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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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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 | |||||||
|
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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Immunedeconv Resource Report Resource Website 10+ mentions |
Immunedeconv (RRID:SCR_023869) | data analysis software, data processing software, software resource, software application | Software R package for unified access to computational methods for estimating immune cell fractions from bulk RNA sequencing data. | computational methods access, estimating immune cell fractions, bulk RNA sequencing data, | PMID:32124323 | Free, Available for download, Freely available | SCR_023869 | 2026-08-13 09:30:51 | 13 | ||||||||||
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Zeiss Zen Lite Resource Report Resource Website 1000+ mentions |
Zeiss Zen Lite (RRID:SCR_023747) | data analysis software, data processing software, software application, data acquisition software, software resource | Software tool for basic image acquisition and analysis. Zeiss ZEN microscopy software to control of axiocam microscope cameras, image transformation and measurements, image processing, image alignment for correlative microscopy, various visualization options. | Zeiss, ZEN microscopy, image acquisition and analysis, axiocam microscope camera control, image transformation and measurements, image processing, image alignment, visualization, | SCR_023747 | ZEISS ZEN lite | 2026-08-13 09:30:49 | 1027 | |||||||||||
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CodonW Resource Report Resource Website 100+ mentions |
CodonW (RRID:SCR_023989) | data analysis software, data processing software, software resource, software application | Software tool designed to simplify Multivariate analysis (correspondence analysis) of codon and amino acid usage. It also calculates standard indices of codon usage. | Multivariate analysis, correspondence analysis, codon and amino acid usage, calculate standard indices, codon usage, | is listed by: Debian | Free, Available for download, Freely available | OMICS_08756 | https://sources.debian.org/src/codonw/ | SCR_023989 | codonw | 2026-08-13 09:31:11 | 322 | |||||||
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bibliometrix Resource Report Resource Website 50+ mentions |
bibliometrix (RRID:SCR_023744) | data analysis software, data processing software, software application, software toolkit, software resource | Software R package for comprehensive science mapping analysis. Used for quantitative research in scientometrics and bibliometrics that includes all main bibliometric methods of analysis. | comprehensive science mapping analysis, quantitative research in scientometrics and bibliometrics, bibliometric analysis, | is listed by: CRAN | DOI:10.1016/j.joi.2017.08.007 | Free, Available for download, Freely available | https://github.com/massimoaria/bibliometrix, https://CRAN.R-project.org/package=bibliometrix | SCR_023744 | 2026-08-13 09:31:09 | 50 | ||||||||
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VarFish Resource Report Resource Website 1+ mentions |
VarFish (RRID:SCR_023710) | data analysis software, data processing software, software resource, software application | Web application for quality control, filtering, prioritization, analysis, and user based annotation of DNA variant data with focus on rare disease genetics. Comprehensive DNA variant analysis for diagnostics and research. | Genetics, Variant Call Format, Filtering, Quality control, | Berlin Institute of Health Charité funds ; Stiftung Charité |
DOI:10.1093/nar/gkaa241 | Free, Available for download, Freely available | https://github.com/bihealth/varfish-server | SCR_023710 | 2026-08-13 09:31:09 | 2 | ||||||||
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LOHHLA Resource Report Resource Website 1+ mentions |
LOHHLA (RRID:SCR_023690) | data analysis software, data processing software, software resource, software application | Software tool to evaluate HLA loss using next-generation sequencing data. Computational tool to determine HLA allele-specific copy number from sequencing data. | evaluate HLA loss, Human Leukocyte Antigen loss, next-generation sequencing data, determine HLA allele-specific copy number, sequencing data, | Cancer Research UK ; University College London Hospitals Biomedical Research Centre ; European Union Seventh Framework Programme ; UK Medical Research Council ; Wellcome Trust ; Rosetrees Trust ; NovoNordisk Foundation ; Prostate Cancer Foundation ; Breast Cancer Research Foundation ; European Research Council ; Marie Curie Network PloidyNet |
PMID:29107330 | Restricted | SCR_023690 | Loss Of Heterozygosity in Human Leukocyte Antigen | 2026-08-13 09:30:49 | 6 | ||||||||
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oncoboxlib Resource Report Resource Website 1+ mentions |
oncoboxlib (RRID:SCR_023722) | software toolkit, software resource, software library | Software library to calculate Pathways Activation Levels. It takes file that contains gene symbols in HGNC format, their expression levels for one or more samples and calculates PAL values for each pathway in each sample. | calculate Pathways Activation Levels, Pathways Activation Levels, gene symbols, HGNC format, gene expression levels, PAL values calculation, | is related to: OncoboxPD | Russian Foundation for basic research | PMID:33633781 | Free, Available for download, Freely available | SCR_023722 | oncoboxlib | 2026-08-13 09:31:08 | 2 | |||||||
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Edlib Resource Report Resource Website 1+ mentions |
Edlib (RRID:SCR_024078) | data processing software, software application, image analysis software, alignment software, software resource | Software C/C++ (and Python) library for sequence alignment using edit (Levenshtein) distance. | sequence alignment, edit Levenshtein distance. | is listed by: Debian | Free, Available for download, Freely available, | OMICS_15611 | https://sources.debian.org/src/libedlib/, http://martinsos.github.io/edlib/ | SCR_024078 | libedlib, Edib: A lightweight and super fast C/C++ library for sequence alignment using edit distance. | 2026-08-13 09:31:13 | 2 | |||||||
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MindTheGap Resource Report Resource Website 1+ mentions |
MindTheGap (RRID:SCR_024115) | data analysis software, data processing software, software resource, software application | Software tool to perform detection and assembly of DNA insertion variants in NGS read datasets with respect to reference genome.Used to call insertions of any size, whether they are novel or duplicated, homozygous or heterozygous in the donor genome. | perform detection and assembly of DNA insertion variants, NGS read datasets, reference genome, call insertions, donor genome, | is listed by: Debian | Free, Available for download, Freely available, | OMICS_05472 | https://sources.debian.org/src/mindthegap/ | SCR_024115 | mindthegap | 2026-08-13 09:30:53 | 3 |
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