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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Avogadro Resource Report Resource Website 1000+ mentions |
Avogadro (RRID:SCR_015983) | data analysis software, data processing software, data visualization software, software application, software resource, software toolkit | Software for semantic chemical editing, visualization, and analysis. It is designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. | semantic, optimization, crystallography, chemical, editor, visualization, analysis, molecular, modeling, drug, design, biomolecule, simulation, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools |
Engineering Research Development Center W912HZ-11-P-0019; NSF DMR-1005413 |
PMID:22889332 DOI:10.1186/1758-2946-4-17 |
Open source, Free, Free to download | OMICS_04967, biotools:avogadro | http://avogadro.openmolecules.net/, https://github.com/avogadro, https://bio.tools/avogadro, https://sources.debian.org/src/axe-demultiplexer/ | SCR_015983 | SciCrunch Registry | 2026-09-26 02:15:40 | 2237 | ||||||
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redcap-importer Resource Report Resource Website |
redcap-importer (RRID:SCR_016032) | data acquisition software, data processing software, software application, software resource | Software that automates the process of retrieving and converting data to the format of a RedCap table and allows selection of directories and files for import. | automate, process, retrvinig, converting, data, format, research, electronic, data, capture, table, selection, directory, import | is related to: University of California at San Diego; California; USA | NIDA U24 DA041123 | Free, Available for download | SCR_016032 | SciCrunch Registry | 2026-09-26 02:15:40 | 0 | |||||||||
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ABCDreport Resource Report Resource Website |
ABCDreport (RRID:SCR_016030) | data analysis software, data processing software, software application, software resource | Software application as a simple system to review study progress. Used in ABCD study. | system, simple, review, study, progress, development, adolescence, brain, cognitive, report | is related to: University of California at San Diego; California; USA | NIDA U24 DA041123 | Free, Available for download | SCR_016030 | SciCrunch Registry | 2026-09-26 02:15:40 | 0 | |||||||||
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Belvu Resource Report Resource Website 10+ mentions |
Belvu (RRID:SCR_015989) | alignment software, data processing software, image analysis software, software application, software resource | Software for multiple sequence alignment viewing, editing and phylogeny. It includes a set of user-configurable modes to color residues used to create high-quality reference alignments. | editing, phylogeny, sequence, alignment, phylogenetic, viewer, multiple, editor, color, residue, reference |
is related to: SEQtools has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
NHGRI U54 HG00455; Wellcome Trust Grant 098051 |
PMID:26801397 | Free, Available for download | SCR_015989 | SciCrunch Registry | 2026-09-26 02:15:40 | 18 | ||||||||
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Hybrid-denovo Resource Report Resource Website 1+ mentions |
Hybrid-denovo (RRID:SCR_015866) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software for a de novo OTU-picking pipeline integrating single- and paired-end 16S sequence tags. It is designed to take Illumina paired-end sequencing reads as input and output the OTU BIOM table, together with their representative sequences and a phylogenetic tree of OTUs. | hybrid-denovo, 16S rRNA, microbiota pipeline, single-end, paired-end, illumina read, de novo, otu-picking pipeline, phylogenetic tree, python, bio.tools |
is listed by: bio.tools is listed by: Debian |
biotools:hybrid-denovo | https://bio.tools/hybrid-denovo | SCR_015866 | SciCrunch Registry | 2026-09-26 02:15:38 | 3 | |||||||||
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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 | SciCrunch Registry | ChimeraX | 2026-09-26 02:15:38 | 2366 | |||||||||
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Bio-tradis Resource Report Resource Website 50+ mentions |
Bio-tradis (RRID:SCR_015993) | TraDIS:Transposon Directed Insertion Sequencing | data analysis software, data processing software, sequence analysis software, software application, software resource, software toolkit | Analysis software for the output from TraDIS (Transposon Directed Insertion Sequencing) analyses of dense transposon mutant libraries. The Bio-Tradis analysis pipeline is implemented as an extensible Perl library which can either be used as is, or as a basis for the development of more advanced analysis tools. | software, tool, analysis, data, sequencing, insertion, transponson, direct, mutant, library, perl, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
Alexander von Humboldt Stiftung/Foundation ; Medical Research Council G1100100/1; Wellcome Trust WT098051 |
PMID:26794317 DOI:10.1093/bioinformatics/btw022 |
Free, Available for download, Freely available | OMICS_11083, biotools:bio-tradis | https://bio.tools/bio-tradis, https://sources.debian.org/src/bio-tradis/ | SCR_015993 | SciCrunch Registry | 2026-09-26 02:15:40 | 56 | |||||
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m6ASNP: Annotation of genetic variants by m6A function Resource Report Resource Website 1+ mentions |
m6ASNP: Annotation of genetic variants by m6A function (RRID:SCR_016048) | data access protocol, data analysis software, data processing software, data visualization software, software application, software resource, web service | Web server implemented in JAVA and PHP for annotating genetic variants by m6A function. It predicts and annotates N6-methyladenosine (m6A) alterations from genetic variants data such as germline SNPs or cancer somatic mutations. It employs two accurate prediction models for human and mouse using Random Forest algorithm. It conducts a statistical analysis for all the predicted m6A alterations. Provides statistical diagrams and a genome browser to visualize the topology characteristics of predicted m6A alterations. | N6-methyladenosine (m6A), variant annotation, effect prediction, random forest, miclip, m6a, mutant | China Postdoctoral Science Foundation 2017M622864; Fundamental Research Funds for the Central Universities No. 17lgpy106; Guangdong Natural Science Foundation 2014TQ01R387; National Key Research and Development Program 2017YFA0106700; National Natural Science Foundation of China 31771462 |
PMID:29617790 DOI:10.1093/gigascience/giy035 |
Free, Available for download, Freely available | https://github.com/RenLabBioinformatics/m6ASNP | SCR_016048 | SciCrunch Registry | m6ASNP | 2026-09-26 02:15:41 | 3 | |||||||
|
IMAGEN Resource Report Resource Website 100+ mentions |
IMAGEN (RRID:SCR_016045) | consortium, data or information resource, organization portal, portal, project portal | Research project examining how biological, psychological, and environmental factors during adolescence may influence brain development and mental health. Using brain imaging and genetics, the project will help develop prevention strategies and improved therapies for mental health disorders in the future., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | adolescence, teen, mental, health, study, brain, development, neurological, prevention, therapy, disorder, psychology | European Commission ; German Federal Ministry of Research & Education (BMBF) ; Medical Research Council ; National Institute for Health Research UK ; National Institute for Health Research US ; National Institute on Drug Abuse ; Swedish Research Council (Vetenskapsrådet) |
PMID:21102431 | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_016045 | SciCrunch Registry | IMAGEN Consortium, IMAGEN Project, IMAGEN Study | 2026-09-26 02:15:41 | 158 | ||||||||
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Short Read Sequence Typing for Bacterial Pathogens Resource Report Resource Website 10+ mentions |
Short Read Sequence Typing for Bacterial Pathogens (RRID:SCR_015870) | SRST2 | data analysis software, data processing software, sequence analysis software, software application, software resource, source code | Software that is designed to take Illumina sequence data, a MLST database and/or a database of gene sequences (e.g. resistance genes, virulence genes, etc) and report the presence of STs and/or reference genes. | genotype analysis, illumina sequence data, mlst database, gene sequence, st, reference gene, short read |
uses: Bowtie uses: SAMTOOLS is listed by: Debian is listed by: OMICtools requires: SciPy requires: Python Programming Language |
infectious disease | NHMRC of Australia 1043830; NHMRC of Australia 1061409; NHMRC of Australia 1061435; Victorian Life Sciences Computation Initiative (VLSCI) VR0082 |
PMID:25422674 | Free, Available for download | OMICS_12777 | http://katholt.github.io/srst2/, https://sources.debian.org/src/srst2/ | http://srst.sourceforge.net/ | SCR_015870 | SciCrunch Registry | SRST2: Short Read Sequence Typing for Bacterial Pathogens, Short Read Sequence Typing v2 | 2026-09-26 02:15:38 | 24 | ||
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GrowthToolbox Resource Report Resource Website 1+ mentions |
GrowthToolbox (RRID:SCR_015754) | GFtbox | data analysis software, data processing software, simulation software, software application, software resource | Analysis software for analysis of finite elements and simulations of 3D shape changes in a tissue that result from patterns of growth. It works with Matlab to model biological growth of leaves, petals, and similar organs. | 3d object, finite element, growth, growth pattern, matlab |
uses: MATLAB has parent organization: University of East Anglia; Norwich; United Kingdom |
BBSRC BB/F005997/1; BBSRC BB/F005555/1 |
PMID:21698124 | Free, Available for download | http://cmpdartsvr3.cmp.uea.ac.uk/wiki/BanghamLab/index.php/Main_Page | SCR_015754 | SciCrunch Registry | GFtbox | 2026-09-26 02:15:37 | 3 | |||||
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CMake Resource Report Resource Website 10+ mentions |
CMake (RRID:SCR_015875) | authoring tool, software application, software development environment, software development tool, software resource, software toolkit | Software toolkit designed to build, test and package software. CMake is used to control the software compilation process using simple platform and compiler independent configuration files, and generate native makefiles and workspaces that can be used in the compiler environment of your choice. | software development, compiler, configuration, makefile, workspace | is used by: NiftyPET | PMID:18051095 | Open source, Available for download | SCR_015875 | SciCrunch Registry | 2026-09-26 02:15:38 | 25 | |||||||||
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RIPPLELAB Resource Report Resource Website 10+ mentions |
RIPPLELAB (RRID:SCR_015876) | data processing software, data visualization software, software application, software resource, source code | Source code for processing continuous local field potentials (LFP). The interface implements different documented algorithms for HFO detection, and provides several tools for signal visualization and manipulation. | lfp, local field potential, continuous local field potential, computing platform | Free, Available for download | SCR_015876 | SciCrunch Registry | RIPPLELAB Multi Analysis EEG Project | 2026-09-26 02:15:38 | 16 | ||||||||||
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NiftyPET Resource Report Resource Website 1+ mentions |
NiftyPET (RRID:SCR_015873) | data processing software, data visualization software, image analysis software, software application, software resource, software toolkit, source code | Python software package that offers quantitative PET image reconstruction and analysis with high accuracy and precision. It is written in CUDA C and embedded in Python C extensions. | python, cuda c, python c, pet, image reconstruction, image analysis, bio.tools |
uses: CMake is listed by: Debian is listed by: bio.tools |
DOI:10.1007/s12021-017-9352-y | Free, Available for download, Runs on Windows, Runs on Linux | biotools:niftypet | https://bio.tools/niftypet | SCR_015873 | SciCrunch Registry | 2026-09-26 02:15:38 | 7 | |||||||
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Perseus Resource Report Resource Website 1000+ mentions |
Perseus (RRID:SCR_015753) | data analysis software, data processing software, software application, software resource | Software that supports biological and biomedical researchers in interpreting protein quantification, interaction and post-translational modification data. Perseus contains a comprehensive portfolio of statistical tools for high-dimensional omics data analysis covering normalization, pattern recognition, time-series analysis, cross-omics comparisons and multiplehypothesis testing. | shotgun proteomics data analysis, protein quantification, post-translational modification data, statistical analysis, omics data | European Union 686547; European Union GA ERC-2012-SyG_318987–ToPAG |
PMID:27348712 | Free, Available for download, Runs on Windows, Runs on Mac OS, Tutorial available, Account required | http://www.biochem.mpg.de/5111810/perseus | SCR_015753 | SciCrunch Registry | 2026-09-26 02:15:37 | 4024 | ||||||||
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Barrnap Resource Report Resource Website 500+ mentions |
Barrnap (RRID:SCR_015995) | data analysis software, data processing software, sequence analysis software, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software to predict the location of ribosomal RNA genes in genomes. It supports bacteria, archaea, mitochondria, and eukaryotes. It takes FASTA DNA sequence as input, writes GFF3 as output, and supports multithreading., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | multithreading, fasta, sequencing, software, predict, location, ribosomal, gene, genome, RNA, prediction, bacteria, archaea, mitochondria, eukaryote, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools |
THIS RESOURCE IS NO LONGER IN SERVICE | biotools:barrnap, OMICS_13988 | https://github.com/tseemann/barrnap, https://bio.tools/barrnap, https://sources.debian.org/src/barrnap/ | SCR_015995 | SciCrunch Registry | Barrnap: Basic rapid ribosomal RNA predictor | 2026-09-26 02:15:40 | 722 | |||||||
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CED: Power1401 Resource Report Resource Website 10+ mentions |
CED: Power1401 (RRID:SCR_016040) | instrument resource | Data acquisition interface from Cambridge Electronic Design Limited. Works with Spike2 to provide continuous acquisition tasks. Records waveform data, digital and marker information, and can generate waveform and digital outputs simultaneously for real-time, multi-tasking experiment control. | Cambridge Electronic Design Limited, equipment, hardware, instrument, USEDit |
is listed by: USEDit works with: Spike2 Software |
Restricted | https://drive.google.com/file/d/1fl3Sbk3t-vRgPgDNMBbZQuLSBIdJUPsO/view?usp=drivesdk | SCR_017282 | SCR_016040 | SciCrunch Registry | , POWER1401-3 Data Acquisition Interface, Power1401-3A, CED Power1401 3A | 2026-09-26 02:15:41 | 15 | |||||||
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BMap Resource Report Resource Website 10+ mentions |
BMap (RRID:SCR_016044) | alignment software, data analysis software, data processing software, image analysis software, sequence analysis software, software application, software resource, source code | Software that maps whole-genome and targeted bisulfite sequence reads to reference genomes. It is especially useful for reads obtained using post-bisulfite adaptor tagging (PBAT)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | mapper, whole-genome, bisulfite, sequencing, post-bisulfite, adaptor, tagging, pbat, reads, mapping | PMID:22649061 | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_016044 | SciCrunch Registry | 2026-09-26 02:15:41 | 29 | ||||||||||
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NeuroImage Field-of-View Normalization Tool Resource Report Resource Website 1+ mentions |
NeuroImage Field-of-View Normalization Tool (RRID:SCR_015957) | data or information resource, portal, topical portal | FSoftware for field-of-view normalization to minimize mismatch in different subjects' images. It aids that streamline analysis of large-scale brain MRI datasets. | normalization, fov, field, view, filed of view, brain, mri, magnetic, resonance, neuroimaging, imaging, atlas | DOI:10.1007/s12021-018-9359-z | Free, Available for download | SCR_015957 | SciCrunch Registry | Normalize FOV, normalizefov | 2026-09-26 02:15:39 | 4 | |||||||||
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FIONASITE Resource Report Resource Website 1+ mentions |
FIONASITE (RRID:SCR_016012) | data acquisition software, data management software, data processing software, data transfer software, software application, software resource | Software for uploading data to FIONA and capturing MR images and k-space data from medical image systems. It provides a web-interface to automate the data review (image viewer), integrate with the centralized electronic data record for assigning anonymized id's, and forward the data to the central archive. | automate, data, upload, collection, network, appliance, abcd, study | is related to: University of California at San Diego; California; USA | NIDA U24 DA041123 | Free, Available for download | SCR_016014, SCR_016013 | http://qi.ucsd.edu/news-article.php?id=2342&go=newer | SCR_016012 | SciCrunch Registry | 2026-09-26 02:15:40 | 1 |
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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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