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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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exRNA Atlas Resource Report Resource Website 10+ mentions |
exRNA Atlas (RRID:SCR_017221) | analysis service resource, application programming interface, atlas, consortium, controlled vocabulary, data access protocol, data analysis service, data or information resource, data repository, database, expression atlas, ontology, organization portal, portal, production service resource, service resource, software resource, storage service resource | Software tool as data and metadata repository of Extracellular RNA Communication Consortium. Atlas includes small RNA sequencing and qPCR derived exRNA profiles from human and mouse biofluids. All RNAseq datasets are processed using version 4 of exceRpt small RNAseq pipeline. Atlas accepts submissions for RNAseq or qPCR data. | Differential, expression, RNA, sequencing, qPCR, data, visualization, extracellular, exRNA, atlas, repository, dataset |
is recommended by: National Library of Medicine has parent organization: Baylor College of Medicine; Houston; Texas has parent organization: exRNA |
gastric cancer, colon carcinoma, colorectal cancer, prostate carcinoma, pancreatic carcinoma, multiple sclerosis, glioblastoma multiforme, ulcerative colitis, Alzheimer's disease, ischemic stroke, intraparenchymal hemorrhage of brain, asthma, cardiovascular disorder, myocardial infarction, lupus, nephrotic syndrome, transplanted kidney present, liver disease, transplanted liver present, pre-eclampsia, Parkinson disease, intraventricular brain hemorrhage, subarachnoid hemorrhage | American Cancer Society ResearchProfessor Award ; Frank McGraw Memorial Chair in CancerResearch ; NCATS UH3 TR000906; NCATS UH3 TR000943; NCI CA217685; NCI R01 CA163849; NCI R35 CA209904; NCI U19 CA179512; NHLBI K23 HL127099; NHLBI R01 HL122547; NHLBI R01 HL136685; NIA R01 AG059729; NIDA U54 DA036134; NIDDK P30 DK63720; NIGMS R25 GM056929 |
PMID:30951672 | Restricted | SCR_017221 | 2026-09-19 12:53:36 | 29 | |||||||
|
RNAstructure Resource Report Resource Website 50+ mentions |
RNAstructure (RRID:SCR_017216) | analysis service resource, data access protocol, production service resource, service resource, simulation software, software application, software resource, web service | Web server for RNA and DNA secondary structure prediction and analysis. Software package as RNA folding prediction program. | RNA, DNA, secondary, structure, prediction, analysis |
is listed by: SoftCite has parent organization: University of Rochester; New York; USA |
NIGMS R01 GM076485 | PMID:23620284 | Free, Freely available | SCR_017216 | 2026-09-19 12:53:36 | 58 | ||||||||
|
SerialEM Resource Report Resource Website 100+ mentions |
SerialEM (RRID:SCR_017293) | data acquisition software, data processing software, software application, software resource | Software tool for automated EM data acquisition. Used for efficient tilt series acquisition and interface for image capture, display, and storage and for control of some aspects of microscope function. | automated, data, acquisition, tilt, image, capture, display, storage, microscope | NCRR RR00592; NIGMS P01 GM61306 |
PMID:16182563 | Restricted | SCR_017293 | 2026-09-19 12:53:38 | 228 | |||||||||
|
Protomo Resource Report Resource Website 1+ mentions |
Protomo (RRID:SCR_017296) | data processing software, image processing software, software application, software resource | Software tool for electron tomography and 3D image processing. Software package used in electron tomography for marker free alignment and 3D reconstruction of tilt series. Tomography software package distributed for linux operating system and developed by Hanspeter Winkler. | electron, tomography, 3D, image, processing | NIGMS GM30598; NIGMS GM64346 |
PMID:16973379 | Restricted | SCR_017296 | 2026-09-19 12:53:38 | 5 | |||||||||
|
Brain Imaging Data Structure (BIDs) Resource Report Resource Website 100+ mentions |
Brain Imaging Data Structure (BIDs) (RRID:SCR_016124) | BIDS | data or information resource, narrative resource, portal, standard specification | Standard specification for organizing and describing outputs of neuroimaging experiments. Used to organize and describe neuroimaging and behavioral data by neuroscientific community as standard to organize and share data. BIDS prescribes file naming conventions and folder structure to store data in set of already existing file formats. Provides standardized templates to store associated metadata in form of Javascript Object Notation (JSON) and tab-separated value (TSV) files. Facilitates data sharing, metadata querying, and enables automatic data analysis pipelines. System to curate, aggregate, and annotate neuroimaging databases. Intended for magnetic resonance imaging data, magnetoencephalography data, electroencephalography data, and intracranial encephalography data. | Data storing structure, neuroimaging, standardized template, data sharing, MRI data, MEG data, EEG data, iEEG data, FASEB list |
is used by: OpenNeuro is used by: SPARC Portal is used by: SPARC Data Standard is listed by: FAIRsharing is related to: BIDS-Matlab is related to: NiPoppy works with: MNE-BIDS |
European Regional Development Fund ; German federal state of Sachsen-Anhalt ; International Neuroinformatics Coordinating Facility ; Laura and John Arnold Foundation ; Medical Research Council United Kingdom ; NIAAA U01 AA021697; NIGMS P20 GM103472; NIMH Intramural Research Program ; NSF 1429999; Wellcome Trust |
PMID:27326542 PMID:29917016 PMID:31239435 PMID:31239438 PMID:37744469 |
Free, Freely available | https://bids-specification.readthedocs.io/en/stable/, https://doi.org/10.25504/FAIRsharing.rd1j6t | SCR_016124 | Brain Imaging Data Structure, BIDS, Brain Imaging Data Structure (BIDS), Brain Imaging Data Structure v1.4.0 | 2026-09-19 12:53:18 | 235 | |||||
|
SV-plaudit Resource Report Resource Website 1+ mentions |
SV-plaudit (RRID:SCR_016285) | data analysis software, data processing software, image analysis software, software application, software resource | Software for rapidly curating structural variant (SVs) predictions. SV-plaudit provides a pipeline for creating image views of genomic intervals, automatically storing them in the cloud, deploying a website to view/score them, and retrieving scores for analysis. | genomics, structural, variants, visualization, manual, curation, prediction, image, alignment | NCI U24 CA209999; NHGRI K99 HG009532; NHGRI R01 HG006693; NIGMS R01 GM124355 |
Free, Available for download | SCR_016285 | 2026-09-19 12:53:20 | 2 | ||||||||||
|
star-for-criu Resource Report Resource Website 1+ mentions |
star-for-criu (RRID:SCR_016294) | alignment software, data processing software, image analysis software, software application, software resource | Software as an Hot Start software container for STAR alignment using CRIU (Checkpoint Restore in Userspace) tool to freeze the running container. Can be deployed to align RNA sequencing data. Used in the processing of biomedical big data for better reproducibility and reliability. | hot, start, container, star, aligner, sequencing, data, processing, biomedical, cloud, reproducibility, RNA, analysis, computing, environment | is related to: Systems Transcriptional Activity Reconstruction | AMEDD Advanced Medical Technology Initiative ; NHLBI U54 HL127624; NIGMS R01 GM126019 |
Free, Freely available, Available for download | https://github.com/paizhang/Hotstarting-For-STAR-Alignment | SCR_016294 | 2026-09-19 12:53:20 | 1 | ||||||||
|
MotionCor2 Resource Report Resource Website 100+ mentions |
MotionCor2 (RRID:SCR_016499) | data analysis software, data processing software, software application, software resource | Software tool for anisotropic correction of beam-induced motion for improved cryo-electron microscopy. Used to describe the sample motion as a local deformation that varies smoothly throughout the exposure. A program running on Linux. | anisotropic, correction, beam, induced, motion, cryo, electron, microscopy, exposure, data | has parent organization: University of California at San Francisco; California; USA | NIGMS P01 GM111126; NIH R01 GM031627 |
PMID:28250466 | Restricted | http://msg.ucsf.edu/em/software/motioncor2.html | SCR_016499 | MotionCor | 2026-09-19 12:53:24 | 186 | ||||||
|
Pavian Resource Report Resource Website 10+ mentions |
Pavian (RRID:SCR_016679) | analysis service resource, data analysis service, production service resource, service resource, software resource, web application | Software R package for interactive analysis of metagenomics classification results with a special focus on infectious disease diagnosis. Used for analyzing and visualization of metagenomics classification results from classifiers such as Kraken, Centrifuge and MetaPhlAn. Provides an alignment viewer for validation of matches to a particular genome. | interactive, analysis, metagenomics, classification, result, infectious, disease, diagnosis, data, visualization, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Centrifuge Classifier |
NHGRI R01 HG006677; NIGMS R01 GM083873; U. S. Army Research Office W911NF1410490 |
DOI:10.1101/084715 | Free, Freely available | biotools:pavian | https://fbreitwieser.shinyapps.io/pavian/, https://bio.tools/pavian | SCR_016679 | 2026-09-19 12:53:27 | 33 | ||||||
|
XYalign Resource Report Resource Website 1+ mentions |
XYalign (RRID:SCR_016661) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software tool for identifying, understanding, and correcting technical biases on the sex chromosomes in next generation sequencing data. | correct, technical, bias, sex, chromosome, next, generation, sequencing, data | is listed by: OMICtools | NIGMS R35 GM124827 | DOI:10.1101/346940 | Free, Available for download, Freely available | SCR_016661 | 2026-09-19 12:53:27 | 1 | ||||||||
|
Centrifuge Classifier Resource Report Resource Website 10+ mentions |
Centrifuge Classifier (RRID:SCR_016665) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software for rapid and sensitive classification of metagenomic sequences. Used for the classification of DNA sequences from microbial samples and analysis of large metagenomics data sets on conventional desktop computers. | classification, large, metagenomic, sequence, DNA, microbial, sample, analysis, data, desktop, computer, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools is related to: Pavian has parent organization: Center for Computational Biology at JHU |
NHGRI R01 HG006677; NIGMS R01 GM083873; NSF ABI1356078; U. S. Army Research Office W911NF1410490 |
DOI:10.1101/gr.210641.116 | Free, Available for download, Freely available | biotools:centrifuge, OMICS_12217 | https://github.com/infphilo/centrifuge, https://bio.tools/centrifuge, https://sources.debian.org/src/centrifuge/ | SCR_016665 | 2026-09-19 12:53:27 | 10 | ||||||
|
HISAT2 Resource Report Resource Website 10000+ mentions |
HISAT2 (RRID:SCR_015530) | data analysis software, data processing software, sequence analysis software, software application, software resource, source code | Graph-based alignment of next generation sequencing reads to a population of genomes. | alignment program, mapping reads, population genomics, human genome, bio.tools |
is used by: Fcirc is listed by: Debian is listed by: bio.tools is related to: TopHat has parent organization: Johns Hopkins University; Maryland; USA is required by: SL-quant is hosted by: GitHub |
NLM R01-LM06845; NIGMS R01-GM083873; NSF CCF-0347992 |
PMID:25751142 DOI:10.1038/s41587-019-0201-4 |
Available for download | OMICS_07225, biotools:hisat2 | https://github.com/infphilo/hisat2, https://bio.tools/hisat2, https://sources.debian.org/src/hisat2/ | SCR_015530 | HISAT | 2026-09-19 12:53:09 | 20753 | |||||
|
GenePattern Notebook Resource Report Resource Website 1+ mentions |
GenePattern Notebook (RRID:SCR_015699) | electronic laboratory notebook, software application, software resource, systems interoperability software, web application | Interactive analysis notebook environment that streamlines genomics research by interleaving text, multimedia, and executable code into unified, sharable, reproducible “research narratives.” It integrates the dynamic capabilities of notebook systems with an investigator-focused, simple interface that provides access to hundreds of genomic tools without the need to write code. | gene, genomics research, research narrative, notebook system, analysis notebook, bio.tools |
is listed by: bio.tools is listed by: Debian is affiliated with: GenePattern |
NIGMS R01-GM074024; NCI U24-CA194107 |
PMID:28822753 | Open Source, Free, Available for download, Account required | biotools:GenePattern_notebook | https://bio.tools/GenePattern_notebook | SCR_015699 | GenePattern Notebook environment | 2026-09-19 12:53:11 | 3 | |||||
|
UCSF ChimeraX Resource Report Resource Website 1000+ mentions |
UCSF ChimeraX (RRID:SCR_015872) | 3d visualization software, 4d visualization software, data processing software, data visualization software, software application, software resource | Software for 3D/4D image reconstruction. UCSF ChimeraX is the next-generation molecular visualization program from the Resource for Biocomputing, Visualization, and Informatics (RBVI), following UCSF Chimera. | 3d, 4d, image reconstruction, molecular visualization, biocomputing, informatics, rbvi, ucsf, chimera |
is related to: UCSF Chimera is related to: UCSF Chimera has parent organization: University of California at San Francisco; California; USA has plug in: ISOLDE |
NIGMS P41 GM103311 | SCR_015872 | ChimeraX | 2026-09-19 12:53:14 | 2366 | |||||||||
|
I-TASSER Resource Report Resource Website 1000+ mentions |
I-TASSER (RRID:SCR_014627) | data analysis software, data processing software, software application, software resource | Web server as integrated platform for automated protein structure and function prediction. Used for protein 3D structure prediction. Resource for automated protein structure prediction and structure-based function annotation. | Automated prediction, protein structure prediction, protein function prediction, protein 3D structure, amino acid sequence, alignment, simulation, 3D atomic model, protein, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: SoftCite has parent organization: University of Michigan; Ann Arbor; USA has parent organization: University of Kansas; Kansas; USA |
NIGMS GM083107; NIGMS GM084222 |
DOI:10.1186/1471-2105-9-40 DOI:10.1093/nar/gkv342 PMID:20360767 PMID:18215316 |
Free, Available for download, Freely available | biotools:i-tasser, SCR_018803 | https://bio.tools/i-tasser | SCR_014627 | Iterative Threading Assembly Refinement, Iterative Threading ASSEmbly Refinement | 2026-09-19 12:53:00 | 3874 | |||||
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libRoadRunner Resource Report Resource Website 10+ mentions |
libRoadRunner (RRID:SCR_014763) | simulation software, software application, software resource | Simulation engine for systems and synthetic biology to be used with other software applications. It retains the original functionality of RoadRunner but has changes in performance, back-end design, event handling, new C++ API, and stochastic simulation support. | simulation engine, simulation software, road runner, roadrunner, systems biology, synthetic biology |
is listed by: Debian is listed by: OMICtools |
NIGMS GM081070 | DOI:10.1093/bioinformatics/btv363 | Open source, Available for download | OMICS_09368 | https://sources.debian.org/src/libroadrunner-dev/ | SCR_014763 | 2026-09-19 12:53:02 | 11 | ||||||
|
NMRbox Resource Report Resource Website 50+ mentions |
NMRbox (RRID:SCR_014827) | software resource, software toolkit, web application | Computing platform for biomolecular NMR available to not-for-profit or government users. It consists of a virtual machine (VM) provisioned with dozens of widely-used NMR software packages, and is available as a cloud-based Platform-as-a-Service (PaaS) or as a downloadable VM for local execution. | Nuclear Magnetic Resonance, nmr, spectra, computing platform, platform, virtual machine, cloud, software toolbox | NIGMS P41GM111135 | Account required | SCR_014827 | , Nuclear Magnetic Resonance box, NMRbox.org | 2026-09-19 12:53:02 | 92 | |||||||||
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Motif Mutation Analysis for Regulatory Genomic Elements Resource Report Resource Website 500+ mentions |
Motif Mutation Analysis for Regulatory Genomic Elements (RRID:SCR_021902) | MMARGE | data analysis software, data processing software, software application, software resource, software toolkit | Software package that integrates genome wide genetic variation with epigenetic data to identify collaborative transcription factor pairs. Optimized to work with chromatin accessibility assays such as ATAC-seq or DNase I hypersensitivity, as well as transcription factor binding data collected by ChIP-seq. Used to identify combinations of cell type specific transcription factors while simultaneously interpreting functional effects of non-coding genetic variation. | genome wide genetic variation, epigenetic data, identify collaborative transcription factor pairs, interpreting functional effects, non-coding genetic variation | NCI CA173903; NHLBI R00 123485; NIDDK DK091183; NIGMS GM085764 |
PMID:29893919 | Free, Available for download, Freely available | SCR_021902 | 2026-09-19 12:54:59 | 608 | ||||||||
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3DRefine Resource Report Resource Website 10+ mentions |
3DRefine (RRID:SCR_021883) | data access protocol, software resource, web service | Interactive web server for efficient protein structure refinement with capability to perform web based statistical and visual analysis. | efficient protein structure refinement, statistical and visual analysis | NIGMS R01 GM093123 | DOI:10.1093/nar/gkw336 | Free, Freely available | SCR_021883 | 2026-09-19 12:54:59 | 32 | |||||||||
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trRosetta Resource Report Resource Website 100+ mentions |
trRosetta (RRID:SCR_021181) | service resource, simulation software, software application, software resource | Software tool for fast and accurate protein structure prediction. Builds protein structure based on direct energy minimizations with restrained Rosetta. Restraints include inter-residue distance and orientation distributions, predicted by deep residual neural network. Homologous templates are included in network prediction to improve accuracy for easy targets. | protein structure, restraint-guided structure generation, protein structure prediction | uses: Rosetta | China Scholarship Council ; Fok Ying-Tong Education Foundation ; Key Laboratory for Medical Data Analysis and Statistical Research of Tianjin ; National Natural Science Foundation of China ; NIGMS R01 GM092802; NIH Office of the Director DP5 OD026389; Thousand Youth Talents Plan of China |
PMID:31896580 | Free, Freely available | https://github.com/gjoni/trRosetta | SCR_021181 | transformed restrained Rosetta | 2026-09-19 12:54:49 | 100 |
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