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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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JuGEx Resource Report Resource Website 1+ mentions |
JuGEx (RRID:SCR_023838) | software application, software resource | Software tool for integrating tissue transcriptome and cytoarchitectonic segregation. Combines data from Allen Human Brain Atlas and the EBRAINS Human Brain Atlas, specifically to discover how gene activities and microanatomical architectures contribute to brain function and dysfunction. Both tissue transcriptome and probabilistic brain segregation data allow for integrating genetic expression, brain structure, and function knowledge. | Allen Human Brain Atlas, EBRAINS Human Brain Atlas, tissue transcriptome, cytoarchitectonic segregation, integrating tissue transcriptome and cytoarchitectonic segregation, brain function, | is related to: Allen Institute for Brain Science | PMID:29478144 | Free, Available for download, Freely available | https://www.fz-juelich.de/de/inm/inm-1/leistungen/tools-services-und-forschungsdaten/jugex/jugex-download | SCR_023838 | 2026-08-09 09:08:48 | 1 | ||||||||
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easyPubMed Resource Report Resource Website 1+ mentions |
easyPubMed (RRID:SCR_023570) | software toolkit, software resource | Software R package for query NCBI Entrez and retrieve PubMed records in XML or text format. Used to process PubMed records by extracting and aggregating data from selected fields. Large number of records can be downloaded via this simple-to-use interface to NCBI PubMed API. Used to search and retrieve scientific publication records from PubMed. | Search and retrieve scientific publication records, scientific publication records, PubMed | Free, Available for download, Freely available | https://www.data-pulse.com/dev_site/easypubmed/ | SCR_023570 | 2026-08-09 09:08:17 | 9 | ||||||||||
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Preprocessing tools for oligonucleotide arrays Resource Report Resource Website 10+ mentions |
Preprocessing tools for oligonucleotide arrays (RRID:SCR_023726) | software toolkit, software resource | Software R package to analyze oligonucleotide arrays at probe level. Supports Affymetrix (CEL files) and NimbleGen arrays (XYS files). Used for annotation of Affymetrix Gene Array data. | analyze oligonucleotide arrays, Affymetrix Gene Array, NimbleGen array, Affymetrix Gene Array data annotation, | Brazilian Funding Agency CAPES ; NCRR R01 RR021967; NHGRI P41 HG004059 |
PMID:20688976 | Free, Available for download, Freely available | SCR_023726 | affycoretools | 2026-08-09 09:08:40 | 15 | ||||||||
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AP-histology Resource Report Resource Website 10+ mentions |
AP-histology (RRID:SCR_023847) | software application, software resource | Software data pipeline which aligns histology images to the Allen CCF. | Allen Common Coordinate Framework, histology images aligning to Allen CCF, Allen CCF, aligns histology images, histology images, | is related to: Allen Institute for Brain Science | Free, Available for download, Freely available | SCR_023847 | 2026-08-09 09:08:20 | 13 | ||||||||||
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ListDiff Resource Report Resource Website 1+ mentions |
ListDiff (RRID:SCR_023569) | software application, software resource | Software tool that performs SET Operations including Set Intersections, Set Unions and Set Differences over lists of words, numbers etc with formatted results . Used for comparing differences between two lists. | comparing differences, list comparison, SET Operations, Set Intersections, Set Unions, Set Differences, lists of words, numbers, formatted results, | Free, Freely available | SCR_023569 | 2026-08-09 09:08:38 | 1 | |||||||||||
|
NamSor Resource Report Resource Website 10+ mentions |
NamSor (RRID:SCR_023935) | software application, software resource | Software tool accurately classifies personal names by gender, country of origin or ethnicity. Can infer gender, translate Chinese names and Japanese names, format phone number, and split full name via user interface and API. Used as name checker for gender, origin and ethnicity determination. | name checker for gender, origin and ethnicity determination, infer gender, translate Chinese names and Japanese names, format phone number, | Free, Freely available | SCR_023935 | 2026-08-09 09:08:20 | 15 | |||||||||||
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VarDict Resource Report Resource Website 10+ mentions |
VarDict (RRID:SCR_023658) | software application, software resource | Software tool as variant caller for both single and paired sample variant calling from BAM files. Implements amplicon bias aware variant calling from targeted sequencing experiments, rescue of long indels by realigning bwa soft clipped reads.Novel and versatile variant caller for next generation sequencing in cancer research. | variant caller, BAM files, amplicon bias aware variant calling, sequencing experiments, next generation sequencing, long indels, | is related to: vardictcpp | AstraZeneca | PMID:27060149 | Free, Available for download, Freely available | SCR_023658 | 2026-08-09 09:08:39 | 38 | ||||||||
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Grammarly Resource Report Resource Website 50+ mentions |
Grammarly (RRID:SCR_023778) | software application, software resource | Software to correct spelling and grammar. | English, spelling, grammar, correction, | Free, Freely available | SCR_023778 | 2026-08-09 09:08:19 | 79 | |||||||||||
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Molecular Operating Environment Resource Report Resource Website 10+ mentions |
Molecular Operating Environment (RRID:SCR_023932) | MOE | software application, software resource | Drug discovery platform to integrate visualization, modeling and simulation in single package. Integrated computer aided molecular design platform. | Chemical Computing Group ULC., drug discovery, visualization, modeling, simulation, molecular design, | Restricted | SCR_023932 | Chemical Computing Group ULC Molecular Operating Environment, Molecular Operating Environment (MOE) | 2026-08-09 09:08:50 | 27 | |||||||||
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ChatGPT Resource Report Resource Website 500+ mentions |
ChatGPT (RRID:SCR_023775) | software application, software resource | Artificial Iinteligence chatbot that uses natural language processing to create humanlike conversational dialogue. Notable for enabling users to refine and steer conversation towards desired length, format, style, level of detail, and language used. Sibling model to InstructGPT, which is trained to follow instruction in prompt and provide detailed response. | natural language processing, humanlike conversational dialogue, provide detailed response, | Restricted | SCR_023775 | 2026-08-09 09:08:19 | 695 | |||||||||||
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CeleScope Resource Report Resource Website 100+ mentions |
CeleScope (RRID:SCR_023553) | software application, software resource | Software tool as collection of bioinfomatics analysis pipelines to process single cell sequencing data generated with Singleron products. Single cell analysis pipelines developed by Singleron Biotechnologies. | Single cell analysis, process single cell sequencing data, Singleron Biotechnologies, | Free, Available for download, Freely available | https://pypi.org/project/celescope/ | SCR_023553 | 2026-08-09 09:08:38 | 177 | ||||||||||
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ARA Tools Resource Report Resource Website 1+ mentions |
ARA Tools (RRID:SCR_023826) | software toolkit, software resource | Software package for analysis of mouse brain STP data with respect to the Allen Reference Atlas. Collection of MATLAB functions to analyze mouse whole brain imaging data and the associated "sparse" point data such as cell locations, traced neurite trees, or traced projections from a bulk injection. This package relates sparse data to the Allen Mouse Brain Reference Atlas. | Allen Mouse Brain Reference Atlas, analyze mouse whole brain imaging data, cell locations, traced neurite trees, traced projections from bulk injection, | is related to: Allen Institute for Brain Science | Free, Available for download, Freely available | SCR_023826 | 2026-08-09 09:08:41 | 3 | ||||||||||
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VirusDetect Resource Report Resource Website 10+ mentions |
VirusDetect (RRID:SCR_023669) | software toolkit, software resource | Software package to efficiently and exhaustively analyze large scale sRNA datasets for virus identification. Automated pipeline for virus discovery using deep sequencing of small RNAs. | Virus discovery, analyze large scale sRNA datasets, virus identification, deep sequencing of small RNAs, sequencing, small RNAs | NSF | PMID:27825033 | Free, Available for download, Freely available | https://github.com/kentnf/VirusDetect | SCR_023669 | 2026-08-09 09:08:18 | 18 | ||||||||
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Process Genes List Resource Report Resource Website |
Process Genes List (RRID:SCR_023823) | PGL | software toolkit, software resource | Software R package which links genetics and human brain imaging by using genes associated with disease and calculating normalized mRNA expression average of those genes in each brain region. By uploading lists of genes and brain regions of interest, this package will return csv with the results. | Allen Human Brain Atlas | is related to: Allen Institute for Brain Science | PMID:32201351 | Free, Available for download, Freely available | SCR_023823 | 2026-08-09 09:08:41 | 0 | ||||||||
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PET-CT mouse brain toolbox Resource Report Resource Website |
PET-CT mouse brain toolbox (RRID:SCR_023821) | software toolkit, software resource | Software toolbox provides multi-modality murine image templates, all of which are spatially registered to the Allen Common Coordinate Framework. The images have been optimized for in-vivo preclinical imaging in terms of resolution and region-of-interest size. The ROIs have been derived from the Allen Brain Atlas. This image analysis tool can be used to facilitate the analysis of mouse PET-CT brain images. | Allen Mouse Brain Atlas, murine image template, mouse PET-CT brain images, | is related to: Allen Institute for Brain Science | DOI:10.1038/s41598-022-19872-4 | Free, Freely available | SCR_023821 | 2026-08-09 09:08:19 | 0 | |||||||||
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GeneWalk Resource Report Resource Website 1+ mentions |
GeneWalk (RRID:SCR_023787) | software application, software resource | Software for individual genes functions determination that are relevant in particular biological context and experimental condition. Quantifies similarity between vector representations of gene and annotated GO terms through representation learning with random walks on condition specific gene regulatory network. Similarity significance is determined through comparison with node similarities from randomized networks. | genes functions determination, vector representations of gene, annotated GO terms, similarity significance, node similarities, randomized networks, | NHGRI R01 HG007173 | PMID:33526072 | Free, Available for download, Freely available | https://churchman.med.harvard.edu/genewalk | SCR_023787 | 2026-08-09 09:08:41 | 4 | ||||||||
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samclip Resource Report Resource Website 1+ mentions |
samclip (RRID:SCR_024330) | software application, software resource | Software tool to filter SAM file for soft and hard clipped alignments | filter SAM file, soft and hard clipped alignments, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/samclip/ | SCR_024330 | 2026-08-09 09:08:52 | 2 | |||||||||
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seqwish Resource Report Resource Website 1+ mentions |
seqwish (RRID:SCR_024332) | software application, software resource | Software tool for alignment to variation graph inducer. | alignment, variation graph inducer, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/seqwish/ | SCR_024332 | 2026-08-09 09:09:02 | 2 | |||||||||
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sigviewer Resource Report Resource Website |
sigviewer (RRID:SCR_024340) | software application, software resource | Software viewing application for biosignals such as EEG or MEG time series. In addition to viewing raw data, SigViewer can also create, edit, and display event information such as annotations or artifact selections. | viewing application for biosignals, EEG, MEG, time series, viewing raw data, create event information, edit event information, display event information, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/sigviewer/ | SCR_024340 | 2026-08-09 09:08:52 | 0 | |||||||||
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pyomo Resource Report Resource Website 1+ mentions |
pyomo (RRID:SCR_024188) | software application, software resource | Open source Python-based optimization modeling language with diverse set of optimization capabilities. | Python, optimization modeling language, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/pyomo/ | SCR_024188 | 2026-08-09 09:08:48 | 5 |
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