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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Scrattch.Hicat Resource Report Resource Website 10+ mentions |
Scrattch.Hicat (RRID:SCR_018099) | data analytics software, software application, software resource | Software R package as hierarchical, iterative clustering for analysis of transcriptomics data.Used for single cell RNA-seq analysis for transcriptomic type characterization from Allen Institute. | Hierarchical, iterative clustering, analysis, transcriptomics, data, single cell RNAseq, Allen Institute | has parent organization: Allen Institute | Free, Available for download, Freely available | SCR_018099 | Scrattch Hierarchical, Iterative Clustering for Analysis of Transcriptomics | 2026-09-12 01:02:55 | 32 | |||||||||
|
QGIS Resource Report Resource Website 100+ mentions |
QGIS (RRID:SCR_018507) | software application, software resource | Open source cross platform desktop geographic information system application that supports viewing, editing, and analysis of geospatial data. Functions as geographic information system software, allowing users to analyze and edit spatial information, in addition to composing and exporting graphical maps. | Geographic information system, viewing, editing, analysis, geospatial data, spatial information analysis, graphical map, bio.tools |
is listed by: Debian is listed by: bio.tools |
Free, Available for download, Freely available | biotools:QGIS | https://bio.tools/QGIS | SCR_018507 | 2026-09-12 01:02:56 | 488 | ||||||||
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GeneMerge Resource Report Resource Website 10+ mentions |
GeneMerge (RRID:SCR_005744) | GeneMerge | analysis service resource, data analysis service, production service resource, service resource, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. Web-based and standalone application that returns a wide range of functional genomic data for a given set of study genes and provides rank scores for over-representation of particular functions or categories in the data. It uses the hypergeometric test statistic which returns statistically correct results for samples of all sizes and is the #2 fastest GO tool available (Khatri and Draghici, 2005). GeneMerge can be used with any discrete, locus-based annotation data, including, literature references, genetic interactions, mutant phenotypes as well as traditional Gene Ontology queries. GeneMerge is particularly useful for the analysis of microarray data and other large biological datasets. The big advantage of GeneMerge over other similar programs is that you are not limited to analyzing your data from the perspective of a pre-packaged set of gene-association data. You can download or create gene-association files to analyze your data from an unlimited number of perspectives. Platform: Online tool, Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | gene, genomics, functional genomic data, analysis, post-genomic analysis, data mining, hypothesis testing, statistical analysis, slimmer-type tool, term enrichment, text mining, false discovery rate, bonferroni correction, false discovery rate and bonferroni correction, perl, microarray |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: Harvard University; Cambridge; United States |
PMID:12724301 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_149203 | http://genemerge.cbcb.umd.edu/ | SCR_005744 | 2026-09-12 01:00:11 | 26 | ||||||
|
Synapse Resource Report Resource Website 1000+ mentions |
Synapse (RRID:SCR_006307) | Synapse | data or information resource, data repository, database, service resource, storage service resource | A cloud-based collaborative platform which co-locates data, code, and computing resources for analyzing genome-scale data and seamlessly integrates these services allowing scientists to share and analyze data together. Synapse consists of a web portal integrated with the R/Bioconductor statistical package and will be integrated with additional tools. The web portal is organized around the concept of a Project which is an environment where you can interact, share data, and analysis methods with a specific group of users or broadly across open collaborations. Projects provide an organizational structure to interact with data, code and analyses, and to track data provenance. A project can be created by anyone with a Synapse account and can be shared among all Synapse users or restricted to a specific team. Public data projects include the Synapse Commons Repository (SCR) (syn150935) and the metaGenomics project (syn275039). The SCR provides access to raw data and phenotypic information for publicly available genomic data sets, such as GEO and TCGA. The metaGenomics project provides standardized preprocessed data and precomputed analysis of the public SCR data. | data sharing, collaboration, data management, analysis, genome, phenotype, crowd sourcing, open data, provenance, resource management, annotation, authoring, markup, r, python, java, command-line, cloud, FASEB list |
is used by: NF Data Portal is listed by: FORCE11 is listed by: DataCite is listed by: re3data.org is related to: clearScience is related to: Exemplar Microscopy Images of Tissues has parent organization: Sage Bionetworks |
Cancer, Normal, Cardiovascular disease, Floppy hat syndrome | Life Sciences Discovery Fund ; NCI ; NHLBI ; Alfred P. Sloan Foundation |
The community can contribute to this resource | nlx_151983, DOI:10.17616/R3B934, r3d100011894, DOI:10.7303 | https://doi.org/10.17616/R3B934, https://doi.org/10.48550/arxiv.1506.00272, https://doi.org/10.7303/, https://dx.doi.org/10.7303, https://doi.org/10.17616/R3B934 | SCR_006307 | 2026-09-12 01:00:12 | 1104 | |||||
|
Clair library Resource Report Resource Website |
Clair library (RRID:SCR_007019) | Clairlib | data analysis software, data processing software, software application, software resource, software toolkit, text extraction software, text-mining software | A suite of open-source Perl modules intended to simplify a number of generic tasks in natural language processing (NLP), information retrieval (IR), and network analysis (NA). Its architecture also allows for external software to be plugged in with very little effort. The latest version of clairlib is 1.06 which was released on March 2009 and includes about 130 modules implementing a wide range of functionalities. Clairlib is distributed in two forms: * Clairlib-core, which has essential functionality and minimal dependence on external software, and * Clairlib-ext, which has extended functionality that may be of interest to a smaller audience. Much can be done using Clairlib on its own. Some of the things that Clairlib can do are: Tokenization, Summarization, Document Clustering, Document Indexing, Web Graph Analysis, Network Generation, Power Law Distribution Analysis, Network Analysis, RandomWalks on Graphs, Tf-IDF, Perceptron Learning and Classification, and Phrase Based Retrieval and Fuzzy OR Queries. | analysis, information, linguistic, module, network, process, retrieval, perl, natural language processing, information retrieval, network analysis |
is listed by: Biositemaps has parent organization: University of Michigan; Ann Arbor; USA |
NSF IIS 0534323; NSF IIS 0329043; NSF BCS 0527513; NLM R01 LM008106; NIDA U54 DA021519 |
Open unspecified license: Content is available under GNU Free Documentation License 1.3 or later. | nif-0000-33210 | SCR_007019 | Computational Linguistics And Information Retrieval Library | 2026-09-12 01:00:12 | 0 | ||||||
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GIMME Resource Report Resource Website 1+ mentions |
GIMME (RRID:SCR_014115) | GIMME | data analysis software, data processing software, software application, software resource, software toolkit | Software Matlab toolbox for directed functional connectivity analysis of fMRI BOLD signal from predefined regions of interest. It recovers true structure of connections and estimates weights attributed to each connection. Obtains patterns at group and individual levels. | Functional, connectivity, analysis, fMRI, BOLD, signal, predefined, region, pattern, BRAIN Initiative |
uses: MATLAB is recommended by: BRAIN Initiative is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of Pennsylvania; Philadelphia; USA has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA |
NIBIB EB022904; NIBIB R21 EB015573; NSF 0852147 |
PMID:22732562 | Free, Available for download, Freely available | SCR_014115 | Group Iterative Multiple Model Estimation | 2026-09-12 01:00:16 | 2 | ||||||
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DESeq2 Resource Report Resource Website 10000+ mentions |
DESeq2 (RRID:SCR_015687) | data analysis software, data processing software, software application, software resource, software tool | Software package for differential gene expression analysis based on the negative binomial distribution. Used for analyzing RNA-seq data for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates. | differential, gene, expression, analysis, binominal, distribution, RNA-seq data, Bioconductor, bio.tools |
is used by: Glimma is used by: TEtranscripts is listed by: Bioconductor is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: SARTools works with: tximport |
European Union’s 7th Framework Programme ; International Max Planck Research School for Computational Biology and Scientific Computing ; NCI T32 CA009337 |
Free, Available for download, Freely available | biotools:deseq2 | https://github.com/mikelove/DESeq2, https://bio.tools/deseq2 | SCR_015687 | 2026-09-12 01:00:17 | 50789 | |||||||
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Pipeline Pilot Resource Report Resource Website 100+ mentions |
Pipeline Pilot (RRID:SCR_014917) | data analysis software, data processing software, software application, software resource | Software used to automate the process of accessing, analyzing and reporting scientific data. This software can be used by a person with little or no software development experience can create scientific protocols that can be executed through a variety of interfaces including: BIOVIA Web Port, other BIOVIA solutions such as BIOVIA Electronic Lab Notebook, Isentris, Chemical Registration and third-party applications such as Microsoft SharePoint. The protocols aggregate and provide immediate access to volumes of research data, they automate the scientific analysis of data and allow researchers to explore, visualize and report results. | automation, accessing, analysis, analyzing, scientific data, aggregation. aggregate, research, scientific | is listed by: SoftCite | Commercial | SCR_014917 | 2026-09-12 01:00:17 | 358 | ||||||||||
|
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 | |||||||||
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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 | |||||||
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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 | ||||||
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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 | |||||||||
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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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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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