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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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University of Freiburg; Baden-Wurttemberg; Germany Resource Report Resource Website |
University of Freiburg; Baden-Wurttemberg; Germany (RRID:SCR_004825) | Uni Freiburg | university | Public research university located in Freiburg im Breisgau, Baden-Württemberg, Germany. |
is related to: MIP-DILI is related to: Mass spectrometry imaging workbench is related to: NanoGalaxy is parent organization of: Images of the Drosophila Nervous System is parent organization of: DTI and Fibertools Software Package is parent organization of: EPILEPSIE database is parent organization of: GraphProt is parent organization of: ViBE-Z is parent organization of: Electroencephalogram Database: Prediction of Epileptic Seizures is parent organization of: University of Freiburg Bioinformatics Group: Servers and Web-Applications is parent organization of: FlyBrain is parent organization of: XuvTools is parent organization of: MIRROR: FlyBrain, An Online Atlas and Database of the Drosophila Nervous System is parent organization of: Braincon Platform Software is parent organization of: GraphClust2 is parent organization of: meta is parent organization of: University of Freiburg Life Imaging Center Core Facility is parent organization of: PottersWheel is parent organization of: FreemoVR project is parent organization of: MutaRNA is parent organization of: Data independent acquisition proteomics workbench is parent organization of: University of Freiburg Magnetic Resonance Development and Application Center Core Facility is parent organization of: University of Freiburg Medical Center Lighthouse Core Facility is parent organization of: Freibox is parent organization of: University of Freiburg Cryo-Electron Microscopy Core Facility |
nlx_80780 | http://www.uni-freiburg.de/start-en.html?set_language=en | SCR_004825 | Albert Ludwig University of Freiburg | 2026-07-25 12:05:54 | 0 | ||||||||
|
VariationHunter Resource Report Resource Website 10+ mentions |
VariationHunter (RRID:SCR_004865) | VariationHunter | software resource | A software tool for discovery of structural variation in one or more individuals simultaneously using high throughput technologies. | structural variation, genome, next-generation sequencing |
is listed by: OMICtools is related to: SPLITREAD has parent organization: Simon Fraser University; British Columbia; Canada has parent organization: SourceForge |
PMID:22048523 PMID:20529927 |
OMICS_00328 | SCR_004865 | VariationHunter-CommonLaw | 2026-07-25 12:05:56 | 12 | |||||||
|
Boston Biochem Resource Report Resource Website 100+ mentions |
Boston Biochem (RRID:SCR_004761) | commercial organization | THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 17, 2021. An Antibody supplier. | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_152321 | SCR_004761 | Boston Biochem Inc. | 2026-07-25 12:05:54 | 108 | ||||||||||
|
University of Genoa; Genoa; Italy Resource Report Resource Website 1+ mentions |
University of Genoa; Genoa; Italy (RRID:SCR_004878) | university | UniGe, is one of the largest universities in Italy. It is located in the city of Genoa and regional Metropolitan City of Genoa, on the Italian Riviera in the Liguria region of northwestern Italy. The original university was founded in 1481. |
is related to: PharmaCog is parent organization of: EyesWeb |
grid.5606.5, ISNI:0000 0001 2151 3065, nlx_14821, Crossref funder ID:501100004702, Wikidata:Q593321 | https://ror.org/0107c5v14 | SCR_004878 | Universit� degli Studi di Genova, University of Genoa, Universita degli Studi di Genova, Universita di Genova, Universit� di Genova | 2026-07-25 12:05:58 | 2 | |||||||||
|
XNAT Extras Resource Report Resource Website 1+ mentions |
XNAT Extras (RRID:SCR_004759) | XNAT Extras | software resource | User software contributions for XNAT - The Extensible Neuroimaging Archive Toolkit, http://www.xnat.org | computed tomography, database application, java, magnetic resonance, pet, spect, posix/unix-like, python, xnat pipeline |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: XNAT - The Extensible Neuroimaging Archive Toolkit |
PMID:25071542 | nlx_156023 | SCR_004759 | 2026-07-25 12:05:56 | 1 | ||||||||
|
Phymm and PhymmBL Resource Report Resource Website 10+ mentions |
Phymm and PhymmBL (RRID:SCR_004751) | Phymm, PhymmBL | software resource | Software for Phylogenetic Classification of Metagenomic Data with Interpolated Markov Models to taxonomically classify DNA sequences and accurately classify reads as short as 100 bp. PhymmBL, the hybrid classifier included in this distribution which combines analysis from both Phymm and BLAST, produces even higher accuracy. | metagenome, sequence, taxonomy, classification, phylogenetic classification, genome, short read |
is listed by: OMICtools has parent organization: University of Maryland; Maryland; USA |
NLM R01-LM006845 | PMID:19648916 PMID:21527926 |
Open-source license | OMICS_01461 | SCR_004751 | 2026-07-25 12:05:53 | 12 | ||||||
|
deStruct Resource Report Resource Website 1+ mentions |
deStruct (RRID:SCR_004747) | deStruct | software resource | A software tool for identifying structural variation in tumour genomes from whole genome illumina sequencing. | structural variation, genome, genomics |
is listed by: OMICtools has parent organization: Google Code |
Tumor, Cancer | Open unspecified license | OMICS_00314 | SCR_004747 | deStruct - Bioinformatics tool for identifying structural variation in tumour genomes | 2026-07-25 12:05:53 | 7 | ||||||
|
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 | 2026-07-25 12:05:57 | 2 | |||||||||
|
Neo Resource Report Resource Website 10+ mentions |
Neo (RRID:SCR_000634) | neo | software resource | A Python package for representing electrophysiology data, together with support for reading a wide range of neurophysiology file formats, including Spike2, NeuroExplorer, AlphaOmega, Axon, Blackrock, Plexon, Tdt, and support for writing to a subset of these formats plus non-proprietary formats including HDF5. The goal of Neo is to improve interoperability between Python tools for analyzing, visualizing and generating electrophysiology data (such as OpenElectrophy, NeuroTools, G-node, Helmholtz, PyNN) by providing a common, shared object model. In order to be as lightweight a dependency as possible, Neo is deliberately limited to represention of data, with no functions for data analysis or visualization. Neo implements a hierarchical data model well adapted to intracellular and extracellular electrophysiology and EEG data with support for multi-electrodes (for example tetrodes). Neo's data objects build on the quantities package, which in turn builds on NumPy by adding support for physical dimensions. Thus Neo objects behave just like normal NumPy arrays, but with additional metadata, checks for dimensional consistency and automatic unit conversion. | neurophysiology, electrophysiology, python, interoperability, intracellular, extracellular, eeg, electrode |
is used by: Elephant is used by: OpenElectrophy is used by: NetworkUnit has parent organization: NeuralEnsemble |
PMID:24600386 | Free, Available for download, Freely available | nlx_151874 | SCR_000634 | 2026-07-25 12:04:48 | 18 | |||||||
|
BEBaC Resource Report Resource Website |
BEBaC (RRID:SCR_000621) | BEBaC | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software for Bayesian estimation of bacterial communities. | linux, bayesian |
is listed by: OMICtools has parent organization: University of Helsinki; Helsinki; Finland |
PMID:22406836 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01440 | SCR_000621 | Bayesian estimation of bacterial communities | 2026-07-25 12:04:48 | 0 | ||||||
|
FlipFlop Resource Report Resource Website |
FlipFlop (RRID:SCR_000625) | software resource | Software that discovers which isoforms of a gene are expressed in a given sample together with their abundances, based on RNA-Seq read data. | standalone software, unix/linux, mac os x, windows, r, rna-seq, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
PMID:24813214 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_04028, biotools:flipflop | https://bio.tools/flipflop | SCR_000625 | flipflop - Fast lasso-based isoform prediction as a flow problem | 2026-07-25 12:04:47 | 0 | ||||||
|
CryptoBase Resource Report Resource Website 1+ mentions |
CryptoBase (RRID:SCR_000780) | software resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented July 19, 2016. This site is built and maintained by the Madhani Lab, Dept. of Biochemistry and Biophysics at the University of California, San Francisco | has parent organization: University of California at San Francisco; California; USA | Herb and Marion Sandler Foundation | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-30395 | http://archive.is/YgVX4 | SCR_000780 | 2026-07-25 12:04:51 | 2 | ||||||||
|
GlycoWorkbench Resource Report Resource Website 1+ mentions |
GlycoWorkbench (RRID:SCR_000782) | software resource | A suite of software tools designed for the rapid drawing of glycan structures and for assisting the process of structure determination from mass spectrometry data. | rapid drawing of glycan structures |
is listed by: OMICtools has parent organization: Google Code |
PMID:23109548 | Free, Available for download, Freely available | OMICS_05691 | SCR_000782 | 2026-07-25 12:04:50 | 6 | ||||||||
|
Australian Wool Innovation Limited Resource Report Resource Website |
Australian Wool Innovation Limited (RRID:SCR_000775) | commercial organization | Company focused on animal welfare and pest prevention in the wool industry. | wool, innovation, animal, health, welfare, prevention, parasite, science, resource, weed, pest, feral predator, breeding | nif-0000-30047 | http://www.wool.com.au/LivePage.aspx?pageId=116 | SCR_000775 | AWI | 2026-07-25 12:04:50 | 0 | |||||||||
|
BLASR Resource Report Resource Website 10+ mentions Discontinued |
BLASR (RRID:SCR_000764) | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. C++ long-read aligner for PacBio reads., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | standalone software, c++, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: Proovread |
PMID:22988817 DOI:10.1186/1471-2105-13-23 |
THIS RESOURCE IS NO LONGER IN SERVICE | biotools:blasr, OMICS_05134 | https://bio.tools/blasr, https://sources.debian.org/src/blasr/ | SCR_000764 | Basic Local Alignment with Successive Refinement, BLASR: The PacBio long read aligner | 2026-07-25 12:04:50 | 15 | ||||||
|
GMcloser Resource Report Resource Website 1+ mentions |
GMcloser (RRID:SCR_000646) | GMcloser | software resource | Software that fills and closes the gaps present in scaffold assemblies, especially those generated by the de novo assembly of whole genomes with next-generation sequencing (NGS) reads. Unlike other gap-closing tools that use only NGS reads, GMcloser uses preassembled contig sets or long read sets as the sequences to close gaps and uses paired-end (PE) reads and a likelihood-based algorithm to improve the accuracy and efficiency of gap closure. The efficiency of gap closure can be increased by successive treatments with different contig sets. | scaffolding, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:26261222 | Free, Available for download, Freely available | biotools:gmcloser, OMICS_00042 | https://bio.tools/gmcloser | SCR_000646 | Gmcloser - Closing the gaps in scaffolds with preassembled contigs | 2026-07-25 12:04:48 | 3 | |||||
|
detecttd Resource Report Resource Website |
detecttd (RRID:SCR_000681) | detecttd | software resource | Software tool to detect tandem duplications in sequencing reads. It is written in Python and requires NCBI Blast standalone. | tandem duplication, sequencing read, python, next-generation sequencing |
is listed by: OMICtools has parent organization: SourceForge |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00315 | SCR_000681 | detecttd - Tool to detect tandem duplications in NGS reads | 2026-07-25 12:04:50 | 0 | |||||||
|
FastUniq Resource Report Resource Website 1+ mentions |
FastUniq (RRID:SCR_000682) | software resource | A software tool for removal of de novo duplicates in paired short DNA sequences. | de novo, dna, sequence, duplicate, |
is listed by: OMICtools has parent organization: SourceForge |
DOI:10.1371/journal.pone.0052249 | Free, Available for download, Freely available | OMICS_01044 | SCR_000682 | 2026-07-25 12:04:48 | 3 | ||||||||
|
Sequencing Analysis Software Resource Report Resource Website 1+ mentions |
Sequencing Analysis Software (RRID:SCR_000718) | Sequencing Analysis Software | software resource | A software that gives the user the ability to basecall, trim, display, edit, and print data for the entire line of capillary DNA sequencing instruments for data analysis and quality control. This software benefits from being able to obtain longer read lengths, greater accuracy on the 5' end, and the ability to filter out low-quality sequence ends. | basecall, capillary dna, quality control, low-quality sequence ends | is listed by: OMICtools | Restricted | OMICS_01814 | SCR_000718 | 2026-07-25 12:04:49 | 1 | ||||||||
|
Stanford University Psychiatry and Behavioral Sciences Resource Report Resource Website |
Stanford University Psychiatry and Behavioral Sciences (RRID:SCR_000719) | university | A Stanford-affiliated organization which is primarily concerned with the study and treatment of sleep disorders, the treatment of psychological illnesses, and the training of medical students, residents and research fellows in psychiatry and sleep medicine. | stanford, sleep disorder, psychiatry, medical, psychological illness, research, medicine | nif-0000-02073 | SCR_000719 | Stanford | 2026-07-25 12:04:50 | 0 |
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