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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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metagear Resource Report Resource Website |
metagear (RRID:SCR_017085) | software resource, software toolkit | Software R package for research synthesis taxonomy from applying systematic review approach to assemble and screen literature, to extract data from studies, and to summarize and analyze these data with statistics of meta analysis. | sythesis, taxonomy, systematic, review, assemble, screen, literature, extract, meta, data, analysis, statistical |
is listed by: CRAN is related to: R Project for Statistical Computing has parent organization: University of South Carolina; South Carolina; USA |
NSF DBI-1262545; NSF DEB-1451031 |
DOI:10.1111/2041-210X.12472 | Free, Available for download, Freely available | https://github.com/cran/metagear, https://lajeunesse.myweb.usf.edu | SCR_017085 | 2026-09-12 01:02:54 | 0 | |||||||
|
CIBERSORT Resource Report Resource Website 1000+ mentions |
CIBERSORT (RRID:SCR_016955) | data analytics software, software application, software resource | Software tool to provide an estimation of the abundances of member cell types in a mixed cell population, using gene expression data. Used for characterizing cell composition of complex tissues from their gene expression profiles, large scale analysis of RNA mixtures for cellular biomarkers and therapeutic targets. | estimation, abundance, cell, type, mixed, population, gene, expression, data, tissue, complex, analysis, RNA, biomarker, therapeutic, target, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Stanford University; Stanford; California |
B&J Cardan Oncology Research Fund ; Damon Runyon Cancer Research Foundation ; Doris Duke Charitable Foundation ; Ludwig Institute for Cancer Research ; NCI T32 CA09302; NCI U01 CA154969; NIAID U19 AI090019; Siebel Stem Cell Institute ; Thomas and Stacey Siebel Foundation ; US Department of Defense |
PMID:25822800 | Not freely available for download or distribution, Available for non commercial users, Registration required | biotools:CIbERSORt | https://bio.tools/CIBERSORT | SCR_016955 | 2026-09-12 01:02:54 | 1908 | ||||||
|
Lab Streaming Layer Resource Report Resource Website 50+ mentions |
Lab Streaming Layer (RRID:SCR_017631) | LSL | software application, software resource | System for unified collection of measurement time series in research experiments that handles networking, time synchronization, near real time access as well as optionally centralized collection, viewing and disk recording of data. System for synchronizing streaming data for live analysis or recording. | Synchronizing, streaming, data, live, analysis, recording, collection, time, series, EEG | has parent organization: University of California at San Diego; California; USA | Army Research Laboratory ; NINDS R01 NS047293 |
Free, Freely available | SCR_017631 | Lab Streaming Layer | 2026-09-12 01:02:55 | 86 | |||||||
|
Astrophysics Source Code Library Resource Report Resource Website 1+ mentions |
Astrophysics Source Code Library (RRID:SCR_017604) | ASCL | software repository, software resource | Registry for source codes of interest to astronomers and astrophysicists, including solar system astronomers, and lists codes that have been used in research that has appeared in, or been submitted to, peer-reviewed publications. ASCL is indexed by SAO/NASA Astrophysics Data System (ADS) and Web of Science and is citable by using unique ascl ID assigned to each code. The ascl ID can be used to link to the code entry by prefacing the number with ascl.net . | Sorce, code, astronomer, astrophysicist, data, list, publication | Free, Freely available | SCR_017604 | 2026-09-12 01:02:55 | 2 | ||||||||||
|
BVA import/export EEGLAB plugin Resource Report Resource Website 1+ mentions |
BVA import/export EEGLAB plugin (RRID:SCR_016333) | bva-io | software application, software resource, software toolkit | Software package for interfacing the Brain Vision Analyser data files (load/save) for ongoing development of Matlab routines . This package is also compatible with the EEGLAB software, and may be uncompressed in the plugin folder of this software. | interfacing, brain, vision, analyser, data, file, load, save, Matlab, routine, compatible, EEGLAB |
is related to: SourceForge is related to: EEGLAB is related to: MATLAB |
Free, Available for download, Freely available | SCR_016333 | Brain Vision Analyser | 2026-09-12 01:02:53 | 4 | ||||||||
|
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 | |||||||||
|
clustLasso Resource Report Resource Website 1+ mentions |
clustLasso (RRID:SCR_018820) | software resource, software toolkit | Software R package to build predictive signatures of microbial phenotypes. Software package implementing cluster lasso approach. | Predictive signatures, microbial phenotype, cluster lasso approach, build predictive signature, phenotype, data, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Freely available | biotools:clustlasso | https://bio.tools/clustlasso | SCR_018820 | 2026-09-12 01:02:56 | 1 | ||||||||
|
ODDPub Resource Report Resource Website 1+ mentions |
ODDPub (RRID:SCR_018385) | algorithm resource, software resource | Text mining algorithm to screen biomedical publications to find data sharing statements. Algorithm that parses set of publications and detects which publications disseminated Open Data or Open Code together with publication. Tailored towards biomedical literature. | Text mining, biomedical publication screening, data sharing statement detection, open data, open code, publication, data, biomedical literature, Berlin Institute of Health, ASWG | is used by: rtransparent | Free, Available for download, Freely available | SCR_018385 | 2026-09-12 01:02:56 | 6 | ||||||||||
|
Statistical Analysis System Resource Report Resource Website 5000+ mentions |
Statistical Analysis System (RRID:SCR_008567) | SAS | data analytics software, data management software, software application, software resource | Software platform to explore, analyze and visualize data. SAS 9.4 is part of SAS Platform. Standardized data governance and management from statistical software company SAS. | Explore, analyze, visualize, data, standardized, management, statistics | is listed by: SoftCite | Restircted | nif-0000-31484 | https://www.sas.com/en_us/software/platform.html, https://www.sas.com/en_us/software/sas9.html | SCR_008567 | Statistical Analysis System, SAS Intelligence Platform, SAS 9.3, SAS 9.4 | 2026-09-12 01:02:38 | 7485 | ||||||
|
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 | |||||||
|
pearson-central-end-point Resource Report Resource Website |
pearson-central-end-point (RRID:SCR_016034) | data acquisition software, data processing software, data storage software, software application, software resource | Data collection software as an end-point for centrally storing data from the Pearsons Q-Interactive. | data, collection, end-point, central, storage, Pearson Q-Interactive, electronic, abcd | is related to: University of California at San Diego; California; USA | NIDA U24 DA041123 | Free, Available for download | SCR_016034 | 2026-09-12 01:00:18 | 0 | |||||||||
|
GeMoMa Resource Report Resource Website 100+ mentions |
GeMoMa (RRID:SCR_017646) | simulation software, software application, software resource | Software tool as homology based gene prediction program that predicts gene models in target species based on gene models in evolutionary related reference species. Utilizes amino acid sequence conservation, intron position conservation, and RNA-seq data to accurately predict protein-coding transcripts. Supports combination of predictions based on several reference species allowing to transfer high quality annotation of different reference species to target species. | Homology, based, gene, prediction, model, target, evolutionary, related, reference, species, sequence, conservation, intron, position, RNAseq, data, protein, coding, transcript, bio.tools |
is listed by: bio.tools is listed by: Debian works with: GUSHR |
PMID:31020559 | Free, Available for download, Freely available | biotools:gemoma | https://bio.tools/gemoma | SCR_017646 | Gene Model Mapper | 2026-09-12 01:00:20 | 158 | ||||||
|
BioDepot-workflow-builder Resource Report Resource Website 1+ mentions |
BioDepot-workflow-builder (RRID:SCR_017402) | Bwb | data processing software, software application, software resource, workflow software | Software tool to create and execute reproducible bioinformatics workflows using drag and drop interface. Graphical widgets represent Docker containers executing modular task. Widgets are linked graphically to build bioinformatics workflows that can be reproducibly deployed across different local and cloud platforms. Each widget contains form-based user interface to facilitate parameter entry and console to display intermediate results. | bioinformatics, big, data, workflow, reproducible, Docker | NHGRI U24HG012674; NHLBI U54 HL127624; NIAID R03AI159286; NIGMS R01 GM126019 |
DOI:10.1016/j.cels.2019.08.007 | Free, Available for download, Freely available | SCR_017402 | 2026-09-12 01:00:20 | 2 | ||||||||
|
dMRIPrep Resource Report Resource Website |
dMRIPrep (RRID:SCR_017412) | 3d spatial image, data analysis software, data or information resource, data processing software, diffusion-weighted mri 3d image, image, image processing software, mri 3d image, software application, software resource | Software tool as preprocessing pipeline for diffusion MRI. Pipeline used for preprocessing of diverse dMRI data. Workflow dispenses of manual intervention, thereby ensuring reproducibility of results. | Preprocessing, diffusion, MRI, imaging, data | Free, Available for download, Freely available | https://doi.org/10.5281/zenodo.3392201 | SCR_017412 | 2026-09-12 01:00:20 | 0 | ||||||||||
|
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 | |||||||||
|
CMap Resource Report Resource Website 500+ mentions |
CMap (RRID:SCR_016204) | data or information resource, data set, database, software resource, web application | Dataset of cellular signatures that catalogs transcriptional responses of human cells to chemical and genetic perturbation. CMap contains perturbagens, expression signatures, and small molecules from cell lines. | data, set, connectivity, gene, expression, database, heat map, drug, tool, perturbational, perturbagen, signature, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian is listed by: SoftCite has parent organization: Broad Institute |
Free for academic use, Subscription for commercial use, Available for download, Acknowledgement requested | biotools:CMap | https://bio.tools/CMap | SCR_016204 | LINCS CMap L1000, LINCS L1000, LINCS CMap, ConnectivityMap, Connectivity Map | 2026-09-12 01:00:18 | 789 | |||||||
|
fastp Resource Report Resource Website 1000+ mentions |
fastp (RRID:SCR_016962) | data analysis software, data processing software, software application, software resource | Software tool to provide fast all in one preprocessing for FastQ files. Developed in C++ with multithreading supported to afford high performance. Performs quality control, adapter trimming, quality filtering, per read quality pruning and many other operations with a single scan of the FASTQ data. | fast, all in one, preprocessing, FastQ, file, data, read, quality, control, adapter, trimming, filtering | is listed by: OMICtools | National Science Foundation of China ; Special Funds for Future Industries of Shenzhen |
PMID:30423086 | Free, Available for download, Freely available | SCR_016962 | 2026-09-12 01:00:19 | 1745 | ||||||||
|
RecView Resource Report Resource Website 1+ mentions |
RecView (RRID:SCR_016531) | data processing software, image analysis software, image processing software, image reconstruction software, software application, software resource | Software tool as a program for tomographic reconstruction and image processing of micro/nano-CT data taken at SPring8 and APS Argonne. | computational, tomographic, reconstruction, image, processing, micro, nano, CT, data | Japan Society for the Promotion of Science | Free, Available for download, Freely available | SCR_016531 | 2026-09-12 01:00:19 | 4 | ||||||||||
|
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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SMARTdenovo Resource Report Resource Website 100+ mentions |
SMARTdenovo (RRID:SCR_017622) | alignment software, data processing software, image analysis software, software application, software resource | Software tool as de novo assembler for PacBio and Oxford Nanopore data. It produces assembly from all-vs-all raw read alignments without error correction stage. Allows to read overlapping, rescue missing overlaps, identify low-quality regions and chimaera and produce better consensus. | De novo, assembler, PacBio, Oxford Nanopore, data, sequence, raw, read, alignment, error, bio.tools |
is listed by: Debian is listed by: bio.tools |
Free, Available for download, Freely available | BioTools:SMARTdenovo, biotools:SMARtdenovo | https://bio.tools/SMARTdenovo, https://bio.tools/SMARTdenovo, https://bio.tools/SMARTdenovo | SCR_017622 | 2026-09-12 01:00:20 | 191 |
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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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