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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Rtsne Resource Report Resource Website 100+ mentions |
Rtsne (RRID:SCR_016342) | data processing software, data visualization software, software application, software resource, software toolkit | Software as R wrapper for Van der Maaten's Barnes-Hut implementation of t-Distributed Stochastic Neighbor Embedding. Used for high-dimentional data visualisation. | data, visualisation, high-dimentional, van der Maaten, Barnes-Hut, implementation, distribution, stochastic, neighbor, embedding |
is listed by: CRAN is related to: R Project for Statistical Computing is related to: University of Toronto; Ontario; Canada |
European Union Seventh Framework Program ; the Netherlands Organization for Scientific Research (NWO) |
Free, Available for download, Freely available | SCR_016900 | https://cran.r-project.org/web/packages/Rtsne/index.html | SCR_016342 | SciCrunch Registry | , R t-distributed stochastic neighbor embedding, R t-Distributed Stochastic Neighbor Embedding | 2026-09-26 02:15:45 | 190 | ||||||
|
BioJupies Resource Report Resource Website 50+ mentions |
BioJupies (RRID:SCR_016346) | software resource, web application | Software as an open source web server that automatically generates RNA-seq data analysis of jupyter notebooks. It allows creation and containment of documents that have live code, visualizations and narrative text. | automatically, generate, RNAseq, data, analysis, notebook, create, visualize, report, custom, raw, processed, user, interface | is affiliated with: Icahn School of Medicine at Mount Sinai; New York; USA | Free, Available for download, Freely available | SCR_016346 | SciCrunch Registry | 2026-09-26 02:15:45 | 72 | ||||||||||
|
MAST Resource Report Resource Website 100+ mentions |
MAST (RRID:SCR_016340) | MAST | data analysis software, data processing software, software application, software resource, software toolkit | Software as an open source package for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data. | model, based, analysis, single, cell, transcriptomics, RNA, sequencing, data | Bill and Melinda Gates Foundation OPP1032317; NIBIB R01 EB008400; NIH DP2 DE023321 |
DOI:10.5281/zenodo.18539 | Free, Available for download, Freely available | https://github.com/RGLab/MAST/ | SCR_016340 | SciCrunch Registry | Model based Analysis of Single Cell Transcriptomics | 2026-09-26 02:15:45 | 106 | ||||||
|
MGnify Resource Report Resource Website 50+ mentions |
MGnify (RRID:SCR_016429) | data or information resource, data repository, portal, service resource, storage service resource | Portal for the analysis and exploration of metagenomic, metatranscriptomic, amplicon and assembly data. Provides functional and taxonomic analyses of user-submitted sequences, as well as analysis of publicly available metagenomic datasets held within the European Nucleotide Archive (ENA).Microbiome analysis resource in 2020. | analysis, exploration, metagenomic, metatranscriptomic, amplicon, assembly, data, sequence, ENA, microbial, population, environment, bio.tools |
is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: Debian is listed by: bio.tools is related to: NIDDK Information Network (dkNET) |
EMBL ; EU Seventh Framework Programme for Research MICROB3; InnovateUK 102513; Research Councils UK (RCUK) ; the Biotechnology and Biological Sciences Research Council (BBSRC) BBM0117551; the Biotechnology and Biological Sciences Research Council (BBSRC) BBN0183541; the Biotechnology and Biological Sciences Research Council BBI02612X1; the Biotechnology and Biological Sciences Research Council BBM0117551; the European Commission within the Research Infrastructures programme of Horizon 2020 676559 |
PMID:31696235 | Free, Freely available, Training online available | r3d100011192, biotools:MGnify | https://bio.tools/MGnify, https://doi.org/10.17616/R34W68 | SCR_016429 | SciCrunch Registry | , MGnify, EBI Metagenomics | 2026-09-26 02:15:47 | 74 | |||||
|
ViewTool Cheng Lab Resource Report Resource Website |
ViewTool Cheng Lab (RRID:SCR_016430) | software resource, web application | Web application viewer for large microscopy data. | microscope, microscopy, data, portal, penn, state | Freely available | http://3d.fish/ | SCR_016430 | SciCrunch Registry | ViewTool ChengLab, muCT Viewer, ChengLab ViewTool | 2026-09-26 02:15:47 | 0 | |||||||||
|
Diabetes Epigenome Atlas Resource Report Resource Website 1+ mentions |
Diabetes Epigenome Atlas (RRID:SCR_016441) | atlas, data or information resource, database, disease-related portal, portal, topical portal | Collects and provides data on the human genome and epigenome to facilitate genetic studies of type 2 diabetes and its complications. A component of the AMP T2D consortium, which includes the National Institute for Diabetes and Digestive and Kidney Diseases (NIDDK) and an international collaboration of researchers. | collect, provide, data, human, genome, epigenome, genetic, study, type 2 diabetes |
has parent organization: Stanford University; Stanford; California has parent organization: University of California at San Diego; California; USA |
type 2 diabetes | NIDDK U01 DK100554 | Free, Proprietary data are available only to approved AMP consortium users with user accounts | SCR_016537 | SCR_016441 | SciCrunch Registry | 2026-09-26 02:15:47 | 2 | |||||||
|
MyAssays Resource Report Resource Website 100+ mentions |
MyAssays (RRID:SCR_016562) | data analysis software, data processing software, service resource, software application, software resource | Software tool for assay data analysis. | assay, data, analysis | Free, Freely available, Registration required, Tutorial available | SCR_016562 | SciCrunch Registry | 2026-09-26 02:15:48 | 102 | |||||||||||
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GEO2R Resource Report Resource Website 50+ mentions |
GEO2R (RRID:SCR_016569) | data analysis software, data processing software, software application, software resource | Software as an interactive web tool to compare two or more groups of samples in a Gene Expression Omnibus (GEO) series regardless of data type and quality. Used to identify genes that are differentially expressed across experimental conditions. Results are presented as a table of genes ordered by significance. | compare, group, sample, gene, expression, omnibus, data, identify, differentially, expressed, across, condition, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: Bioconductor is related to: GEOquery is related to: LIMMA |
Free, Available for download, Freely available | biotools:GEO2R | https://bio.tools/GEO2R | SCR_016569 | SciCrunch Registry | 2026-09-26 02:15:48 | 76 | ||||||||
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Respironics Actiware Resource Report Resource Website 1+ mentions |
Respironics Actiware (RRID:SCR_016440) | data analysis software, data management software, data processing software, software application, software resource, software toolkit | Software package to analyze, manage, and export recorded activity data from all Actiwatch models. Used to view long-term sleep/wake patterns, activity, illuminance, and event markers in an easy-to-read actogram format. | Philips, Respironics, analyze, manage, export, recorded, activity, data, view, long, term, sleep, wake, pattern, actogram | Commercially available, Free trial available | SCR_016440 | SciCrunch Registry | 2026-09-26 02:15:47 | 8 | |||||||||||
|
Venny 2.1 Resource Report Resource Website 100+ mentions |
Venny 2.1 (RRID:SCR_016561) | data analysis software, data processing software, software application, software resource | Software tool for comparing lists with Venn's diagrams. | compare, list, data, Venn, diagram | Open source | http://www.citeulike.org/user/hroest/article/6994833 | SCR_016561 | SciCrunch Registry | 2026-09-26 02:15:48 | 458 | ||||||||||
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Splicing Express Resource Report Resource Website 1+ mentions |
Splicing Express (RRID:SCR_016498) | data analysis software, data processing software, data visualization software, software application, software resource | Software suite for Alternative Splicing Events (ASEs) analysis from transcriptome sequencing data in any transcriptome. Used for identification, annotation and visualization. Written in Perl and suitable to run only in UNIX-like systems. | alternative, splicing, analysis, next, generation, sequencing, data, transcriptome, identify, annotate, visualize, Perl, UNIX, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:26618088 | Free, Available for download, Freely available | biotools:splicing_express | https://bio.tools/splicing_express | SCR_016498 | SciCrunch Registry | 2026-09-26 02:15:48 | 3 | |||||||
|
SARTools Resource Report Resource Website 100+ mentions |
SARTools (RRID:SCR_016533) | data analysis software, data processing software, software application, software resource, software toolkit | Software package as a DESeq2- and EdgeR-Based R Pipeline for Comprehensive Differential Analysis of RNA-Seq Data. | R package, DESeq2, EdgeR, comprehensive, analysis, RNAseq, data, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: DESeq2 is related to: edgeR has parent organization: Pasteur Institute |
the France Génomique National Infrastructure | PMID:27280887 | Free, Available for download, Freely available | biotools:sartools | https://bio.tools/sartools | SCR_016533 | SciCrunch Registry | 2026-09-26 02:15:48 | 151 | ||||||
|
TRANSIT Resource Report Resource Website 1+ mentions |
TRANSIT (RRID:SCR_016492) | data analysis software, data processing software, software application, software resource | Software tool Python based and open source for statistical analysis of TnSeq data. Provides a graphical interface to three different statistical methods for analyzing TnSeq data capable of identifying essential genes in individual datasets as well as comparative analysis between conditions. | statistical, analysis, TnSeq, data, identify, gene, dataset, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Texas A and M University; Texas; USA |
PMID:26447887 | Free, Available for download, Freely available | biotools:transit | https://github.com/mad-lab/transit, https://bio.tools/transit | SCR_016492 | SciCrunch Registry | 2026-09-26 02:15:47 | 4 | |||||||
|
PiGx Resource Report Resource Website 1+ mentions |
PiGx (RRID:SCR_016476) | PiGx | data analysis software, data processing software, sequence analysis software, software application, software resource, software toolkit | Software application as a collection of genomic pipelines used for raw fastq read data of bisulfite experiments, RNAseq samples, single cell dropseq analysis, reads from ChIPseq experiments, analysis of sequence mutations in CRISPR-CAS9 targeted amplicon sequencing data. | collection, genomic, pipeline, bisulfite, sequencing, rnaseq, chipseq, single, cell, reproducibility, sample, analysis, mutation, data | European Union Horizon 2020 No 654248; German Federal Ministry of Education and Research (BMBF) 031 A538C RBC (de.NBI) |
Free, Available for download, Freely available | https://github.com/BIMSBbioinfo/pigx | SCR_016476 | SciCrunch Registry | Pipelines in Genomics | 2026-09-26 02:15:47 | 6 | |||||||
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Unpaywall Resource Report Resource Website 10+ mentions |
Unpaywall (RRID:SCR_016471) | data access protocol, data or information resource, data repository, database, service resource, software resource, storage service resource, web service | Database of free scholary articles. Content from over 50,000 publishers and repositories easy to find, track, and use. A website featuring web-based tools created and maintained by Impactstory, Inc. | Impactstory, data, scholary, research, articles, repository, find, track, use, open, reusable, non profit | Open source, Some features require purchase, Unpaywall and Impactstory Privacy Policy, Persons under the age of 13 are not permitted to use the Service | SCR_016471 | SciCrunch Registry | 2026-09-26 02:15:47 | 20 | |||||||||||
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Transcriptome Analysis Console Resource Report Resource Website 10+ mentions |
Transcriptome Analysis Console (RRID:SCR_016519) | TAC | data analysis software, data processing software, sequence analysis software, software application, software resource | Software tool for microarray analysis designed for biologists . Used for identification of differential expression by providing interactive visualizations. | transcriptome, analysis, console, data, array, gene, visualization, identify | Commercially available | SCR_016519 | SciCrunch Registry | TAC:Transcriptome Analysis Console | 2026-09-26 02:15:48 | 21 | |||||||||
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Viewbox4, Cephalometric software Resource Report Resource Website 1+ mentions |
Viewbox4, Cephalometric software (RRID:SCR_016481) | data analysis software, data processing software, image analysis software, software application, software resource | Software for cephalometric analysis. Customizable. Allows rendering, viewing and measuring of 3D data from CT scanners. Used in orthodontic departments for analysis of the dental and skeletal relationships of a human skull. | dHAL Software - The Company, cephalometric, analysis, rendering, viewing, measuring, data, CT scan, orthodontic, dental, skeletal, relationship, human, skull | Commercially available, Tutorial available | SCR_016481 | SciCrunch Registry | 2026-09-26 02:15:47 | 6 | |||||||||||
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National Sleep Research Resource (NSRR) Resource Report Resource Website 50+ mentions |
National Sleep Research Resource (NSRR) (RRID:SCR_016576) | NSRR | data or information resource, organization portal, portal | System for sharing sleep data. Organization portal that aggregates, harmonizes, and organizes sleep and clinical data from individuals studied as part of cohort studies or clinical trials and provides suite of tools to facilitate data exploration and data visualization. National Heart, Lung, and Blood Institute resource designed to provide big data resources to sleep research community. | sleep, clinical, data, cohort, study, trial, dataset, visualization, exploration |
is recommended by: National Library of Medicine lists: Apnea, Bariatric surgery, and CPAP study lists: Sleep Heart Health Study lists: Honolulu-Asia Aging Study of Sleep Apnea lists: Cleveland Family Study lists: Cleveland Children's Sleep and Health Study lists: Best Apnea Interventions for Research (BestAIR) sleep study |
sleep apnea | NHLBI | PMID:29860441 | Free, Freely available, Registration required for membership | https://sleepdata.org/share, https://sleepdata.org/datasets | SCR_016576 | SciCrunch Registry | National Sleep Research Resource | 2026-09-26 02:15:48 | 88 | ||||
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eulerAPE Resource Report Resource Website 10+ mentions |
eulerAPE (RRID:SCR_016457) | data processing software, data visualization software, software application, software resource | Software that uses ellipses to automatically draw accurate area-proportional Venn diagrams for 3-set data. It generates an exact diagram for most of the cases, and when it fails, the best diagram obtained through the hill climbing search is displayed, together with the inaccuracy values for each region. | euler, venn, diagram, graph, mathematics, math, data, draw | School of Computing ; University of Kent ; UK |
PMID:25032825 | SCR_016457 | SciCrunch Registry | Euler Ape | 2026-09-26 02:15:47 | 32 | |||||||||
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Assemblosis Resource Report Resource Website 1+ mentions |
Assemblosis (RRID:SCR_016571) | data or information resource, data processing software, narrative resource, software application, software resource, training material, workflow | Software tool as a Common Workflow Language (CWL) based automated bioinformatics workflow to assemble haploid/diploid eukaryote genomes of non-model organisms using PacBio long-reads and Illumina short-reads. | common, workflow, language, automated, assemble, haploid, diploid, eukaryote, genome, longread, shortread, data | Free, Available for download, Freely available | SCR_016571 | SciCrunch Registry | 2026-09-26 02:15:48 | 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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