as a standalone viewer for accessing slides locally, or connected to Digital Image Hub for remote review. | windows 7, windows xp | is listed by: OMICtools | OMICS_00818 | SCR_005597 | SlidePath Gateway, SlidePath Gateway Client Viewer, SlidePath Gateway Client | 2026-08-08 12:05:44 | 44 | ||||||||
|
FinchTV Resource Report Resource Website 500+ mentions |
FinchTV (RRID:SCR_005584) | FinchTV | commercial organization, software resource | Chromatogram viewer that can display an entire trace in a scalable multi-pane view, allows raw data views, BLAST searching and the ability to reverse complement sequences and traces., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | chromatogram, linux, mac osx, windows, solaris, dna sequence trace, dna sequence, trace |
is listed by: OMICtools has parent organization: Geospiza |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01019 | SCR_005584 | FinchTV - A Brilliant Trace Viewer | 2026-08-08 12:05:44 | 646 | |||||||
|
Geneious Microsatellite Plugin Resource Report Resource Website 1+ mentions |
Geneious Microsatellite Plugin (RRID:SCR_005466) | Geneious Microsatellite Plugin | commercial organization, software resource | Free plugin that imports ABI fragment analysis ?les and allows you to visualize traces, ?t ladders, call peaks, predict bins, display alleles in a tabular format and export your data. | matlab |
is listed by: OMICtools has parent organization: Geneious |
Free | OMICS_00104 | SCR_005466 | Streamlined microsatellite genotyping for quick analysis | 2026-08-08 12:05:44 | 1 | |||||||
|
PhenoFam Resource Report Resource Website |
PhenoFam (RRID:SCR_000640) | PhenoFam | software resource, software application | A web-based application that performs gene set enrichment analysis (GSEA) by employing structural and functional information on families of protein domains as annotation terms. | java, javascript, gene, gene set enrichment analysis, structure, function, protein domain, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:20478033 | Free, Available for download, Freely available | OMICS_02230, biotools:phenofam | https://bio.tools/phenofam | SCR_000640 | 2026-08-08 12:04:37 | 0 | ||||||
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iOMICS Resource Report Resource Website |
iOMICS (RRID:SCR_000239) | iOMICS | software resource, service resource | A genomics data analysis platform which generates decision models for healthcare organizations and medical research. This service is meant to utilize data through machine learning methods. | genomic, decision model, machine learning, healthcare, machine learning, medical research | is listed by: OMICtools | Restricted | OMICS_02159 | http://www.iomics.in/overview | SCR_000239 | 2026-08-08 12:04:46 | 0 | |||||||
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ILLUMINUS Resource Report Resource Website |
ILLUMINUS (RRID:SCR_000388) | Illuminus | software resource, software application | A fast and accurate algorithm for assigning single nucleotide polymorphism (SNP) genotypes to microarray data from the Illumina BeadArray technology. | gene, genetic, genomic, c++, single nucleotide polymorphism, genotype, microarray, illumina beadarray, illumina |
is listed by: OMICtools is listed by: Genetic Analysis Software has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
PMID:17846035 | Free, Available for download, Freely available | OMICS_00726, nlx_154408 | http://www.sanger.ac.uk/resources/software/illuminus/ | http://www.sanger.ac.uk/science/tools/illuminus | SCR_000388 | Illuminus: the genotype calling algorithm | 2026-08-08 12:04:46 | 0 | ||||
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Magnolya Resource Report Resource Website 1+ mentions |
Magnolya (RRID:SCR_000164) | software resource, data analytics software, software application | A software which enables copy number variation (CNV) detections without using a reference genome. Magnolya directly compares the two next-generation sequences datasets. | algorithm, copy number, next-generation, reference genome, dataset comparison |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23047563 | Free, Available for download, Freely available | OMICS_00347 | SCR_000164 | 2026-08-08 12:04:36 | 2 |
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