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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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MBCluster.Seq Resource Report Resource Website 1+ mentions |
MBCluster.Seq (RRID:SCR_005079) | MBCluster.Seq | software resource | Software to cluster genes based on Poisson or Negative-Binomial model for RNA-Seq or other digital gene expression (DGE) data. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:24191069 | GNU General Public License, >/=v3 | OMICS_01417, biotools:mbcluster.seq | https://bio.tools/mbcluster.seq | SCR_005079 | MBCluster.Seq: Model-Based Clustering for RNA-seq Data | 2026-08-01 12:02:48 | 1 | |||||
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University of Kansas; Kansas; USA Resource Report Resource Website |
University of Kansas; Kansas; USA (RRID:SCR_005075) | KU | university | Public research university with its main campus in Lawrence, Kansas, and several satellite campuses, research and educational centers, medical centers, and classes across the state of Kansas. |
is parent organization of: HistoWeb: Nervous System is parent organization of: Images from the Clendening Library is parent organization of: Dockground: Benchmarks, Docoys, Templates, and other knowledge resources for DOCKING is parent organization of: DB-PABP: a database of polyanion binding proteins is parent organization of: Autism Genetic Database is parent organization of: University of Kansas Labs and Facilities is parent organization of: University of Kansas Protein Production Group Core Facility is parent organization of: University of Kansas Nuclear Magnetic Resonance Laboratory Core Facility is parent organization of: University of Kansas Molecular Graphics and Modeling Laboratory Core Facility is parent organization of: University of Kansas Medical Center; Kansas; USA is parent organization of: University of Kansas Lawrence Protein Structure and X-ray Crystallography Laboratory Core Facility is parent organization of: University of Kansas Microscopy and Analytical Imaging Research Resource Core Facility is parent organization of: University of Kansas Mass Spectrometry and Analytical Proteomics Core Facility is parent organization of: I-TASSER is parent organization of: University of Kansas Nanofabrication Core Facility |
ISNI:0000 0001 2106 0692, Wikidata:Q52413, nlx_83015, Crossref funder ID:100007859, grid.266515.3 | https://ror.org/001tmjg57 | SCR_005075 | University of Kansas | 2026-08-01 12:02:48 | 0 | ||||||||
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AGORA Resource Report Resource Website 50+ mentions |
AGORA (RRID:SCR_005070) | AGORA | software resource | An algorithm to use optical map information directly within the de Bruijn graph framework to help produce an accurate assembly of a genome that is consistent with the optical map information provided. AGORA takes as input two data structures: OpMap ? an ordered list of fragment sizes representing the optical map; and Edges ? a list of de Bruijn graph edges with their corresponding sequences. | genome assembly, genome, reconstruction | is listed by: OMICtools | PMID:22856673 | OMICS_00039 | SCR_005070 | Assembly Guided by Optical Restriction Alignment | 2026-08-01 12:02:45 | 99 | |||||||
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GRASS Resource Report Resource Website 50+ mentions |
GRASS (RRID:SCR_005071) | GRASS | software resource | A generic algorithm for scaffolding next-generation sequencing assemblies. | next-generation sequencing, scaffolding, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:22492642 | GNU General Public License, v3 | biotools:GRASS, OMICS_00043 | https://bio.tools/GRASS | SCR_005071 | GRASS: a generic algorithm for scaffolding next-generation sequencing assemblies, GeneRic ASembly Scaffolder | 2026-08-01 12:02:48 | 89 | |||||
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Protocol Online - Your labs reference book Resource Report Resource Website 10+ mentions |
Protocol Online - Your labs reference book (RRID:SCR_004937) | Protocol Online | experimental protocol, narrative resource, data or information resource | Database of research protocols in a variety of life science fields, it contains protocols contributed by worldwide researchers as well as links to web protocols hosted by worldwide research labs, biotech companies, personal web sites. The data is stored in a MySql relational database. Protocol Online also hosts discipline specific discussion forums (BioForum), and provides a free PubMed search and alerting service (PubAlert). | bioinformatics, molecular biology, immunology, microbiology, proteomics, cell biology, database |
is used by: NIF Data Federation is used by: Integrated Blogs |
Eppendorf ; Invitrogen ; Chang Bioscience ; Mirus ; KPL ; Oligomaster ; Abcam ; Nature Publishing Group |
nlx_90492 | SCR_004937 | Protocol Online Your lab''s reference book, Protocol-Online | 2026-08-01 12:02:50 | 10 | |||||||
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MapAl Resource Report Resource Website 1+ mentions |
MapAl (RRID:SCR_004938) | MapAl | software resource | A software tool for RNA-Seq expression profiling that builds on the established programs Bowtie and Cufflinks. Allowing an incorporation of ''gene models'' already at the alignment stage almost doubles the number of transcripts that can be measured reliably. | rna?seq |
is listed by: OMICtools has parent organization: BOKU University; Vienna; Austria |
PMID:22485116 | GNU General Public License | OMICS_01261 | SCR_004938 | 2026-08-01 12:02:43 | 1 | |||||||
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Open University; Milton Keynes; United Kingdom Resource Report Resource Website 1+ mentions |
Open University; Milton Keynes; United Kingdom (RRID:SCR_004931) | OU | university | Public research university and the largest university in the UK for undergraduate education. The majority of the OU's undergraduate students are based in the United Kingdom and principally study off-campus; many of its courses can also be studied anywhere in the world. |
is affiliated with: OpenMinTeD is parent organization of: Scholarly Ontologies Project is parent organization of: Cohere is parent organization of: Rexplore |
Wikidata:Q2413375, nlx_19814, grid.10837.3d, ISNI:96069301, Crossref funder ID:100008509 | https://ror.org/05mzfcs16 | SCR_004931 | Open University, The Open University | 2026-08-01 12:02:43 | 3 | ||||||||
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SINA Resource Report Resource Website 100+ mentions |
SINA (RRID:SCR_005067) | SINA | data analysis service, service resource, production service resource, software resource, analysis service resource | Service to align and optionally taxonomically classify your rRNA gene sequences. The results can be combined with any other sequences aligned by SINA or taken from the SILVA databases by concatenation of FASTA files or using the ARB MERGE tool. Note: Submission is currently limited to at most 1000 sequences of at most 6000 bases each. If your requirements exceed this limitation, get Opens internal link in current windowSINA for local installation. | alignment, taxonomic classification, rrna, gene sequence, fasta, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: SILVA is related to: ARB project has parent organization: Max Planck Institute for Marine Microbiology; Bremen; Germany |
PMID:22556368 | Free, Available for download, Freely available | OMICS_01438, biotools:sina | https://bio.tools/sina, https://sources.debian.org/src/sina/, https://github.com/epruesse/SINA | SCR_005067 | SINA Alignment Service, SILVA Incremental Aligner | 2026-08-01 12:02:48 | 369 | |||||
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Bambus Resource Report Resource Website |
Bambus (RRID:SCR_005068) | Bambus | software resource | Software for scaffolding to address some of the challenges encountered when analyzing metagenomes. Scaffolding represents the task of ordering and orienting contigs by incorporating additional information about their relative placement along the genome. While most other scaffolders are closely tied to a specific assembly program, Bambus accepts the output from most current assemblers and provides the user with great flexibility in choosing the scaffolding parameters. In particular, Bambus is able to accept contig linking data other than specified by mate-pairs. Such sources of information include alignment to a reference genome (Bambus can directly use the output of MUMmer), physical mapping data, or information about gene synteny. | scaffolding |
is listed by: OMICtools has parent organization: SourceForge |
PMID:21926123 | Open unspecified license | OMICS_01432 | http://sourceforge.net/apps/mediawiki/amos/index.php?title=Bambus | SCR_005068 | Bambus 2, Bambus 2.0 | 2026-08-01 12:02:53 | 0 | |||||
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Neuron Navigator Resource Report Resource Website |
Neuron Navigator (RRID:SCR_005063) | NNG | data analysis service, data or information resource, database, service resource, d spatial image, production service resource, analysis service resource | Neuron Navigator (NNG) integrates a 3D neuron image database into an easy-to-use visual interface. Via a flexible and user-friendly interface, NNG is designed to help researchers analyze and observe the connectivity within the neural maze and discover possible pathways. With NNG''s 3D neuron image database, researchers can perform volumetric searches using the location of neural terminals, or the occupation of neuron volumes within the 3D brain space. Also, the presence of the neurons under a combination of spatial restrictions can be shown as well. NNG is a result of a multi-discipline collaboration between neuroscientists and computer scientists, and NNG has now been implemented on a coordinated brain space for the Drosophila (fruit fly) brain. Account is required. | image database, connectivity, drosophila, brain, neuron | has parent organization: National Tsing Hua University; Hsinchu; Taiwan | nlx_144057 | SCR_005063 | NNG: Neuron Navigator, NNG: Neuron Navigator - A Database of Drosophila Brain Neurons | 2026-08-01 12:02:48 | 0 | ||||||||
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University of Iowa Carver College of Medicine; Iowa; USA Resource Report Resource Website 1+ mentions |
University of Iowa Carver College of Medicine; Iowa; USA (RRID:SCR_005064) | UI Carver College of Medicine | university | Medical school of the University of Iowa, located in Iowa City, in the U.S. state of Iowa. |
has parent organization: University of Iowa; Iowa; USA is parent organization of: MADS+ - discovery of differential splicing events from Affymetrix exon junction array data is parent organization of: University of Iowa College of Medicine Department of Pharmacology is parent organization of: University of Iowa Magnetic Resonance Research Facility is parent organization of: University of Iowa Center for Gene Therapy Vectore Core is parent organization of: University of Iowa Center for Gene Therapy Clinical Core is parent organization of: University of Iowa Center for Gene Therapy Animal Model Core is parent organization of: University of Iowa Center for Gene Therapy is parent organization of: University of Iowa Center for Gene Therapy Comparative Pathology Core is parent organization of: University of Iowa Center for Gene Therapy Cell Tissue Core |
nlx_68753 | SCR_005064 | University of Iowa Carver College of Medicine, Roy J. and Lucille A. Carver College of Medicine | 2026-08-01 12:02:53 | 1 | |||||||||
|
G-BLASTN Resource Report Resource Website |
G-BLASTN (RRID:SCR_005062) | G-BLASTN | software resource | A GPU-accelerated nucleotide alignment tool based on the widely used NCBI-BLAST. It can produce exactly the same results as NCBI-BLAST, and it also has very similar user commands. It also supports a pipeline mode, which can fully utilize the GPU and CPU resources when handling a batch of medium to large sized queries. | parallel computation 4, blast, alignment, nucleotide, gpu, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: NCBI BLAST has parent organization: Hong Kong Baptist University; Hong Kong; China has parent organization: SourceForge |
Hong Kong Baptist University; Hong Kong; China FRG2/11-12/158; NVIDIA |
PMID:24463183 | Free | OMICS_02263, biotools:g-blastn | http://sourceforge.net/projects/gblastn/, https://bio.tools/g-blastn | SCR_005062 | 2026-08-01 12:02:45 | 0 | |||||
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Classifier for Metagenomic Sequences Resource Report Resource Website 100+ mentions |
Classifier for Metagenomic Sequences (RRID:SCR_004929) | ClaMS | data processing software, data analysis software, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 2nd, 2023. Sequence composition based classifier for metagenomic sequences. It works by capturing signatures of each sequence based on the sequence composition. Each sequence is modeled as a walk in a de Bruijn graph with underlying Markov chain properties. ClaMS captures stationary parameters of the underlying Markov chain as well as structural parameters of the underlying de Bruijn graph to form this signature. In practice, for each sequence to binned, such a signature is computed and matched to similar signatures computed for the training sets. The best match that also qualifies the normalized distance cut-off wins. In the case that the best match does not qualify this cut-off, the sequence remains un-binned. | metagenome, classification, sequence |
is listed by: OMICtools has parent organization: DOE Joint Genome Institute |
DOE contract DE-AC02-05CH11231 | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_005519, nlx_144629, OMICS_01452 | SCR_004929 | 2026-08-01 12:02:46 | 150 | |||||||
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Stanford Research Institute International Resource Report Resource Website 1+ mentions |
Stanford Research Institute International (RRID:SCR_004926) | SRI | institution | Independent, nonprofit research institute conducting client sponsored research and development for government agencies, commercial businesses, foundations, and other organizations. SRI also brings its innovations to the marketplace by licensing its intellectual property and creating new ventures. SRI was founded as Stanford Research Institute in 1946 by a group of West Coast industrialists and Stanford University. SRI formally separated from the University in 1970, and we changed our name to SRI International in 1977. |
is related to: Stanford University; Stanford; California is parent organization of: BioCyc is parent organization of: NIMH Toxicological Screens of Novel Ligands is parent organization of: Project Halo is parent organization of: EcoCyc is parent organization of: NCANDA: Data Integration Component is parent organization of: SRI24 Atlas: Normal Adult Brain Anatomy is parent organization of: HumanCyc: Encyclopedia of Homo sapiens Genes and Metabolism is parent organization of: MetaCyc |
nif-0000-00235 | SCR_004926 | SRI International, Stanford Research Institute | 2026-08-01 12:02:49 | 2 | |||||||||
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MethodBox Resource Report Resource Website 1+ mentions |
MethodBox (RRID:SCR_004928) | MethodBox | data or information resource, data repository, storage service resource, portal, community building portal, service resource, source code, data set, software resource | Collaboration environment for sharing variable sets and statistical methods for analysis across social science survey data. MethodBox enables you to browse and download datasets, share methods and scripts, find fellow researchers with similar interests and share your knowledge. MethodBox source available on Google code. Finding the variables you need to support a particular research question can be time consuming. Wading through hundreds of pages of PDF documents, codebooks and metadata and then trying to find the exact column in a huge spreadsheet can be very frustrating. MethodBox gets you to the variables faster and lets you download only the data you need. You can also share your scripts with others to allow them to adopt best practice quicker than before. | variable, survey data, method, script, data sharing, social science | has parent organization: University of Manchester; Manchester; United Kingdom | ESRC | PMID:20841736 | Account required | nlx_89127 | SCR_004928 | 2026-08-01 12:02:42 | 1 | ||||||
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SLIDE Resource Report Resource Website 10+ mentions |
SLIDE (RRID:SCR_005137) | SLIDE | software resource | Software package that takes exon boundaries and RNA-Seq data as input to discern the set of mRNA isoforms that are most likely to present in an RNA-Seq sample. It is based on a linear model with a design matrix that models the sampling probability of RNA-Seq reads from different mRNA isoforms. To tackle the model unidentifiability issue, SLIDE uses a modified Lasso procedure for parameter estimation. Compared with deterministic isoform assembly algorithms (e.g., Cufflinks), SLIDE considers the stochastic aspects of RNA-Seq reads in exons from different isoforms and thus has increased power in detecting more novel isoforms. Another advantage of SLIDE is its flexibility of incorporating other transcriptomic data such as RACE, CAGE, and EST into its model to further increase isoform discovery accuracy. SLIDE can also work downstream of other RNA-Seq assembly algorithms to integrate newly discovered genes and exons. Besides isoform discovery, SLIDE sequentially uses the same linear model to estimate the abundance of discovered isoforms. |
is listed by: OMICtools has parent organization: University of California at Berkeley; Berkeley; USA |
NIH ; NHGRI HG004695; NHGRI HG005639; NEI EY019094 |
PMID:22135461 | OMICS_01291 | SCR_005137 | sparse linear modeling of RNA-Seq data for isoform discovery and abundance estimation | 2026-08-01 12:02:49 | 32 | |||||||
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VFS Resource Report Resource Website 1+ mentions |
VFS (RRID:SCR_005138) | VFS | software resource | A versatile high-throughput sequencing (HTS) tool for discovering viral integration events and reconstruct fusion transcripts at single-base resolution. It combines soft-clipping information, read-pair analysis, and targeted de novo assembly to discover and annotate viral-human fusion events. A simple yet effective empirical statistical model is used to evaluate the quality of fusion breakpoints. Minimal user defined parameters are required. | ubuntu, debian, high-throughput sequencing, virus, reconstruct, fusion transcript, transcript, integration, fusion, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge has parent organization: Chinese University of Hong Kong; Hong Kong; China |
PMID:23314323 | GNU General Public License, v3 | OMICS_00224, biotools:viralfusionseq | https://bio.tools/viralfusionseq | SCR_005138 | ViralFusionSeq, ViralFusionSeq (VFS) | 2026-08-01 12:02:56 | 1 | |||||
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RetroSeq Resource Report Resource Website 10+ mentions |
RetroSeq (RRID:SCR_005133) | RetroSeq | software resource | A tool for discovery and genotyping of transposable element variants (TEVs) (also known as mobile element insertions) from next-gen sequencing reads aligned to a reference genome in BAM format. The goal is to call TEVs that are not present in the reference genome but present in the sample that has been sequenced. It should be noted that RetroSeq can be used to locate any class of viral insertion in any species where whole-genome sequencing data with a suitable reference genome is available. RetroSeq is a two phase process, the first being the read pair discovery phase where discorandant mate pairs are detected and assigned to a TE class (Alu, SINE, LINE, etc.) by using either the annotated TE elements in the reference and/or aligned with Exonerate to the supplied library of viral sequences. | mobile element insertion, next-gen sequencing, bam, transposable element, genome, sequence |
is listed by: OMICtools has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
PMID:23233656 | Acknowledgement requested, Open unspecified license | OMICS_11232, OMICS_00120 | SCR_005133 | 2026-08-01 12:02:55 | 45 | |||||||
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Cloudbreak Resource Report Resource Website |
Cloudbreak (RRID:SCR_005097) | software resource | Software providing a Hadoop-based genomic structural variation (SV) caller for Illumina paired-end DNA sequencing data. It contains a full pipeline for aligning data in the form of FASTQ files using alignment pipelines that generate many possible mappings for every read, in the Hadoop framework. It then contains Hadoop jobs for computing genomic features from the alignments, and for calling insertion and deletion variants from those features. | illumina, mapreduce, insertion, deletion, genomic | is listed by: OMICtools | OMICS_04078 | SCR_005097 | 2026-08-01 12:02:49 | 0 | ||||||||||
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St. Louis University Alzheimer's Brain Bank Resource Report Resource Website |
St. Louis University Alzheimer's Brain Bank (RRID:SCR_005132) | biomaterial supply resource, tissue bank, material resource, brain bank | A brain bank which provides brain tissue for interdisciplinary research in neurochemical, anatomical, epidemiological and clinical aspects of Alzheimer's disease. It provides brain tissue from Alzheimer's patients and healthy elderly brain donors to investigators who are helping further the understanding of Alzheimer's disease through research. It also gives family members of Alzheimer's patients the opportunity to obtain a confirmed diagnosis through brain autopsy. Through this program, families of individuals with either a clinical diagnosis, or those with suspected Alzheimer's disease, grant permission for a brain autopsy to be performed immediately after death. | brain bank, alzheimer's disease, normal control, dementia, brain tissue, autopsy, healthy donor, material storage repository |
is listed by: One Mind Biospecimen Bank Listing has parent organization: St. Louis University Department of Neurology and Psychiatry has parent organization: Saint Louis University School of Medicine; Missouri; USA |
Alzheimer's disease, Dementia | alz.org | Public, Available to the research community | nlx_144152 | SCR_005132 | SLU Brain Bank, Saint Louis University Alzheimer’s Brain Bank, Saint Louis University Medical Center Alzheimer's Disease Brain Bank | 2026-08-01 12:02:49 | 0 |
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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."
