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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Pilon Resource Report Resource Website 1000+ mentions |
Pilon (RRID:SCR_014731) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software tool to automatically improve draft assemblies and find variation among strains, including large event detection. FASTA files of genome along with one or more BAM files of reads aligned as input. Read alignment analysis is used to identify inconsistencies between input genome and evidence in reads, then attempts to make improvements to genome. | automatically, improve, draft, assembly, variation, strain, genome, read, alignment, analysis, inconsistency, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools is related to: shovill is hosted by: GitHub |
DOI:10.1371/journal.pone.0112963 DOI:10.1371/journal.pone.0112963 |
Available for download, Acknowledgement requested | OMICS_14553, biotools:pilon | https://github.com/broadinstitute/pilon/wiki, https://bio.tools/pilon, https://sources.debian.org/src/pilon/ | SCR_014731 | 2026-09-12 01:00:17 | 3377 | |||||||
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Brain Imaging Analysis Kit Resource Report Resource Website 10+ mentions |
Brain Imaging Analysis Kit (RRID:SCR_014824) | BrainIAK | data processing software, image analysis software, software application, software resource, software toolkit | Open source software package of Python modules for neuroscience, primarily focused on functional Magnetic Resonance Imaging (fMRI) analysis. Used for analyzing neuroimaging data. | brain, python, module, imaging, fmri, data, analysis, neuroimaging |
is related to: Intel has parent organization: Princeton University; New Jersey; USA |
Free, Available for download, Freely available | https://github.com/brainiak/brainiak | SCR_014824 | BrainIAK, Brain Imaging Analysis Kit, Brain Imaging Analysis Kit (BrainIAK) | 2026-09-12 01:00:17 | 30 | |||||||
|
Roary Resource Report Resource Website 500+ mentions |
Roary (RRID:SCR_018172) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software tool for rapid large scale prokaryote pan genome analysis. Builds large scale pan genomes, identifying core and accessory genes. Makes construction of pan genome of thousands of prokaryote samples on standard desktop without compromising on accuracy of results. Not intended for meta genomics or for comparing extremely diverse sets of genomes. | Genome analysis, prokaryote pan genome, pan genome, gene identification, analysis, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools works with: Scoary |
Wellcome Trust | PMID:26198102 | Free, Available for download, Freely available | OMICS_09491, biotools:roary | https://github.com/sanger-pathogens/Roary, https://bio.tools/roary, https://sources.debian.org/src/roary/ | SCR_018172 | 2026-09-12 01:00:20 | 710 | ||||||
|
StringTie Resource Report Resource Website 1000+ mentions |
StringTie (RRID:SCR_016323) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software application for assembling of RNA-Seq alignments into potential transcripts. It enables improved reconstruction of a transcriptome from RNA-seq reads. This transcript assembling and quantification program is implemented in C++ . | assembling, RNA, sequence, transcript, gene, alignment, reconstruction, read, analysis, process, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools |
NCI R01 CA120185; NCI R01 CA134292; NHGRI R01 HG006102; NHGRI R01 HG006677; NIGMS R01 GM105705; the Cancer Prevention and Research Institute of Texas |
PMID:25690850 DOI:10.1038/nbt.3122 |
Open source, Free, Freely available, Available for download | biotools:stringtie, OMICS_07226 | https://github.com/gpertea/stringtie, https://bio.tools/stringtie, https://sources.debian.org/src/stringtie/ | SCR_016323 | 2026-09-12 01:00:18 | 4976 | ||||||
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MrDiffusion Resource Report Resource Website 1+ mentions |
MrDiffusion (RRID:SCR_016567) | data analysis software, data processing software, data visualization software, image analysis software, software application, software resource | Software package for diffusion imaging analysis and visualization. Module of Vistasoft for processing diffusion weighted data and measuring and visualizing fractional anisotropy, mean diffusivity, axial and radial diffusivity, RGB fiber direction maps and analysis of MRI data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | diffusion, imaging, analysis, visualization, data, fractional, anisotropy, MRI |
is related to: MATLAB has parent organization: Stanford University; Stanford; California |
THIS RESOURCE IS NO LONGER IN SERVICE | https://github.com/vistalab/vistasoft/tree/master/mrDiffusion | SCR_016567 | 2026-09-12 01:00:19 | 9 | |||||||||
|
Spyder Resource Report Resource Website 50+ mentions |
Spyder (RRID:SCR_017585) | software application, software development environment, software development tool, software resource | Interactive scientific development environment package for Python. Used for editing, analysis, debugging, and profiling functionality of comprehensive development tool with data exploration, interactive execution, deep inspection, and visualization. | Python, environment, editing, analysis, debugging, profiling, functionality, development, data, exploration, visualization | is related to: Pythonxy | Free, Available for download, Freely available | SCR_017585 | 2026-09-12 01:00:20 | 75 | ||||||||||
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UMMPerfusion Resource Report Resource Website 1+ mentions |
UMMPerfusion (RRID:SCR_015970) | data processing software, image analysis software, software application, software resource, software toolkit | Analysis software for dynamic contrast enhanced magnetic resonance images with implementation of a pixel-by-pixel deconvolution approach. It quantifies T1-weighted contrast-enhanced dynamic MR imaging (DCE-MRI) perfusion data as an OsiriX plug-in. | DCE-MRI, t1, weighted, imaging, mr, magnetic, resonance, analysis, digital, perfusion, parameter, data, set, image, algorithm, contrast, pixel | is affiliated with: Heidelberg University; Baden-Wurttemberg; Germany | Heinrich-Vetter-Stiftung | PMID:22832894 | Open source, Available for download, Runs on Mac OS, Tutorial available | SCR_015970 | OsiriX plugin | 2026-09-12 01:00:18 | 6 | |||||||
|
FreeContact Resource Report Resource Website 10+ mentions |
FreeContact (RRID:SCR_016113) | alignment software, data processing software, image analysis software, software application, software resource | Alignment software for large-scale protein contact or protein-protein interaction prediction optimized for speed through shorter runtimes. FreeContact provides the opportunity to compute contact predictions in any environment (desktop or cloud). | protein, structure, prediction, sequence, analysis, fast, contact, alignment, multiple |
is listed by: OMICtools is related to: Debian |
Alexander von Humboldt Foundation ; German Ministry for Research and Education (BMBF: Bundesministerium fuer Bildung und Forschung) ; Research Council of Norway 208481 |
PMID:24669753 DOI:10.1186/1471-2105-15-85 |
Open source, Free, Available for download | OMICS_03520 | https://rostlab.org/owiki/index.php/FreeContact, https://sources.debian.org/src/libfreecontact-perl/ | SCR_016113 | 2026-09-12 01:00:18 | 22 | ||||||
|
QModeling Resource Report Resource Website 1+ mentions |
QModeling (RRID:SCR_016358) | data analysis software, data processing software, image analysis software, software application, software resource, software toolkit | Software toolbox for Statistical Parametric Mapping (SPM) to fit reference-region kinetic models (SRTM, SRTM2, Patlak Reference and Logan Reference Plot) are currently available in QModeling to dynamic PET studies. Used for the analysis of brain imaging data sequences. | statistical, parametric, mapping, reference, region, kinetic, model, dynamic, analysis, brain, data, imaging, sequence |
is related to: University of Malaga; Andalusia; Spain is related to: MATLAB |
DOI:10.1007/s12021-018-9384-y | Free, Available for download, Available after registration | SCR_016358 | 2026-09-12 01:00:18 | 1 | |||||||||
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SCDE Resource Report Resource Website 10+ mentions |
SCDE (RRID:SCR_015952) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software package that implements a set of statistical methods for analyzing single-cell RNA-seq data, including differential expression analysis (Kharchenko et al.) and pathway and geneset overdispersion analysis (Fan et al.) | statistic, single, cell, rna, seq, rnaseq, differential, analysis, pathway, gene, geneset, dispersion, overdispersion, bayesian, expression, magnitude | Leukemia and Lymphoma Research UK ; Leukemia and Lymphoma Society ; NHLBI R01 HL097794; NIA K25 AG037596; NIDDK R01 DK050234 |
PMID:24836921 | Free, Available for download | SCR_015952 | 2026-09-12 01:00:18 | 32 | |||||||||
|
geomorph Resource Report Resource Website 10+ mentions |
geomorph (RRID:SCR_016482) | geomorph | data analysis software, data processing software, software application, software resource, software toolkit | Software package for performing all stages of geometric morphometric shape analysis of landmark points and curves in 2-and-3-dimensions as well as 3D surfaces in the R statistical computing environment. | geometric, morphometric, shape, analysis, landmark, point, curve, 2D, 3D, surface |
is listed by: CRAN is related to: R Project for Statistical Computing |
Free, Available for download, Freely available | https://github.com/geomorphR/geomorph | SCR_016482 | geometric morphometric | 2026-09-12 01:00:19 | 35 | |||||||
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NanoPipe Resource Report Resource Website 1+ mentions |
NanoPipe (RRID:SCR_016852) | NanoPipe | analysis service resource, data access protocol, data analysis service, production service resource, service resource, software resource, web service | Web tool for analysis of MinION (ONT) long sequencing reads. Used for analysis of reads generated by the Oxford Nanopore sequencing devices. Provides alignments to any target of interest, alignment statistics and information about polymorphisms. | analysis, MinION, long, sequence, read, Oxford Nanopore, alignment, target, statistics, polymorphism, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: University of Muenster; Muenster; Germany |
Institute of Bioinformatics Muenster ; Germany |
PMID:30689855 | Free, Available for download, Freely Available | biotools:NanoPipe | https://github.com/IOB-Muenster/nanopipe2, https://bio.tools/NanoPipe | SCR_016852 | NanoPipe, nanopipe2 | 2026-09-12 01:00:19 | 5 | ||||
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University Medical Center Hamburg-Eppendorf Bioinformatics Core Facility Resource Report Resource Website |
University Medical Center Hamburg-Eppendorf Bioinformatics Core Facility (RRID:SCR_017144) | UKE Bioinformatics Core | access service resource, analysis service resource, core facility, production service resource, service resource, training service resource | Core provides bioinformatics services for researchers at University Medical Center Hamburg Eppendorf and related institutions. Focusing on high throughput sequencing data. Services include data analysis, consulting, software development, and bioinformatical training. | bioinformatics, data, analysis, consulting, software, development, training | has parent organization: University Medical Center Hamburg-Eppendorf | Restricted | SCR_017144 | Bioinformatics Core, University Medical Center Hamburg Eppendorf Core, UKE | 2026-09-12 01:00:20 | 0 | ||||||||
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Brain Gene Expression Analysis toolbox Resource Report Resource Website 1+ mentions |
Brain Gene Expression Analysis toolbox (RRID:SCR_017438) | data analysis software, data processing software, software application, software resource | Software Matlab toolbox for quantitative analysis of digitized brain wide gene expression data from Allen Atlas of adult mouse brain. | Quantitative, analysis, digitized, brain, gene, expression, data, Allen Atlas, adult, mouse, brain, BRAIN Initiative |
is recommended by: BRAIN Initiative is related to: MATLAB is related to: Allen Institute for Brain Science works with: Allen Mouse Brain Reference Atlas |
Free, Available for download, Freely available | SCR_017438 | , Brain, Gene, Expression, Analysis, toolbox | 2026-09-12 01:00:20 | 1 | |||||||||
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GraphWeb Resource Report Resource Website 10+ mentions |
GraphWeb (RRID:SCR_005746) | GraphWeb | analysis service resource, data analysis service, production service resource, service resource | GraphWeb allows the detection of modules from biological, heterogeneous and multi-species networks, and the interpretation of detected modules using Gene Ontology, cis-regulatory motifs and biological pathways. GraphWeb is a public web server for graph-based analysis of biological networks that: * analyses directed and undirected, weighted and unweighted heterogeneous networks of genes, proteins and microarray probesets for many eukaryotic genomes; * integrates multiple diverse datasets into global networks; * incorporates multispecies data using gene orthology mapping; * filters nodes and edges based on dataset support, edge weight and node annotation; * detects gene modules from networks using a collection of algorithms; * interprets discovered modules using Gene Ontology, pathways, and cis-regulatory motifs. Platform: Online tool | analysis, biological network, ontology or annotation visualization, protein interaction, gene id conversion, orthology mapping, network visualization, graph clustering, gene ontology, cis-regulatory motif, module, network, pathway, biological pathway, motif, visualization, protein interaction, orthology mapping, network visualization, graph clustering, analysis, statistical analysis, term enrichment |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: BIIT - Bioinformatics Algorithmics and Data Mining Group |
European Union FP6 ENFIN LSHG-CT-2005-518254; European Union FP6 COBRED LSHB-CT-2007-037730; Estonian Science Foundation ETF7437 |
PMID:18460544 | Open unspecified license - Free for academic use | nlx_149205 | SCR_005746 | 2026-09-12 01:01:39 | 12 | ||||||
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CateGOrizer Resource Report Resource Website 50+ mentions |
CateGOrizer (RRID:SCR_005737) | CateGOrizer | analysis service resource, data analysis service, production service resource, service resource | CateGOrizer takes batch input of GO term IDs in a list format or unformatted plain text file, allows users to choose one of the available classifications such as GO_slim, GOA, EGAD, MGI_GO_slim, GO-ROOT, or a self-defined classification list, find its parental branch and performs an accumulative classification count, and returns the results in a sorted table of counts, percentages, and a pie chart (if it takes longer than standard time out period, it will email the user with a URL link to the results). This tool is comprised with a set of perl CGI programs coupled with a MySQL DBMS that stores the GO terms DAG data. Platform: Online tool | gene ontology, statistical analysis, slimmer-type tool, go term classification, classification, analysis, go slim |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: NAGRP Bioinformatics Coordination Program |
Free for academic use | nlx_149197 | SCR_005737 | GO Terms Classifications Counter | 2026-09-12 01:01:39 | 85 | |||||||
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National Institutes of Health Research Portfolio Online Reporting Tool Resource Report Resource Website 10+ mentions |
National Institutes of Health Research Portfolio Online Reporting Tool (RRID:SCR_006874) | RePORTER, RePORT | data or information resource, database | A database of federally funded biomedical research projects conducted at universities, hospitals, and other research institutions that provides a central point of access to reports, data, and analyses of NIH research. The RePORTER has replaced the CRISP database. The database, maintained by the Office of Extramural Research at the National Institutes of Health, includes projects funded by the National Institutes of Health (NIH), Substance Abuse and Mental Health Services (SAMHSA), Health Resources and Services Administration (HRSA), Food and Drug Administration (FDA), Centers for Disease Control and Prevention (CDCP), Agency for Health Care Research and Quality (AHRQ), and Office of Assistant Secretary of Health (OASH). | government grant information, government grant, grant data, granting agency, grant, funding, award, biomedical, research, report, analysis, nih research |
is used by: Integrated Grants is used by: NIF Data Federation is used by: Ranking Tables of NIH Funding to US Medical Schools in 2010 has parent organization: Office of Extramural Research NIH |
nif-0000-10319 | SCR_006874 | NIH RePORT, NIH RePORTER | 2026-09-12 01:01:44 | 38 | ||||||||
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National Library of Health: Medical Literature Analysis and Retrieval System Online Fact Sheet Resource Report Resource Website 10+ mentions |
National Library of Health: Medical Literature Analysis and Retrieval System Online Fact Sheet (RRID:SCR_006994) | data or information resource, database | MEDLINE (Medical Literature Analysis and Retrieval System Online) is the U.S. National Library of Medicine''s (NLM) premier bibliographic database that contains over 16 million references to journal articles in life sciences with a concentration on biomedicine. MEDLINE is the primary component of PubMed, part of the Entrez series of databases provided by NLM''s National Center for Biotechnology Information (NCBI). MEDLINE may also be searched via the NLM Gateway. Currently, citations from approximately 5,200 worldwide journals in 37 languages; 60 languages for older journals. Citations for MEDLINE are created by the NLM, international partners, and collaborating organizations. The subject scope of MEDLINE is biomedicine and health, broadly defined to encompass those areas of the life sciences, behavioral sciences, chemical sciences, and bioengineering needed by health professionals and others engaged in basic research and clinical care, public health, health policy development, or related educational activities. MEDLINE also covers life sciences vital to biomedical practitioners, researchers, and educators, including aspects of biology, environmental science, marine biology, plant and animal science as well as biophysics and chemistry. Sponsors: Services/products providing access to MEDLINE data are also developed and made available by organizations that lease the database from NLM. | environmental science, analysis, animal science, behavioral science, bioengineering, biology, biomedical practitioner, biomedicine, biophysics, biotechnology, chemical science, chemistry, health, life science, literature, marine biology, medical, plant science, journal article | nif-0000-10470 | SCR_006994 | NIH NLM: Medline Fact Sheet | 2026-09-12 01:01:45 | 11 | ||||||||||
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Public Expression Profiling Resource Resource Report Resource Website 10+ mentions |
Public Expression Profiling Resource (RRID:SCR_007274) | PEPR | data or information resource, database | An experiment in web-database access to large multi-dimensional data sets using a standardized experimental platform to determine if the larger scientific community can be given simple, intuitive, and user-friendly web-based access to large microarray data sets. All data in PEPR is also available via NCBI GEO. The structure and goals of PEPR differ from other mRNA expression profiling databases in a number of important ways. * The experimental platform in PEPR is standardized, and is an Affymetrix - only database. All microarrays available in the PEPR web database should ascribe to quality control and standard operating procedures. A recent publication has described the QC/SOP criteria utilized in PEPR profiles ( The Tumor Analysis Best Practices Working Group 2004 ). * PEPR permits gene-based queries of large Affymetrix array data sets without any specialized software. For example, a number of large time series projects are available within PEPR, containing 40-60 microarrays, yet these can be simply queried via a dynamic web interface with no prior knowledge of microarray data analysis. * Projects in PEPR originate from scientists world-wide, but all data has been generated by the Research Center for Genetic Medicine, Children''''s National Medical Center, Washington DC. Future developments of PEPR will allow remote entry of Affymetrix data ascribing to the same QC/SOP protocols. They have previously described an initial implementation of PEPR, and a dynamic web-queried time series graphical interface ( Chen et al. 2004 ). A publication showing the utility of PEPR for pharmacodynamic data has recently been published ( Almon et al. 2003 ). | microarray, expression profiling, affymetrix, metadata standard, gene, time series, data sharing, visualization, data mining, platform, blood, cell, cancer, bone, brain, eye, gut, heart, kidney, liver, lung, muscle, spinal cord, spleen, analysis |
is listed by: OMICtools is related to: Gene Expression Omnibus |
NINDS ; United States Department of Defense ; NHGRI ; NHLBI |
PMID:14681485 PMID:14596642 |
Public, Account required, (to download, For the analysis and visualization tools), The community can contribute to this resource | nif-0000-00014, OMICS_00776 | SCR_007274 | 2026-09-12 01:01:46 | 16 | ||||||
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Anvi'o Resource Report Resource Website 10+ mentions |
Anvi'o (RRID:SCR_021802) | data analysis software, data processing software, data visualization software, software application, software resource | Open source software analysis and visualization platform for microbial omics including genomics, metagenomics, metatranscriptomics, pangenomics, metapangenomics, phylogenomics, and microbial population genetics in integrated fashion through extensive interactive visualization capabilities. | analysis, visualization, integrated omics, metagenomics, pangenomics, phylogenomics, microbial omics | Alfred P. Sloan Foundation ; Helmholtz Institute for Functional Marine Biodiversity ; Marine Biological Laboratory ; Simons Foundation ; University of Chicago ; W. M. Keck Foundation |
Free, Available for download, Freely available | biotools:anvio | https://github.com/merenlab/anvio, https://bio.tools/anvio | SCR_021802 | Anvi’o | 2026-09-12 01:00:01 | 21 |
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
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