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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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SoftSearch Resource Report Resource Website 1+ mentions |
SoftSearch (RRID:SCR_006683) | SoftSearch | software resource | A sensitive structural variant (SV) detection software tool for Illumina paired-end next-generation sequencing data. It simultaneously utilizes soft-clipping and read-pair strategies for detecting SVs to increase sensitivity. Soft clips are proxies for split-reads that indicate part of the read maps to the reference genome, but the other part is not localized at the same place (e.g. breakpoint spanning reads). Discordant read-pairs refer to a read and its mate, where the insert size is greater (or less than) the expected distribution of the dataset ? or ? where the mapping orientation of the reads is unexpected (e.g. both on the same strand). SoftSearch looks for areas with soft-clipping in the genome that have discordant read pairs supporting the anomaly. Once areas with both these conditions are identified, the read and mate information is extracted directly from the BAM file containing the discordant reads, obviating the need for time-consuming and error-prone complex alignment strategies. Only a small number of soft-masked bases discordant read-pairs are necessary to identify an SV, which on their own would not be sufficient to make an SV call, thus highlighting SoftSearch?s improved sensitivity. SoftSearch is well suited to be ?plugged in? to most sequence analysis workflows, since it requires standard file inputs, such as a BAM file using almost any aligner and a reference genome FASTA file. Because SoftSearch requires soft-masked bases, the only requirement is that the aligner must have this functionality, which is usually turned on by default by many standard aligners (e.g. BWA, Novoalign, etc). | illumina, structural variant, next-generation sequencing, perl, academic |
is listed by: OMICtools has parent organization: Google Code |
GNU General Public License, v2 | OMICS_00322 | SCR_006683 | SoftSearch - Detecting Structural Variations Using Split Reads and Discordant Read Pairs | 2026-07-25 12:06:28 | 5 | |||||||
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GREC Corpus Resource Report Resource Website 1+ mentions |
GREC Corpus (RRID:SCR_006719) | GREC | training set | A semantically annotated corpus of 240 MEDLINE abstracts (167 on the subject of E. coli species and 73 on the subject of the Human species) intended for training information extraction (IE) systems and/or resources which are used to extract events from biomedical literature. The corpus has been manually annotated with events relating to gene regulation by biologists. Each event is centered on either a verb (e.g. transcribe) or nominalized verb (e.g. transcription) and annotation consists of identifying, as exhaustively as possible, the structurally-related arguments of the verb or nominalized verb within the same sentence. Each event argument is then assigned the following information: * A semantic role from a fixed set of 13 roles which are tailored to the biomedical domain. * A biomedical concept type (where appropriate). The corpus in available for download in 2 formats: * A standoff format, based on the BioNLP'09 Shared Task format * An XML format, based on the GENIA event annotation format | annotation, information extraction, text mining, semantic role, semantic search, gene, computational linguistics, gene regulation |
is listed by: FORCE11 is related to: MEDLINE has parent organization: National Centre for Text Mining |
JISC | PMID:19852798 | Creative Commons Attribution-NonCommercial-ShareAlike License, v3 Unported, For Copyright of abstracts refer to PubMed. | nif-0000-06688 | SCR_006719 | Gene Event Regulation Corpus | 2026-07-25 12:06:29 | 3 | |||||
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InnateDB Resource Report Resource Website 100+ mentions |
InnateDB (RRID:SCR_006714) | InnateDB | database, data or information resource | Publicly available database of the genes, proteins, experimentally-verified interactions and signaling pathways involved in the innate immune response of humans, mice and bovines to microbial infection. The database captures coverage of the innate immunity interactome by integrating known interactions and pathways from major public databases together with manually-curated data into a centralized resource. The database can be mined as a knowledgebase or used with the integrated bioinformatics and visualization tools for the systems level analysis of the innate immune response. Although InnateDB curation focuses on innate immunity-relevant interactions and pathways, it also incorporates detailed annotation on the entire human, mouse and bovine interactomes by integrating data (178,000+ interactions & 3,900+ pathways) from several of the major public interaction and pathway databases. InnateDB also has integrated human, mouse and bovine orthology predictions generated using Ortholgue software. Ortholgue uses a phylogenetic distance-based method to identify possible paralogs in high-throughput orthology predictions. Integrated human and mouse conserved gene order and synteny information has also been determined to provide further support for orthology predictions. InnateDB Capabilities: * View statistics for manually-curated innate immunity relevant molecular interactions. New manually curated interactions are submitted weekly. * Search for genes and proteins of interest. * Search for experimentally-verified molecular interactions by gene/protein name, interaction type, cell type, etc. * Search genes/interactions belonging to 3,900 pathways. * Visualize interactions using an intuitive subcellular localization-based layout in Cerebral. * Upload your own list of genes along with associated gene expression data (from up to 10 experimental conditions) to interactively analyze this data in a molecular interaction network context. Once you have uploaded your data, you will be able to interactively visualize interaction networks with expression data overlaid; carry out Pathway, Gene Ontology and Transcription Factor Binding Site over-representation analyses; construct orthologous interaction networks in other species; and much more. * Access curated interaction data via a dedicated PSICQUIC webservice. | gene, immune response, pathway, protein, signaling pathway, interaction, immune, signaling response, gene, orthology prediction, orthology, ortholg, annotation, interactome, gene expression, molecule, protein-protein interaction, molecular interaction, visualization, nucleic acid-protein, nucleic acid, network, web service, transcription factor binding site, software resource, FASEB list |
is listed by: re3data.org is related to: IMEx - The International Molecular Exchange Consortium is related to: Interaction Reference Index is related to: ConsensusPathDB is related to: IMEx - The International Molecular Exchange Consortium is related to: PSICQUIC Registry is related to: PSICQUIC Registry is related to: Gene Ontology is related to: IntAct has parent organization: Simon Fraser University; British Columbia; Canada has parent organization: University of British Columbia; British Columbia; Canada works with: IMEx - The International Molecular Exchange Consortium |
Microbial infection, Allergy, Asthma | Michael Smith Foundation for Health Research ; AllerGen 12ASI1; AllerGen 12B&B2; Teagasc RMIS6018; European Union PSIMEx project contract FP7-HEALTH-2007-223411 |
PMID:23180781 PMID:18766178 |
Free, Freely available | nif-0000-20808, r3d100010676 | https://doi.org/10.17616/R36S43 | SCR_006714 | A Knowledge Resource for Innate Immunity Interactions and Pathways, InnateDB: Systems Biology of the Innate Immune Response, InnateDB - A Knowledge Resource for Innate Immunity Interactions and Pathways | 2026-07-25 12:06:25 | 496 | |||
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EDASeq Resource Report Resource Website 100+ mentions |
EDASeq (RRID:SCR_006751) | EDASeq | software resource | Software for numerical and graphical summaries of RNA-Seq read data. Within-lane normalization procedures to adjust for GC-content effect (or other gene-level effects) on read counts: loess robust local regression, global-scaling, and full-quantile normalization (Risso et al., 2011). Between-lane normalization procedures to adjust for distributional differences between lanes (e.g., sequencing depth): global-scaling and full-quantile normalization (Bullard et al., 2010)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | data analysis, normalization, rna-seq |
is listed by: OMICtools has parent organization: Bioconductor has parent organization: National Cancer Institute |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01231 | SCR_006751 | EDASeq: Exploratory Data Analysis and Normalization for RNA-Seq data | 2026-07-25 12:06:27 | 254 | |||||||
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POLGUI - Matlab Polhemus Interface Resource Report Resource Website 1+ mentions |
POLGUI - Matlab Polhemus Interface (RRID:SCR_006752) | POLGUI | software resource | An interface between MATLAB and the Polhemus Fastrak digitizer used to digitize fiducial locations and scalp EEG electrode locations. There are 5 versions all of which work under MATLAB R14 (on both linux and windows platforms), # polgui_ver1_r14 : works with 1 receiver (stylus pen) # polgui_ver2_r14 : works with 2 receivers (including the pen) # polgui_ver3_r14 : works with 3 receivers(including the pen) # polgui_ver4_r14 : works with 4 receivers (including the pen) # polgui_ver5_r14 : Generic version which works with 1/2/3/4 receivers (WARNING: Ver 5 might be buggy; not fully tested) Requirements: MATLAB R14 (Linux/Windows) | eeg, meg, electrocorticography, linux, matlab, microsoft, magnetic resonance, posix/unix-like, win32 (ms windows), windows |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: SourceForge |
BSD License | nlx_155915 | http://www.nitrc.org/projects/polgui | SCR_006752 | POLGUI - Matlab GUI for Polhemus Fastrak | 2026-07-25 12:06:30 | 4 | ||||||
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mubiomics Resource Report Resource Website 1+ mentions |
mubiomics (RRID:SCR_006785) | mubiomics | software resource | A set of scripts (mostly python) for processing reads generated by the Roche 454 or Illumina next-gen sequencing platforms. Included are quality control, read demultiplexing and microbiome characterisation scripts for use with usearch, pplacer and RDP classifier. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_01059 | SCR_006785 | mubiomics - Scripts for processing next-gen sequencing data | 2026-07-25 12:06:28 | 3 | |||||||||
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ShortRead Resource Report Resource Website 100+ mentions |
ShortRead (RRID:SCR_006813) | ShortRead | software resource | Software package for input, quality assessment and exploration of high-throughput sequence data. Used for input, quality assurance, and basic manipulation of `short read'' DNA sequences such as those produced by Solexa, 454, and related technologies, including exible import of common short read data formats. | high throughput sequence data, short read, DNA sequences, short read data |
is listed by: OMICtools is listed by: Debian is listed by: SoftCite has parent organization: Bioconductor |
PMID:19654119 | Free, Available for download, Freely available | OMICS_01076 | https://sources.debian.org/src/r-bioc-shortread/ | SCR_006813 | ShortRead - Classes and methods for high-throughput short-read sequencing data. | 2026-07-25 12:06:29 | 225 | |||||
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mutationSeq Resource Report Resource Website 10+ mentions |
mutationSeq (RRID:SCR_006815) | mutationSeq | software resource | A software suite using feature-based classifiers for somatic mutation prediction from paired tumour/normal next-generation sequencing data. mutationSeq has the advantages of integrating different features (e.g., base qualities, mapping qualities, strand bias, and tailed distance features), and validated somatic mutations to make predictions. Given paired normal/tumour bam files, mutationSeq will output the probability of each candidate site being somatic. | next-generation sequencing, somatic mutation, tumor, normal |
is listed by: OMICtools is related to: JointSNVMix has parent organization: BC Cancer Agency |
Tumor, Normal | PMID:22084253 | OMICS_00086 | SCR_006815 | 2026-07-25 12:06:28 | 24 | |||||||
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University of Rostock; Mecklenburg-Vorpommern; Germany Resource Report Resource Website 1+ mentions |
University of Rostock; Mecklenburg-Vorpommern; Germany (RRID:SCR_006816) | university | Public university located in Rostock, Mecklenburg-Vorpommern, Germany. Founded in 1419. |
is parent organization of: neuroVIISAS is parent organization of: SysZNF - C2H2 Zinc Finger genes |
nlx_151399, grid.10493.3f, Wikidata:Q159895, ISNI:121858338 | https://ror.org/03zdwsf69 | SCR_006816 | Universit�t Rostock, University of Rostock, Universitat Rostock | 2026-07-25 12:06:29 | 1 | |||||||||
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RIPSeeker Resource Report Resource Website 10+ mentions |
RIPSeeker (RRID:SCR_006810) | RIPSeeker | software resource | A statistical software package for identifying protein-associated transcripts from RIP-seq experiments. Infer and discriminate RIP peaks from RIP-seq alignments using two-state HMM with negative binomial emission probability. While RIPSeeker is specifically tailored for RIP-seq data analysis, it also provides a suite of bioinformatics tools integrated within this self-contained software package comprehensively addressing issues ranging from post-alignments processing to visualization and annotation. | rip-seq |
is listed by: OMICtools has parent organization: Bioconductor |
GNU General Public License, v2 | OMICS_00569 | SCR_006810 | RIPSeeker: a statistical package for identifying protein-associated transcripts from RIP-seq experiments | 2026-07-25 12:06:29 | 10 | |||||||
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BioBricks Foundation Resource Report Resource Website 10+ mentions |
BioBricks Foundation (RRID:SCR_006779) | BBF | institution | The BioBricks Foundation (BBF) is dedicated to advancing synthetic biology to benefit all people and the planet. To achieve this, we must make engineering biology easier, safer, equitable, and more open. We do this in the following ways: by ensuring that the fundamental building blocks of synthetic biology are freely available for open innovation; by creating community, common values and shared standards; and by promoting biotechnology for all constructive interests. We envision a world in which scientists and engineers work together using BioBric parts freely available standardized biological parts to create safe, ethical solutions to the problems facing humanity. We envision synthetic biology as a force for good in the world. We see a future in which architecture, medicine, environmental remediation, agriculture, and many other fields are using the technology of synthetic biology. Our supporters are many and include corporations, individuals, institutions, foundations, government, corporations, and others. Currently, the BBF''s key programs include: * BIOFAB * BioBrick Public Agreement * Technical Standards Framework * Conferences and Workshops * BBF Global Network * OpenWetWare | is parent organization of: OpenWetWare | grid.487833.3, nlx_19572 | https://ror.org/03kqtp318 | SCR_006779 | 2026-07-25 12:06:30 | 35 | |||||||||
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PeproTech Resource Report Resource Website 10000+ mentions |
PeproTech (RRID:SCR_006802) | commercial organization | An Antibody supplier | nlx_152428 | SCR_006802 | 2026-07-25 12:06:31 | 27848 | ||||||||||||
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Life Sciences Discovery Fund Resource Report Resource Website 1+ mentions |
Life Sciences Discovery Fund (RRID:SCR_006845) | LSDF | institution | Funds innovative research and development in Washington state to promote life sciences competitiveness, enhance economic vitality, and improve health and health care. Its grantmaking opportunities are designed to leverage the state''s investment in research and development by achieving three goals: promoting health; making the life sciences sector more competitive; and strengthening Washington''s economy. LSDF currently offers two different types of granting mechanisms for both for-profit and non-profit organizations in Washington: * Proof of Concept grants to enhance the commercial viability of intellectual property developed by non-profit organizations or enhance the competitiveness of early-stage companies for private equity investment. (This grant mechanism combines the Commercialization and PreCede mechanisms offered in prior years.) * Opportunity grants to fund extraordinary research and development proposals having the ability to significantly leverage LSDF dollars against those from other sources. | life science, health, health care, economic well being, grant | nlx_151984, grid.475232.5 | https://ror.org/05tzak412 | SCR_006845 | 2026-07-25 12:06:28 | 3 | |||||||||
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NeuronVisio Resource Report Resource Website 1+ mentions |
NeuronVisio (RRID:SCR_006839) | Neuronvisio | d visualization software | A Graphical User Interface for NEURON simulator environment with 3D capabilities. Neuronvisio makes easy to select and investigate sections'''' properties and it offers easy integration with matplotlib for plotting the results. The geometry can be saved using NeuroML and the computational results in a customized and extensible HDF5 format; the results can then be reload in the software and analyzed in a later stage, without re-running the simulation. Featuring 3D visualization of the model with the possibility to change it runtime; creation of vectors to record any variables present in the section; pylab integration to plot directly the result of the simulation; exploration of the timecourse of any variable among time using a color coded scale; saving the results simulation for later analysis; automatic download and running of models in ModelDB. | 3d visualization, electrophysiological model, hdf storage, matplotlib integration, neuron model, visualization, neuron, visualization, electrophysiology |
is related to: INCF Software Center is related to: NEURON is related to: ModelDB has parent organization: European Bioinformatics Institute |
Wellcome Trust | PMID:22685429 | GNU General Public License, Acknowledgement requested | nlx_156723 | SCR_006839 | Neuron visio | 2026-07-25 12:06:28 | 3 | |||||
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EBCall Resource Report Resource Website 10+ mentions |
EBCall (RRID:SCR_006791) | EBCall | software resource | A software package for somatic mutation detection (including InDels). EBCall uses not only paired tumor/normal sequence data of a target sample, but also multiple non-paired normal reference samples for evaluating distribution of sequencing errors, which leads to an accurate mutaiton detection even in case of low sequencing depths and low allele frequencies. | mutation, cancer, genome, sequencing, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Tokyo; Tokyo; Japan |
PMID:23471004 | Copyright conditions, Acknowledgement required | biotools:ebcall, OMICS_00084 | https://bio.tools/ebcall | SCR_006791 | EBCall (Empirical Baysian mutation Calling), Empirical Baysian mutation Calling | 2026-07-25 12:06:27 | 19 | |||||
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Pel-Freez Biologicals Resource Report Resource Website 100+ mentions |
Pel-Freez Biologicals (RRID:SCR_006827) | commercial organization | An Antibody supplier | nlx_152427 | SCR_006827 | Pel-Freez | 2026-07-25 12:06:32 | 143 | |||||||||||
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BAMStats Resource Report Resource Website 10+ mentions |
BAMStats (RRID:SCR_006973) | BAMStats | software resource | A GUI desktop tool for calculating and displaying metrics to assess the success of Next Generation Sequencing mapping tools. BAMstats is written in Java and based around the Picard API. | matlab, next generation sequencing, java |
is listed by: OMICtools has parent organization: SourceForge |
GNU General Public License | OMICS_01034 | SCR_006973 | 2026-07-25 12:06:31 | 10 | ||||||||
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University of Wyoming; Wyoming; USA Resource Report Resource Website 1+ mentions |
University of Wyoming; Wyoming; USA (RRID:SCR_007020) | UW | university | Public land grant research university in Laramie, Wyoming. |
is parent organization of: bamova is parent organization of: TAED - The Adaptive Evolution Database is parent organization of: University of Wyoming School of Pharmacy is parent organization of: University of Wyoming Stable Isotope Core Facility is parent organization of: University of Wyoming Center for Advanced Scientific Instrumentation CASI Core Facility |
Wikidata:Q1326975, ISNI:0000 0001 2109 0381, nlx_97727, Crossref funder ID:100008106, grid.135963.b | https://ror.org/01485tq96 | SCR_007020 | UWYO | 2026-07-25 12:06:32 | 1 | ||||||||
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RamiGO Resource Report Resource Website 10+ mentions |
RamiGO (RRID:SCR_006922) | RamiGO | software resource | Software package with an R interface sending requests to AmiGO visualize, retrieving DAG GO trees, parsing GraphViz DOT format files and exporting GML files for Cytoscape. Also uses RCytoscape to interactively display AmiGO trees in Cytoscape. | visualization, analysis, ontology or annotation search engine, ontology or annotation visualization, other analysis, classification, go, graph, network, third party client, windows, mac os x, linux, unix, bio.tools |
is listed by: Gene Ontology Tools is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: Gene Ontology is related to: Cytoscape is related to: AmiGO has parent organization: Dana-Farber Cancer Institute has parent organization: Bioconductor |
PMID:23297033 | Artistic License, v2 | biotools:ramigo, OMICS_02267, nlx_149331 | http://bioconductor.org/packages/release/bioc/html/RamiGO.html, https://bio.tools/ramigo | SCR_006922 | ramigo, RamiGO - AmiGO visualize R interface | 2026-07-25 12:06:30 | 11 | |||||
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RazerS Resource Report Resource Website 10+ mentions |
RazerS (RRID:SCR_006889) | RazerS | software resource | A read mapping software program with adjustable sensitivity based on counting q-grams. RazerS 3 supports shared-memory parallelism, an additional seed-based filter with adjustable sensitivity, a much faster, banded version of the Myers? bit-vector algorithm for verification, memory saving measures and support for the SAM output format. This leads to a much improved performance for mapping reads, in particular long reads with many errors. | next-generation sequencing, c++, openmp, linux, mac os x, windows |
is listed by: OMICtools has parent organization: Free University of Berlin; Berlin; Germany |
PMID:22923295 PMID:19592482 |
GNU General Public License | OMICS_00679 | SCR_006889 | 2026-07-25 12:06:29 | 13 |
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Data set from Kravitz, Owen and Kretizer's 2012 paper "Optogenetic identification of striatal projection neuron subtypes during in vivo recordings."
