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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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NanoString GeoMx Tools Resource Report Resource Website 10+ mentions |
NanoString GeoMx Tools (RRID:SCR_023424) | data analysis software, data processing software, software resource, software application | Software package contains tools for analyzing data from NanoString GeoMx Digital Spatial Profiler. Provides functions to read, quality control and normalize starting from Nanostring DCC and PKC files generated from NanoString GeoMx DSP. Contains definition of NanoStringGeoMxSet class which inherits from Biobase’s ExpressionSet class and NanoStringRCCSet class. | NanoString GeoMx Digital Spatial Profiler, Nanostring DCC, PKC files, NanoString GeoMx DSP, Biobase ExpressionSet class, NanoStringRCCSet class, | Free, Available for download, Freely available | https://bioconductor.org/packages/GeomxTools/ | SCR_023424 | GeoMxTools | 2026-08-13 09:31:04 | 41 | |||||||||
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DeepCT Resource Report Resource Website 1+ mentions |
DeepCT (RRID:SCR_023302) | data analysis software, data processing software, software resource, software application | Software tool can learn complex interconnections of epigenetic features and infer unmeasured data from any available input. Can learn cell type-specific properties, build biologically meaningful vector representations of cell types, and utilize these representations to generate cell type-specific predictions of effects of non-coding variations in human genome. | interconnections of epigenetic features, infer unmeasured data, human genome | DOI:10.1101/2021.12.31.474623 | Free, Available for download, Freely available | SCR_023302 | 2026-08-13 09:31:01 | 1 | ||||||||||
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IGoR Resource Report Resource Website 10+ mentions |
IGoR (RRID:SCR_024053) | data analysis software, data processing software, software resource, software application | C++ software designed to infer V(D)J recombination related processes from sequencing data. | infer V(D)J recombination related processes, sequencing data, | is listed by: Debian | PMID:29422654 | Free, Available for download, Freely available, | OMICS_18534 | https://sources.debian.org/src/igor/, https://qmarcou.github.io/IGoR/ | SCR_024053 | Inference and Generation Of Repertoires, igor | 2026-08-13 09:31:11 | 13 | ||||||
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Proteinortho Resource Report Resource Website 50+ mentions |
Proteinortho (RRID:SCR_024177) | data analysis software, data processing software, software resource, software application | Software tool to detect orthologous genes within different species. Stand-alone tool for large datasets for orthology analysis. | Stand-alone tool, detect orthologous genes, different species, large datasets, orthology analysis, | is listed by: Debian | PMID:21526987 | Free, Available for download, Freely available, | OMICS_05355 | https://sources.debian.org/src/proteinortho/ | SCR_024177 | 2026-08-13 09:31:14 | 99 | |||||||
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KmerResistance Resource Report Resource Website 1+ mentions |
KmerResistance (RRID:SCR_024058) | data analysis software, data processing software, software resource, software application | Software tool to correlate mapped genes with the predicted species of WGS samples, where this allows for identification of genes in samples which have been poorly sequenced or high accuracy predictions for samples with contamination. KmerResistance has one dependency, namely KMA to perform the mapping, which is also freely available. | correlate mapped genes, predicted species, WGS samples, identification of genes, | is listed by: Debian | PMID:27365186 | Free, Available for download, Freely available, | https://sources.debian.org/src/kmerresistance/ | SCR_024058 | kmerresistance | 2026-08-13 09:30:52 | 1 | |||||||
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ProDA Resource Report Resource Website 1+ mentions |
ProDA (RRID:SCR_024171) | data processing software, software application, image analysis software, alignment software, software resource | Software for multiple alignment of protein sequences with repeated and shuffled elements.Used for automated detection and alignment of homologous regions in collections of proteins with arbitrary domain architectures. | sequence alignment, protein sequences, protein sequences multiple alignment, repeated sequences, shuffled elements, | is listed by: Debian | DOI:10.1093/nar/gkl511 | Free, Available for download, Freely available, | OMICS_21692 | https://sources.debian.org/src/proda/ | SCR_024171 | proda | 2026-08-13 09:31:16 | 1 | ||||||
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Kleborate Resource Report Resource Website 10+ mentions |
Kleborate (RRID:SCR_024051) | data analysis software, data processing software, software resource, software application | Software tool to screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) for MLST sequence type, species (e.g. K. pneumoniae, K. quasipneumoniae, K. variicola, etc.), ICEKp associated virulence loci (yersiniabactin (ybt), colibactin (clb), salmochelin (iro), hypermucoidy (rmpA)), virulence plasmid associated loci (salmochelin (iro), aerobactin (iuc), hypermucoidy (rmpA, rmpA2)), antimicrobial resistance determinants (acquired genes, SNPs, gene truncations and intrinsic ?-lactamases), and K (capsule) and O antigen (LPS) serotype prediction, via wzi alleles and Kaptive. | screen genome assemblies, Klebsiella pneumoniae, Klebsiella pneumoniae species complex, genome assemblies, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/kleborate/ | SCR_024051 | KLEBORATE, kleborate | 2026-08-13 09:31:13 | 27 | ||||||||
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SwissTargetPrediction Resource Report Resource Website 1000+ mentions |
SwissTargetPrediction (RRID:SCR_023756) | data access protocol, software resource, web service | Web tool to estimate the most probable macromolecular targets of small molecule, assumed as bioactive. Prediction is founded on combination of 2D and 3D similarity with library of known actives on proteins from three different species. | protein targets, small molecule, bioactive small molecule, macromolecular target estimation, target prediction, | Swiss Institute of Bioinformatics | PMID:31106366 | Free, Freely available | SCR_023756 | 2026-08-13 09:31:09 | 2774 | |||||||||
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VIGRA Resource Report Resource Website 1+ mentions |
VIGRA (RRID:SCR_024100) | , data processing software, software application, image analysis software, software toolkit, software library, software resource, image processing software | Software image processing and analysis library that puts its main emphasis on customizable algorithms and data structures. VIGRA is especially strong for multi-dimensional images. By using template techniques similar to those in the C++ Standard Template Library, you can easily adapt any VIGRA component to the needs of your application, without thereby giving up execution speed. As of version 1.7.1, VIGRA also provides extensive Python bindings on the basis of the popular numpy framework. | image processing and analysis library, customizable algorithms and data structures, multi-dimensional image, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/libvigraimpex/ | SCR_024100 | , The VIGRA Computer Vision Library, Vision with Generic Algorithms, libvigraimpex | 2026-08-13 09:31:14 | 1 | ||||||||
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pynast Resource Report Resource Website 50+ mentions |
pynast (RRID:SCR_024189) | data processing software, software application, image analysis software, alignment software, software resource | Software tool for aligning sequences to template alignment. | aligning sequences to template alignment, | is listed by: Debian | PMID:19914921 | Free, Available for download, Freely available, | OMICS_15419 | https://sources.debian.org/src/pynast/ | SCR_024189 | Python Nearest Alignment Space Termination tool | 2026-08-13 09:31:16 | 65 | ||||||
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Patristic Resource Report Resource Website 1+ mentions |
Patristic (RRID:SCR_024154) | data analysis software, data processing software, software resource, software application | Software Java program for calculating patristic distances and graphically comparing the components of genetic change. | calculating patristic distances, graphically comparing the components of genetic change, | is listed by: Debian | PMID:16388682 | Free, Available for download, Freely available, | https://sources.debian.org/src/patristic/ | SCR_024154 | patristic | 2026-08-13 09:31:13 | 5 | |||||||
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IgDiscover Resource Report Resource Website 10+ mentions |
IgDiscover (RRID:SCR_024037) | data analysis software, data processing software, software resource, software application | Software to analyze antibody repertoires and discover new V genes from high-throughput sequencing reads.Heavy chains, kappa and lambda light chains are supported (to discover VH, VK and VL genes)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | analyze antibody repertoires, discover new V genes, high-throughput sequencing reads, | is listed by: Debian | PMID:27995928 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_16456 | https://sources.debian.org/src/igdiscover/, https://github.com/NBISweden/IgDiscover/ | SCR_024037 | igdiscover | 2026-08-13 09:31:11 | 11 | ||||||
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BOLT-LMM Resource Report Resource Website 1+ mentions |
BOLT-LMM (RRID:SCR_023978) | data analysis software, data processing software, software resource, software application | Software statistical tool for identifying genetic associations. Used for genome wide association studies in large cohorts. | statistical tool, identifying genetic associations, genome wide association studies, large cohorts, | is listed by: Debian | PMID:25642633 | Free, Available for download, Freely available | OMICS_13504 | https://sources.debian.org/src/bolt-lmm/ | SCR_023978 | bolt-lmm | 2026-08-13 09:30:51 | 2 | ||||||
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QUINT Resource Report Resource Website 1+ mentions |
QUINT (RRID:SCR_023856) | workflow software, data processing software, software resource, software application | Software workflow includes suite of various software to form analysis pipeline of atlas-based quantifuication of labbeled features in histological images from mouse or rat brain. This workflow also suggests and explains with instructional videos the way these software work together. Used for quantification and spatial analysis of labelling in series of rodent brain section images based on available 3D reference atlases. | Allen Common Coordinate Framework, labelling quantification and spatial analysis, analysis pipeline of atlas based quantifuication of labbeled features, histological images, mouse brain, rat brain, images, brain section images, 3D reference atlases, |
is used by: WebNutil is related to: Allen Institute for Brain Science is related to: SeriesZoom has parent organization: University of Oslo; Oslo; Norway |
European Union’s Horizon 2020 Framework Programme for Research and Innovation under the Framework Partnership Agreement No. 650003 (HBP FPA) and the European Union’s Horizon Europe Programme for Research Infrastructures Grant Agreement No. 101147319 (EBRAINS 2.0). | PMID:31849633 | Free, Freely available | SCR_023856 | 2026-08-13 09:31:10 | 5 | ||||||||
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Global Alzheimers Association Interaction Network Resource Report Resource Website 10+ mentions |
Global Alzheimers Association Interaction Network (RRID:SCR_023699) | GAAIN | topical portal, data or information resource, disease-related portal, portal | Open access integrated research platform, which links scientists, shared data, and analysis tools to accelerate Alzheimer’s disease research, disease preventions, treatments and cure. Unites diverse and geographically distributed network of data partners to foster cohort discovery, collaboration and sharing. Researchers can discover clinical, genetic, imaging and other data collected across many independent studies. | USC Mark and Mary Stevens Neuroimaging and Informatics Institute, Alzheimer’s disease research, disease preventions, treatments and cure, network of data partners, cohort discovery, collaboration and sharing, clinical data, genetic data, imaging data, Alzheimer data discovery, | has parent organization: University of Southern California; Los Angeles; USA | Alzheimer’s disease | Alzheimer Association | Free, Freely available | SCR_023699 | 2026-08-13 09:31:08 | 30 | |||||||
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Brainreg-segment Resource Report Resource Website 1+ mentions |
Brainreg-segment (RRID:SCR_023853) | segmentation software, data processing software, software application, image analysis software, software resource | Software tool for manual segmentation of regions/objects within the brain. Brainreg-segment will only work if the user registers their data with brainreg first. Used for segmentation of 3D shapes in common anatomical space. | Allen Mouse Brain Atlas, Allen Human Brain Atlas, brain imaging, regions segmentation, objects segmentation, segmentation within the brain, | is related to: Allen Institute for Brain Science | Free, Available for download, Freely available | SCR_023853 | 2026-08-13 09:31:10 | 5 | ||||||||||
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IVA Resource Report Resource Website 1+ mentions |
IVA (RRID:SCR_024044) | data analysis software, data processing software, software resource, software application | Software tool as de novo assembler designed to assemble virus genomes that have no repeat sequences,using Illumina read pairs sequenced from mixed populations at extremely high and variable depth. | de novo assembler, assemble virus genomes, no repeat sequences, Illumina reads, pairs sequenced from mixed populations, | is listed by: Debian | PMID:25725497 | Free, Available for download, Freely available, | OMICS_08188 | https://sources.debian.org/src/iva/, http://sanger-pathogens.github.io/iva/ | SCR_024044 | Iterative Virus Assembler - de novo virus assembler of Illumina paired reads., iva | 2026-08-13 09:31:12 | 1 | ||||||
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PlasmidSeeker Resource Report Resource Website 10+ mentions |
PlasmidSeeker (RRID:SCR_024167) | data analysis software, data processing software, software resource, software application | Software tool as k-mer based program for identification of known plasmids from whole genome sequencing reads. Used for identification of known plasmids from bacterial whole genome sequencing reads. | k-mer based program, identification of known plasmids, whole genome sequencing reads, | is listed by: Debian | PMID:29629246 | Free, Available for download, Freely available, | OMICS_28371 | https://sources.debian.org/src/plasmidseeker/ | SCR_024167 | plasmidseeker | 2026-08-13 09:31:14 | 17 | ||||||
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Cancer Genome Interpreter Resource Report Resource Website 10+ mentions |
Cancer Genome Interpreter (RRID:SCR_023752) | CGI | data access protocol, software resource, web service | Platform that systematizes interpretation of cancer genomes and makes it automatic. Web tool to annotate genomic alterations and interpret their possible role in tumorigenesis and in response to anti cancer therapies. Used to support identification of tumor alterations that drive disease and/or which may be therapeutically actionable. Analyses mutations including single nucleotide changes and small insertions/deletions, copy number alterations including gene amplifications and deletions and translocations. | cancer genomes, annotate genomic alterations, tumor alterations identification, mutations analysis, single nucleotide change, copy number alteration, gene amplifications, gene deletions, gene translocation, | European Union Horizon 2020 ; European Research Council ; Spanish Ministry of Economy and Competitiveness ; CERCA |
DOI:10.1101/140475 | Free, Freely available | SCR_023752 | 2026-08-13 09:30:49 | 21 | ||||||||
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ViewPoint MicroZebraLab Resource Report Resource Website 1+ mentions |
ViewPoint MicroZebraLab (RRID:SCR_023750) | data acquisition software, data processing software, software resource, software application | Software tool to extract cardiovascular parameters from transmitted light videos of zebrafish embryos or larvae. Used to investigate live and in non-invasive way scope of zebrafish larvae physiological parameters. Measures heartbeat and blood flow. | ViewPoint, extract cardiovascular parameters, transmitted light videos, zebrafish embryos video, larvae video, physiological parameters, heartbeat measurement, blood flow measurement, | Restricted | SCR_023750 | MicroZebraLab | 2026-08-13 09:31:09 | 1 |
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