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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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University of Tennessee Genome Science and Technology Graduate Program Resource Report Resource Website |
University of Tennessee Genome Science and Technology Graduate Program (RRID:SCR_000038) | UTK GST, UT Knoxville GST | data or information resource, portal, graduate program resource, organization portal | Graduate School of Genome Science and Technology (GST) is a Life Science graduate program founded on two premises. First, whole-genome sequences and related large-scale datasets have transformed how we perform biological research, a trend that is gathering momentum and is anticipated to frame the way the biology research is accomplished for many years to come. Second, advances in technology, whether at the level of instrumentation, computation, or wet lab reagents, have long been a powerful driving force in biology. The GST program is home to faculty mentors from many walks of life. The virulence factors of pathogenic fungi and the engineering of photosynthetic reaction complexes for bioenergy harvesting are just two examples from the cornucopia of research projects being pursued in GST. | genome, molecular genetics, biochemistry, bioinformatics | has parent organization: University of Tennessee Knoxville; Tennessee; USA | nlx_149162 | SCR_000038 | UTK Genome Science & Technology, UT Genome Science & Technology, UT-ORNL Graduate School of Genome Science and Technology, Graduate School of Genome Science and Technology, University of Tennessee Genome Science & Technology, University of Tennessee Genome Science Technology | 2026-08-08 11:57:11 | 0 | ||||||||
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BlackOPs Resource Report Resource Website |
BlackOPs (RRID:SCR_000032) | sequence analysis software, software resource, software application, data analysis software, data processing software | Open source software tool that simulates experimental RNA-seq and DNA whole exome sequences derived from reference genome, aligns these sequences by custom parameters, detects variants and outputs blacklist of positions and alleles caused by mismapping. Used to characterize mappability of RNA-Seq reads and create blacklist of genomic positions of mismapped reads. This blacklist is used to filter potential false positives from variant or RNA editing calls. | rna seq, false positive, genome editing, rna editing, mismapped reads | has parent organization: SourceForge | PMID:23935067 | Free, Available for download, Freely available | OMICS_01229 | SCR_000032 | BlackOPs: RNA-Seq Variant Blacklist Tool | 2026-08-08 11:57:11 | 0 | |||||||
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RCSB PDB Software Tools Resource Report Resource Website 1+ mentions |
RCSB PDB Software Tools (RRID:SCR_000035) | data or information resource, portal, software resource, topical portal | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Information Portal to Biological Macromolecular Structures provides variety of software tools made available through the RCSB. These tools include: data extraction and deposition preparation tools, data format conversion and validation tools, data parsing tools, dictionary and data management tools, visualization tools that support PDBx/mmCIF, and other PDBx/mmCIF software library tools. | Information Portal, Biological Macromolecular Structure, RCSB, RCSB software tools, data extraction, format conversion, data parsing, data management, visualization, pdbx/mmcif, pdbx, mmcif |
is listed by: LabWorm is related to: Protein Data Bank Markup Language has parent organization: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-31399 | SCR_000035 | RCSB Software Tools | 2026-08-08 11:57:10 | 2 | ||||||||
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RmiR.Hs.miRNA Resource Report Resource Website |
RmiR.Hs.miRNA (RRID:SCR_000101) | software resource | Software package for various databases of microRNA Targets. | software package, unix/linux, mac os x, windows, r, annotation data, custom db schema, mirna |
is listed by: OMICtools is related to: CRAN has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_05797 | SCR_000101 | RmiR.Hs.miRNA: Various databases of microRNA Targets | 2026-08-08 11:57:13 | 0 | ||||||||
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GeneTex Resource Report Resource Website 500+ mentions |
GeneTex (RRID:SCR_000069) | commercial organization | An antibody supplier for the purposes of life science and biomedical research. This company has a wide variety of immunological reagents that focus on areas of research such as cancer, cell biology, epigenetics, immunology and infectious diseases. | antibody, antibodies, supplier, immunology, research, cell biology, cancer, epigenetics, infectious diseases, reagents | nlx_152372 | SCR_000069 | 2026-08-08 11:57:12 | 691 | |||||||||||
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nFuse Resource Report Resource Website 1+ mentions |
nFuse (RRID:SCR_000066) | nFuse | software resource | Software that predicts fusion transcripts and associated CGRs from matched RNA-seq and Whole Genome Shotgun Sequencing (WGSS). | cancer, genomics |
is listed by: OMICtools is listed by: Google Code has parent organization: Simon Fraser University; British Columbia; Canada |
Cancer | PMID:22745232 | Free, Available for download, Freely available, | OMICS_01353 | SCR_000066 | nFuse: Discovery of Complex Genomic Rearrangements in Cancer | 2026-08-08 11:57:12 | 2 | |||||
|
GASV Resource Report Resource Website 1+ mentions |
GASV (RRID:SCR_000061) | GASV | software resource, software application, data analysis software, data processing software | Software tool for identifying structural variants (SVs) from paired-end sequencing data.GASV distribution includes three components that are typically run in succession: the BAM file of unique paired-read mappings is processed; structural variants are identified by clustering discordant fragments; and a probabilistic algorithm improves the specificity of GASV predictions. | paired-end sequencing data, structural variant, probabilistic algorithm, discordant fragment, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: GASVPro has parent organization: Brown University; Rhode Island; USA |
Burroughs Wellcome Fund ; Department of Defense Breast Cancer Research ; ADVANCE Program at Brown University ; NSF 0548311 |
PMID:19477992 | Free, Available for download, Freely available | biotools:gasv, OMICS_01352 | http://compbio.cs.brown.edu/projects/gasv/, https://bio.tools/gasv | SCR_000061 | Geometric Analysis of Structural Variants | 2026-08-08 11:57:12 | 4 | ||||
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ChIPmeta Resource Report Resource Website |
ChIPmeta (RRID:SCR_000054) | software resource, software application, data analysis software, data processing software | Software using a Hierarchical hidden Markov model for jointly analyzing ChIP-chip and ChIP-seq datasets. | chip-chip, chip-seq, ChIP-chip and ChIP-seq datasets analysis, | is listed by: OMICtools | Free, Available for download, Freely available | OMICS_02172 | SCR_000054 | ChIPmeta with HHM | 2026-08-08 11:57:12 | 0 | ||||||||
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FACS Resource Report Resource Website 1+ mentions |
FACS (RRID:SCR_000055) | FACS | software resource | Software for classification of Sequences using Bloom filters that can accurately and rapidly align sequences to a reference sequence. | unix/linux, sequence, bio.tools |
is listed by: OMICtools is listed by: GitHub is listed by: bio.tools is listed by: Debian is listed by: SoftCite has parent organization: SciLifeLab |
PMID:20472541 | Free, Available for download, Freely available | OMICS_02147, biotools:facs | https://bio.tools/facs | SCR_000055 | Fast and Accurate Classification of Sequences | 2026-08-08 11:57:11 | 6 | |||||
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Batman-Seq Resource Report Resource Website |
Batman-Seq (RRID:SCR_000048) | Batman-Seq | software resource | A fast BWT-based short reads mapping tools which uses additional statistical method to model error profile of the sequencing experiment. | c++ | is hosted by: SourceForge | Free, Available for download, Freely available | OMICS_00651 | SCR_000048 | Basic Alignment Tool for MAny Nucleotides | 2026-08-08 11:57:11 | 0 | |||||||
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Indelocator Resource Report Resource Website 10+ mentions |
Indelocator (RRID:SCR_005258) | Indelocator | software resource | A software tool for calling short indels in next generation sequencing data. |
is listed by: OMICtools has parent organization: Broad Institute |
OMICS_00098 | SCR_005258 | 2026-08-08 11:58:32 | 45 | ||||||||||
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Bioinformatics Knowledgeblog Resource Report Resource Website |
Bioinformatics Knowledgeblog (RRID:SCR_005379) | Bioinformatics Knowledgeblog | training material, data or information resource, blog, narrative resource | Series of tutorial material covering a broad selection of topics in bioinformatics. Categories include: Bioinformatics APIs, Data integration, Events, Grid and Cloud Computing, Metabolic modelling, Reviews, Software Comparisons, Statistics, Systems Biology, Transcriptomics, Tutorials. | bioinformatics, application programming interface, data integration, event, grid computing, cloud computing, metabolic modelling, review, statistics, systems biology, transcriptomics, tutorial, software | has parent organization: Knowledge Blog | JISC | Acknowledgement requested, The community can contribute to this resource | nlx_144450 | SCR_005379 | Bioinformatics Knowledge Blog | 2026-08-08 11:58:27 | 0 | ||||||
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GASVPro Resource Report Resource Website 1+ mentions |
GASVPro (RRID:SCR_005259) | GASVPro | sequence analysis software, software resource, software application, data analysis software, data processing software | Software tool combining both paired read and read depth signals into probabilistic model which can analyze multiple alignments of reads. Used to find structural variation in both normal and cancer genomes using data from variety of next-generation sequencing platforms. Used to predict structural variants directly from aligned reads in SAM/BAM format.Combines read depth information along with discordant paired read mappings into single probabilistic model two common signals of structural variation. When multiple alignments of read are given, GASVPro utilizes Markov Chain Monte Carlo procedure to sample over the space of possible alignments. | structural variation, genome, genomics, alignment, sequencing, variant, variation, detection, dna, paired, end, read, sequence |
is listed by: OMICtools is related to: GASV has parent organization: Brown University; Rhode Island; USA |
NHGRI R01 HG5690; Burroughs Wellcome Career Award at the Scientific Interface |
PMID:22452995 | Free, Available for download, Freely available | OMICS_00317 | http://code.google.com/p/gasv/downloads/list | SCR_005259 | GASVPro: Geometric Analysis of Structural Variants | 2026-08-08 11:58:36 | 8 | ||||
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PRISM (Stanford database) Resource Report Resource Website 10000+ mentions |
PRISM (Stanford database) (RRID:SCR_005375) | PRISM | data or information resource, production service resource, data analysis service, database, analysis service resource, service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 5,2022.Tool that predicts interactions between transcription factors and their regulated genes from binding motifs. Understanding vertebrate development requires unraveling the cis-regulatory architecture of gene regulation. PRISM provides accurate genome-wide computational predictions of transcription factor binding sites for the human and mouse genomes, and integrates the predictions with GREAT to provide functional biological context. Together, accurate computational binding site prediction and GREAT produce for each transcription factor: 1. putative binding sites, 2. putative target genes, 3. putative biological roles of the transcription factor, and 4. putative cis-regulatory elements through which the factor regulates each target in each functional role., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | genomic, transcription factor, function, transcription factor binding site, transcription factor regulator, biological role, target gene, target genomic region, genome, FASEB list |
is listed by: OMICtools is listed by: SoftCite is related to: GREAT: Genomic Regions Enrichment of Annotations Tool has parent organization: Stanford University School of Medicine; California; USA |
PMID:23382538 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00489 | SCR_005375 | Predicting Regulatory Information from Single Motifs | 2026-08-08 11:58:38 | 40822 | ||||||
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Knime4Bio Resource Report Resource Website 1+ mentions |
Knime4Bio (RRID:SCR_005376) | Knime4Bio | software resource | A set of custom nodes for the KNIME (The Konstanz Information Miner) graphical workbench, for analysing next-generation sequencing (NGS) data without the requirement of programming skills. | node, next-generation sequencing, knime, bioinformatics, workflow, sequencing, flow, data, bam, wig, bed, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Google Code |
PMID:21984761 | GNU General Public License, v3 | biotools:knime4bio, OMICS_01143 | https://bio.tools/knime4bio | SCR_005376 | Knime4Bio: custom nodes for the interpretation of Next Generation Sequencing data with KNIME | 2026-08-08 11:58:27 | 2 | |||||
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Ergatis Resource Report Resource Website 1+ mentions |
Ergatis (RRID:SCR_005377) | Ergatis | software resource | A web interface and scalable software system for bioinformatics workflows that is used to create, run, and monitor reusable computational analysis pipelines. It contains pre-built components for common bioinformatics analysis tasks. These components can be arranged graphically to form highly-configurable pipelines. Each analysis component supports multiple output formats, including the Bioinformatic Sequence Markup Language (BSML). The current implementation includes support for data loading into project databases following the CHADO schema, a highly normalized, community-supported schema for storage of biological annotation data. Ergatis uses the Workflow engine to process its work on a compute grid. Workflow provides an XML language and processing engine for specifying the steps of a computational pipeline. It provides detailed execution status and logging for process auditing, facilitates error recovery from point of failure, and is highly scalable with support for distributed computing environments. The XML format employed enables commands to be run serially, in parallel, and in any combination or nesting level. | workflow, bioinformatics, workflow management, pipeline, computation, genomics, genome, processing |
is listed by: OMICtools has parent organization: SourceForge has parent organization: University of Maryland School of Medicine; Maryland; USA |
PMID:20413634 | Artistic License | OMICS_01140 | SCR_005377 | ergatis: workflow creation and monitoring interface | 2026-08-08 11:58:33 | 2 | ||||||
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CREST Resource Report Resource Website 50+ mentions |
CREST (RRID:SCR_005257) | CREST | software resource | An algorithm for detecting genomic structural variations at base-pair resolution using next-generation sequencing data. CREST uses pieces of DNA called soft clips to find structural variations. Soft clips are the DNA segments produced during sequencing that fail to properly align to the reference genome as the sample genome is reassembled. CREST uses the soft clips to precisely identify sites of chromosomal rearrangement or where pieces of DNA are inserted or deleted. | genome, structural variation, next-generation sequencing, soft clip |
is listed by: OMICtools has parent organization: Pennsylvania State University |
PMID:21666668 | OMICS_00312 | SCR_005257 | 2026-08-08 11:58:26 | 57 | ||||||||
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MRC Mammalian Genetics Unit Resource Report Resource Website 100+ mentions |
MRC Mammalian Genetics Unit (RRID:SCR_005378) | MGU | data or information resource, portal, topical portal | It is now widely known that animals share many genes with humans and can suffer from the same diseases, for example diabetes or deafness. Investigating these diseases in animals can provide vital leads to understanding both their causes and ways to treat them in humans. This approach to medical research lies at the heart of work at the MRC Mammalian Genetics Unit (MGU) at Harwell in Oxfordshire. In 1995 the MRC Radiobiology Unit was reconstituted to form two new units, the Radiation and Genome Stability Unit and the MGU. These opened in January 1996, together with the UK Mouse Genome Centre which is now part of MGU, making MRC Harwell a unique campus for multi-disciplinary genetics research. Since MGU's Director Steve Brown took the reins in 1996, the unit has dramatically expanded its scientific scope and increased its personnel from 40 to over 100. It now has 13 research programs encompassing molecular genetics, genomics, genetic manipulation and data analysis at all levels, from single genes to the whole genome. With a combination of cutting-edge facilities and expertise unrivaled in Europe, MGU Harwell has become firmly established as one of the world's leading academic centres for mouse genetics. | mouse, genetics, gene |
is parent organization of: European Mouse Phenotyping Resource of Standardised Screens is parent organization of: Europhenome Mouse Phenotyping Resource is parent organization of: International Mouse Strain Resource |
nlx_144449 | http://www.mrc.ac.uk/Ourresearch/Unitscentresinstitutes/Profiles/MGU/index.htm | SCR_005378 | Medical Research Council Mammalian Genetics Unit, MGU Harwell, MRC MGU | 2026-08-08 11:58:38 | 236 | |||||||
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Werblin Lab Resource Report Resource Website |
Werblin Lab (RRID:SCR_005251) | Werblin Lab | video resource, data or information resource, image, laboratory portal, portal, organization portal | The goal of our research is to uncover the neural circuitry that mediates some of the remarkable processing capabilities of the retina. The retina to operates at high spatial and temporal resolution over more than 7 orders of magnitude, to detect the direction of motion, to blank and then recover after saccades, to generate at least a dozen different abstract representations of the visual world. How is all of this, and much more, possible in this tissuepaper-thin array of neurons? Videos and images describing this include: * The retinal hypercircuit. * How the Retina Works * Take a Tour through the Retina * Cartoon of the retina showing layering of neurons * Directional Selectivity * Feedback and Crossover inhibition * Multiple Representations of the Visual Scene ** Pseudo Array Recording Methods ** Multiple Representations of the Visual World ** Regions of Frequency Space * Regions of space/time frequency * Space-time rasters for ON and OFF cells * Patching a neuron in a retinal slice * Targeting Retinal Neuron Subregions with Arficial Rhodopsins | retina, hypercircuit, neuron, ganglion | has parent organization: University of California at Berkeley; Berkeley; USA | nlx_144274 | SCR_005251 | Werblin Lab: Division of Neurobiology; Department of Molecular and Cell Biology | 2026-08-08 11:58:26 | 0 | ||||||||
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MolBioLib Resource Report Resource Website |
MolBioLib (RRID:SCR_005372) | MolBioLib | software resource | A compact, portable, and extensively tested C++11 software framework and set of applications tailored to the demands of next-generation sequencing data and applicable to many other applications. It is designed to work with common file formats and data types used both in genomic analysis and general data analysis. A central relational-database-like Table class is a flexible and powerful object to intuitively represent and work with a wide variety of tabular datasets, ranging from alignment data to annotations. MolBioLib includes programs to perform a wide variety of analysis tasks such as computing read coverage, annotating genomic intervals, and novel peak calling with a wavelet algorithm. This package assumes fluency in both UNIX and C++. | c++, next-generation sequencing, genomic, analysis, genome |
is listed by: OMICtools has parent organization: SourceForge |
PMID:22815363 | OMICS_01145 | SCR_005372 | MolBioLib: C++11 framework for rapid develop and deploy of bioinformatic tasks | 2026-08-08 11:58:38 | 0 |
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