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Resource Name Proper Citation Abbreviations Resource Type Description Keywords Resource Relationships Related Condition Funding Defining Citation Availability Specification URL Alternate IDs Alternate URLs Old URLs Parent Organization Resource ID Synonyms Record Last Update Mentions Count
ORMAN
 
Resource Report
Resource Website
1+ mentions
ORMAN (RRID:SCR_005188) ORMAN software resource A software tool for resolving multi-mappings within an RNA-Seq SAM file. bio.tools is listed by: OMICtools
is listed by: Debian
is listed by: bio.tools
has parent organization: SourceForge
PMID:24130305 OMICS_01284, biotools:orman https://bio.tools/orman SCR_005188 ORMAN : Optimal Resolution of Ambiguous RNA-Seq Multi-mappings in the Presence of Novel Isoforms 2026-08-08 11:58:25 4
FRCbam
 
Resource Report
Resource Website
10+ mentions
FRCbam (RRID:SCR_005189) software resource Software package containing tools to process bam files in order to evaluate and analyze de novo assembly / assemblers and identify Structural Variations suspicious genomics regions. The tools have been already successfully applied in several de novo and resequencing projects. This package contains two tools: # FRCbam: tool to compute Feature Response Curves in order to validate and rank assemblies and assemblers # FindTranslocations: tool to identify chromosomal rearrangements using Mate Pairs standalone software, sam, bam is listed by: OMICtools PMID:23284938 GNU General Public License, v3 OMICS_04070 SCR_005189 2026-08-08 11:58:32 11
University of KwaZulu-Natal; Durban; South Africa
 
Resource Report
Resource Website
1+ mentions
University of KwaZulu-Natal; Durban; South Africa (RRID:SCR_005222) UKZN university University with five campuses in the province of KwaZulu-Natal in South Africa. It was formed on 1 January 2004 after the merger between the University of Natal and the University of Durban-Westville. is parent organization of: Africa Centre Biobank
is parent organization of: BioAfrica HIV Informatics in Africa
is parent organization of: Africa Centre for Health and Population Studies
nlx_51412, ISNI:0000 0001 0723 4123, Wikidata:Q727516, grid.16463.36, Crossref funder ID:501100004695 https://ror.org/04qzfn040 SCR_005222 University of KwaZulu-Natal, University of KwaZulu Natal 2026-08-08 11:58:25 4
SeqAnt
 
Resource Report
Resource Website
1+ mentions
SeqAnt (RRID:SCR_005186) SeqAnt production service resource, software resource, data analysis service, analysis service resource, service resource A free web service and open source software package that performs rapid, automated annotation of DNA sequence variants (single base mutations, insertions, deletions) discovered with any sequencing platform. Variant sites are characterized with respect to their functional type (Silent, Replacement, 5' UTR, 3' UTR, Intronic, Intergenic), whether they have been previously submitted to dbSNP, and their evolutionary conservation. Annotated variants can be viewed directly on the web browser, downloaded in a tab delimited text file, or directly uploaded in a Browser Extended Data (BED) format to the UCSC genome browser. SeqAnt further identifies all loci harboring two or more coding sequence variants that help investigators identify potential compound heterozygous loci within exome sequencing experiments. In total, SeqAnt resolves a significant bottleneck by allowing an investigator to rapidly prioritize the functional analysis of those variants of interest. annotation, dna sequence variant, single base mutation, insertion, deletion, sequencing, mutation, variant, sequence variant, perl, sequence, genome is listed by: OMICtools
has parent organization: Emory University; Georgia; USA
has parent organization: SourceForge
PMID:20854673 GNU General Public License, v2 OMICS_00182 SCR_005186 SeqAnt - Sequence Annotator 2026-08-08 11:58:32 2
NGS-SNP
 
Resource Report
Resource Website
10+ mentions
NGS-SNP (RRID:SCR_005182) NGS-SNP software resource A collection of command-line scripts for providing rich annotations for SNPs identified by the sequencing of transcripts or whole genomes from organisms with reference sequences in Ensembl. Included among the annotations, several of which are not available from any existing SNP annotation tools, are the results of detailed comparisons with orthologous sequences. These comparisons allow, for example, SNPs to be sorted or filtered based on how drastically the SNP changes the score of a protein alignment. Other fields indicate the names of overlapping protein domains or features, and the conservation of both the SNP site and flanking regions. NCBI, Ensembl, and Uniprot IDs are provided for genes, transcripts, and proteins when applicable, along with Gene Ontology terms, a gene description, phenotypes linked to the gene, and an indication of whether the SNP is novel or known. A ?Model_Annotations? field provides several annotations obtained by transferring in silico the SNP to an orthologous gene, typically in a well-characterized species. annotation, snp, sequencing, transcript, genome, reference sequence, indel, annotate, reference chromosome, reference transcript, gene, command-line is listed by: OMICtools
is related to: Ensembl
has parent organization: University of Alberta; Alberta; Canada
OMICS_00177 SCR_005182 2026-08-08 11:58:34 33
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
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
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
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
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
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
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
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
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
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
Kepler
 
Resource Report
Resource Website
10+ mentions
Kepler (RRID:SCR_005252) Kepler workflow software, software resource, software application, data processing software Kepler is a software application for analyzing and modeling scientific data. Using Kepler''s graphical interface and components, scientists with little background in computer science can create executable models, called scientific workflows, for flexibly accessing scientific data (streaming sensor data, medical and satellite images, simulation output, observational data, etc.) and executing complex analyses on this data. Kepler is developed by a cross-project collaboration led by the Kepler/CORE team. The software builds upon the mature Ptolemy II framework, developed at the University of California, Berkeley. Ptolemy II is a software framework designed for modeling, design, and simulation of concurrent, real-time, embedded systems. The Kepler Project is dedicated to furthering and supporting the capabilities, use, and awareness of the free and open source, scientific workflow application, Kepler. Kepler is designed to help scien��tists, analysts, and computer programmers create, execute, and share models and analyses across a broad range of scientific and engineering disciplines. Kepler can operate on data stored in a variety of formats, locally and over the internet, and is an effective environment for integrating disparate software components, such as merging R scripts with compiled C code, or facilitating remote, distributed execution of models. Using Kepler''s graphical user interface, users simply select and then connect pertinent analytical components and data sources to create a scientific workflowan executable representation of the steps required to generate results. The Kepler software helps users share and reuse data, workflows, and compo��nents developed by the scientific community to address common needs. Kepler is a java-based application that is maintained for the Windows, OSX, and Linux operating systems. The Kepler Project supports the official code-base for Kepler development, as well as provides materials and mechanisms for learning how to use Kepler, sharing experiences with other workflow developers, reporting bugs, suggesting enhancements, etc. The Kepler Project Leadership Team works to assure the long-term technical and financial viability of Kepler by making strategic decisions on behalf of the Kepler user community, as well as providing an official and durable point-of-contact to articulate and represent the interests of the Kepler Project and the Kepler software application. Details about how to get more involved with the Kepler Project can be found in the developer section of this website. software, workflow is listed by: SoftCite
is related to: bioKepler
has parent organization: University of California at Davis; California; USA
has parent organization: University of California at Santa Barbara; California; USA
has parent organization: University of California at San Diego; California; USA
NSF 0722079 nlx_144278 SCR_005252 Kepler Project 2026-08-08 11:58:32 49
HIV Neurobehavioral Research Center
 
Resource Report
Resource Website
10+ mentions
HIV Neurobehavioral Research Center (RRID:SCR_005370) data or information resource, portal, topical portal The mission of the HIV Neurobehavioral Research Center (HNRC) is to increase our understanding of how HIV and other diseases affect the human nervous system. The HNRC conducts local, national, and international research devoted to advancing our knowledge of the prevention, diagnosis and treatment of HIV-related diseases as they affect the brain and nervous system, and result in impairment of everyday functioning. Research areas of the Center include: - The incidence, prevalence, and features of neurocognitive impairment caused by HIV - The attributes of the virus, host, and host-virus interactions that determine the presentation of HIV-associated neurocognitive disorders - Possible molecular and cellular mechanisms of nervous system impairment, including the mechanisms by which host-virus factors generate neural injury and neurobehavioral disorders - The cerebrospinal fluid (CSF) as a window on CNS events * The role of co-pathogens and comorbidities in neuroAIDS (e.g., hepatitis C infection, methamphetamine abuse) - Real life implications of neurocognitive impairment in terms of work, daily life, and survival - The effects of HIV disease and neurocognitive impairment on family and social adaptation - NeuroAIDS in resource limited settings - Treatments for neurocognitive impairment and behavioral interventions HNRC also has a Developmental Grants Program (DGP), the primary goal of which is the initiation of innovative studies by junior faculty and trainees at UCSD or affiliated institutions with the following objectives: 1. Recruitment to neuroAIDS research of new investigators or established investigators without prior experience in the field; 2. Generation and pilot testing of new research initiatives; 3. Fostering collaboration among investigators from throughout Southern California. The program provides to qualified investigators and trainees any appropriate combination of the following forms of support: 1. Small, 1-2 year grants to support pilot studies; 2. Access to HNRC core resources such as data, specimens, participants, equipment, administrative support, or expert consultation and technical assistance. Lastly, The the NHRC Mentored Investigator Program recruits, supports, and follows the progress of graduate students, postdoctoral (Ph.D. or M.D.) fellows, and junior faculty in disciplines relevant to HNRC research. The HNRC is committed to tailoring our training opportunities to the backgrounds and interests of candidates from a variety of disciplines who join us with various levels of training and experience in research. We have and will continue to provide training and mentoring of medical students, doctoral students in clinical psychology, and postdoctoral fellows in Medicine, Psychiatry, Neurology, and Psychology. Sponsors: The Center is supported by public funding from the National Institutes of Health, the State of California, and other sources. abuse, brain, cellular, cerbrospinal fluid (csf), clinical psychology, comorbidity, co-pathogen, diagnosis, disease, disorder, hepatitis c, hiv, host-virus factor, host-virus interaction, human, impairment, infection, mechanism, medicine, methamphetamine, molecular, nervous system, neural, neurobehavioral, neurocognitive, neurology, prevention, psychiatry, psychology, social adaption, virus has parent organization: University of California at San Diego; California; USA nif-0000-10508 SCR_005370 HNRC 2026-08-08 11:58:33 37
University of Liege; Wallonia; Belgium
 
Resource Report
Resource Website
University of Liege; Wallonia; Belgium (RRID:SCR_005369) ULg university Public university in French community of Belgium. International university spreads out over 4 campuses. Its official language is French. is related to: European Gram Negative AntiBacterial Engine
is parent organization of: EnablingOpenScholarship
is parent organization of: fMRI Artefact rejection and Sleep Scoring Toolbox
is parent organization of: Forward: Accurate finite element electromagnetic head models
is parent organization of: University of Liege Interdisciplinary Cluster for Applied Genoproteomics Bioinformatics Core Facility
nlx_155544 SCR_005369 The University of Liege, University of Liège, Université de Liège 2026-08-08 11:58:27 0
PhenoMan
 
Resource Report
Resource Website
1+ mentions
PhenoMan (RRID:SCR_005249) PhenoMan software resource An interactive software program that integrates phenotypic data exploration, selection, management and quality control using a unified platform for association studies of rare and common variants. phenotype, quality control, statistical genetics, association study, python, bio.tools is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
has parent organization: Google Code
has parent organization: Baylor University; Texas; USA
GNU General Public License, v3 biotools:phenoman, OMICS_00301 https://bio.tools/phenoman SCR_005249 phenoman - Phenotypic data exploration selection management and quality control for association studies of rare and common variants 2026-08-08 11:58:36 1
1000 Functional Connectomes Project
 
Resource Report
Resource Website
10+ mentions
1000 Functional Connectomes Project (RRID:SCR_005361) INDI, 1000 FCP, FCP data or information resource, image collection, project portal, catalog, database, service resource, storage service resource, portal, data repository, image repository Collection of resting state fMRI (R-fMRI) datasets from sites around world. It demonstrates open sharing of R-fMRI data and aims to emphasize aggregation and sharing of well-phenotyped datasets. resting state functional mri, fmri, brain, neuroimaging, phenotype, function, data sharing, human, mri, r-fmri, rs-fmri, fc-fmri, rs--fcmri, resting-state, dicom, dti, child, adolescent, brain imaging, neuroinformatics, adult human, phenotype, data set, FASEB list is used by: NIF Data Federation
is used by: DataLad
is used by: Integrated Datasets
is used by: MetaSearch
is listed by: NITRC-IR
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
is listed by: NIH Data Sharing Repositories
is affiliated with: Preprocessed Connectomes Project
is related to: Spanish Resting State Network
is related to: NITRC-IR
is related to: NIH Data Sharing Repositories
is related to: BASH4RfMRI
is related to: 1000 Functional Connectomes Project
has parent organization: NeuroImaging Tools and Resources Collaboratory (NITRC)
is parent organization of: C-PAC
is parent organization of: Neuro Bureau - Berlin Mind and Brain Sample
is parent organization of: Quiron-Valencia Sample
is parent organization of: ABIDE
is parent organization of: Consortium for Reliability and Reproducibility
is parent organization of: ADHD-200 Sample
is parent organization of: FCP Classic Data Sharing Samples
is parent organization of: NKI/Rockland Sample
is parent organization of: NYU Institute for Pediatric Neuroscience Sample
is parent organization of: Virginia Tech Carilion Research Institute Sample
is parent organization of: NKI-RS Multiband Imaging Test-Retest Pilot Dataset
is parent organization of: Beijing: Eyes Open Eyes Closed Study
is parent organization of: Beijing: Short TR Study
is parent organization of: COBRE
NITRIC PMID:23133413
PMID:23123682
Restricted SCR_015771, nlx_144428, r3d100011565, r3d100011555 http://www.nitrc.org/projects/fcon_1000/, https://doi.org/10.17616/R3W05R, https://doi.org/10.17616/R35H0H SCR_005361 INDI, International Neuroimaging Data-Sharing Initiative, fcon_1000, Functional Connectomes Project International Neuroimaging Data-Sharing Initiative (FCP/INDI), 1000 Functional Connectomes Project, FCP/INDI 2026-08-08 11:58:38 48

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