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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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NIAID Overview of Coronaviruses Resource Report Resource Website 1+ mentions |
NIAID Overview of Coronaviruses (RRID:SCR_018290) | funding resource, data or information resource, topical portal, portal | Information about coronaviruses, including COVID-19. NIAID provides research funding and resources for scientific community to facilitate development of vaccines, therapeutics, and diagnostics for infectious diseases, including those caused by coronaviruses. | Coronavirus, COVID-19, data, infectious disease, NIAID |
is listed by: Data and Computational Resources to Address COVID-19 is related to: NIAID |
COVID-19 | NIAID | Free, Freely available | SCR_018290 | 2026-07-28 09:44:39 | 3 | ||||||||
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LeafCutter Resource Report Resource Website 10+ mentions |
LeafCutter (RRID:SCR_017639) | software application, data analysis software, software resource, data processing software, data analytics software | Software tool for identifying and quantifying RNA splicing variation. Used to study sample and population variation in intron splicing. Identifies variable intron splicing events from short read RNA-seq data and finds alternative splicing events of high complexity. Used for detecting differential splicing between sample groups, and for mapping splicing quantitative trait loci (sQTLs). | Identify, quantitate, RNA, splicing, variation, intron, short, read, RNAseq, data, mapping, trait, loci, sQTL | has parent organization: Stanford University; Stanford; California | CEHG Fellowship ; Howard Hughes Medical Institute ; NHGRI HG007036; NHGRI HG008140; NHGRI HG009431; NIMH R01 MH107666 |
PMID:29229983 DOI:10.1038/s41588-017-0004-9 |
Free, Available for download, Freely available | SCR_017639 | 2026-07-28 09:44:39 | 29 | ||||||||
|
tenx Resource Report Resource Website 10+ mentions |
tenx (RRID:SCR_016957) | service resource, data analysis service, software resource, production service resource, analysis service resource, software toolkit | Pipeline for the analysis of 10x single cell RNA sequencing data. Collection of python3 pipelines and Rscripts to analyze data generated with the 10x Genomics platform. The pipelines are based on 10x's Cell Ranger pipeline for mapping and quantitation and the R Seurat package for downstream analysis. | analysis, 10x, single, cell, RNA, sequencing, data, genomic, platform, mapping, quantitation | Free, Available for download, Freely available | SCR_016957 | 2026-07-28 09:44:26 | 11 | |||||||||||
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TSDiffAna Resource Report Resource Website 1+ mentions |
TSDiffAna (RRID:SCR_016656) | software application, data analysis software, software resource, data processing software, image analysis software | Software tool developed for Statistical Parametric Mapping (SPM) that computes slicewise scan by scan difference and standard deviations. Used to examine quality of image timeseries. | SPM, statistical, parametiric, mapping, slicewise, scan, difference, standard, deviation, quality, image, neuroimaging, data |
has parent organization: University College London; London; United Kingdom is provided by: SPM |
Free, Available for download, Freely available | https://sourceforge.net/projects/tsdiffana.spmtools.p/ | SCR_016656 | 2026-07-28 09:44:24 | 2 | |||||||||
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Nutil - Neuroimaging utilities Resource Report Resource Website 10+ mentions |
Nutil - Neuroimaging utilities (RRID:SCR_017183) | Nutil | software application, software toolkit, software resource, data processing software, image processing software, image analysis software | Software toolbox to simplify and streamline mechanism of pre and post processing 2D brain image data. Neuroscience image processing and analysis utilities. Stand alone application that runs on all operating systems. Nutil is part of the QUINT workflow. | neuroscience, 2D, brain, image, data, processing, analysis |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Allen Institute for Brain Science has parent organization: University of Oslo; Oslo; Norway works with: VisuAlign |
European Union’s Horizon 2020 Framework Programme for Research and Innovation under the Framework Partnership Agreement No. 650003 (HBP FPA) and the European Union’s Horizon Europe Programme for Research Infrastructures Grant Agreement No. 101147319 (EBRAINS 2.0). | PMID:32973479 | Free, Available for download, Freely available | https://nutil.readthedocs.io; https://github.com/Neural-Systems-at-UIO/nutil | SCR_017183 | Neuroimaging utilities | 2026-07-28 09:44:27 | 25 | |||||
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Kids First Data Resource Portal Resource Report Resource Website 1+ mentions |
Kids First Data Resource Portal (RRID:SCR_016493) | DRP | service resource, disease-related portal, data or information resource, organization portal, data repository, database, topical portal, storage service resource, portal | Portal for analysis and interpretation of pediatric genomic and clinical data to advance personalized medicine for detection, therapy, and management of childhood cancer and structural birth defects. For patients, researchers, and clinicians to create centralized database of well curated clinical and genetic sequence data from patients with childhood cancer or structural birth defects. | pediatric, genomic, clinical, disease, data, children, cancer, birth, defect, analysis | is recommended by: National Library of Medicine | pediatric cancer, birth defect | the Common Fund’s Gabriella Miller Kids First Pediatric Research Program ; NIH |
Restricted | SCR_016553 | https://commonfund.nih.gov/kidsfirst, https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001168.v1.p1, https://commonfund.nih.gov/kidsfirst | SCR_016493 | Data Resource Portal | 2026-07-28 09:44:19 | 3 | ||||
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NASEM Standing Committee on Emerging Infectious Diseases and 21st Century Health Threats Resource Report Resource Website |
NASEM Standing Committee on Emerging Infectious Diseases and 21st Century Health Threats (RRID:SCR_018289) | data or information resource, organization portal, consortium, portal | Committee provides expert consultation on data elements and systems design for modeling and decision making for COVID-19 pandemic. Assembled at request of White House Office of Science and Technology Policy and Office of Assistant Secretary for Preparedness and Response in response to COVID-19 outbreak. Provides expert consultations on several topics, such as surface stability and incubation, social distancing, and crisis standards of care. | Data, consultation, COVID-19, expertise, crisis standard of care | is listed by: Data and Computational Resources to Address COVID-19 | COVID-19 | Free, Freely available | https://www.nap.edu/read/25755/chapter/1 | SCR_018289 | Engineering, National Academies of Science, and Medicine Standing Committee on Emerging Infectious Diseases and 21st Century Health Threats | 2026-07-28 09:44:53 | 0 | |||||||
|
Nephele Resource Report Resource Website 10+ mentions |
Nephele (RRID:SCR_016595) | service resource, web application, data analysis service, software resource, production service resource, analysis service resource | Cloud based platform for simplified, standardized and reproducible microbiome data analysis. Allows users to process microbiome datasets through pipelines of existing software tools. | microbiome, datasets, process, analyze, metagenome, sequencing, data, bio.tools |
uses: mothur uses: QIIME uses: biobakery uses: A5-miseq is listed by: NIAID is listed by: bio.tools is listed by: Debian has parent organization: OCICB |
NIH Department of Health and Human Services GS35F0373X | PMID:29028892 | Free, Available for download, Freely available | biotools:nephele | https://github.com/niaid/Nephele, https://bio.tools/nephele | SCR_016595 | 2026-07-28 09:44:21 | 27 | ||||||
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Cyflogic Resource Report Resource Website 10+ mentions |
Cyflogic (RRID:SCR_016635) | software application, data analysis software, software resource, data processing software, software toolkit | Software tool for a flow cytometry data analysis for Microsoft Windows enviroment developed by CyFlo Ltd. Has analysis capabilities, such as dot plot, histogram and statistics. | flow, cytometry, data, analysis, CyFlo Ltd., dot, plot, histogram, statistics | PMID:23839300 | Commercially available, Free for non-commercial research use only and not for use in diagnostic or therapeutic procedures | SCR_016635 | 2026-07-28 09:44:23 | 25 | ||||||||||
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PASC Resource Report Resource Website 1+ mentions |
PASC (RRID:SCR_016642) | PASC | service resource, data or information resource, database, data access protocol, software resource, production service resource, web service, analysis service resource | Web tool for analysis of pairwise identity distribution within viral families. Used for virus sequence-based classification. Data in the system are updated every day to reflect changes in virus taxonomy and additions of new virus sequences to the public database. | analysis, pairwise, identity, distribution, viral, family, sequence, classification, data, taxonomy | has parent organization: NCBI | National Library of Medicine | PMID:25119676 | Free, Public | SCR_016642 | PAirwise Sequence Comparison | 2026-07-28 09:44:22 | 4 | ||||||
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SNP2TFBS Resource Report Resource Website 1+ mentions |
SNP2TFBS (RRID:SCR_016885) | SNP2TFBS | data or information resource, database, data access protocol, software resource, web service | Collection of text files providing specific annotations for human single nucleotide polymorphisms (SNPs), namely whether they are predicted to abolish, create or change the affinity of one or several transcription factor (TF) binding sites. Used to investigate the molecular mechanisms underlying regulatory variation in the human genome. SNP2TFBS is also accessible over a web interface, enabling users to view the information provided for an individual SNP, to extract SNPs based on various search criteria, to annotate uploaded sets of SNPs or to display statistics about the frequencies of binding sites affected by selected SNPs. | collection, regulatory, single, polymorphism, SNP, affecting, predicted, transcription, factor, binding, site, affinity, data, human, nucleotide, genome | Swiss National Science Foundation ; Swiss Institute of Bioinformatics |
PMID:27899579 | Free, Freely available | SCR_016885 | Single Nucleotide Polymorphisms 2 Transcription Factor Binding Site, SNP2TFBS | 2026-07-28 09:44:25 | 7 | |||||||
|
University of Manitoba Department of Plant Science Bio Information Technologies Lab Core Facility Resource Report Resource Website |
University of Manitoba Department of Plant Science Bio Information Technologies Lab Core Facility (RRID:SCR_017177) | University of Manitoba BIT Core Facility | service resource, data or information resource, data analysis service, software resource, production service resource, access service resource, analysis service resource, core facility | BIT Core at University of Manitoba, Manitoba, Canada, provides bioinformatics services, resources and collaborations. Support for Genome assembly and annotation, Microarray and Transcriptomics, Systems Biology and Pathway analysis, Databases, Data pipelines, Bioinformatics software, Custom software and programming, Project Wikis, Lab group computer management. | bioinformatics, genome, assembly, microarray, transcriptomics, pathway, data, analysis, management | Restricted | SCR_017177 | University of Manitoba, BIT, Bio Information Technologies Lab, Fritensky Lab, Canada, Department of Plant Science | 2026-07-28 09:44:31 | 0 | |||||||||
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Stress Mice Portal Resource Report Resource Website 1+ mentions |
Stress Mice Portal (RRID:SCR_017572) | data set, project portal, data or information resource, database, portal | Sapienza University of Rome and Cineca consortium portal. Used for analyzing published RNAseq transcriptomes obtained from brain of mice exposed to different kinds of stress protocols, to generate database of stress related differentially expressed genes and to identify factors contributing to vulnerability or resistance to stress. Allows to query database of RNAseq data. | Spienza University of Rome, Cineca, RNA seq, transcriptome, data, brain, mouse, stress, gene, expresison | Free, Available for download, Freely available | SCR_017572 | 2026-07-28 09:44:35 | 1 | |||||||||||
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DrivAER Resource Report Resource Website 1+ mentions |
DrivAER (RRID:SCR_019076) | software application, software resource, data analysis software, data processing software | Software tool as method for identification of driving transcriptional programs based on AutoEncoder derived Relevance scores. Infers relevance scores for transcriptional programs with respect to specified outcomes of interest in single-cell RNA sequencing data, such as psuedotemporal ordering or disease status.Used for manifold interpretation in scRNA-seq data. | Manifold interpretation, scRNAseq data, relevance scores infering, transcriptional program, psuedotemporal ordering, disease status, data, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Available for download, Freely available | biotools:drivaer | https://bio.tools/drivaer | SCR_019076 | Driving transcriptional programs using AutoEncoder based Relevance scores | 2026-07-28 09:44:55 | 1 | |||||||
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OMiCC Resource Report Resource Website 1+ mentions |
OMiCC (RRID:SCR_016604) | OMiCC | service resource, web application, data or information resource, data analysis service, software resource, production service resource, analysis service resource | Community based, biologist friendly web platform for creating and meta analyzing annotated gene expression data compendia., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | creating, metadata, analysis, annotated, gene, expression, data, compendia, human, mouse |
uses: Gene Expression Omnibus has parent organization: NIAID |
PMID:27323300 | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_016604 | OMics Compendia Commons | 2026-07-28 09:44:21 | 1 | |||||||
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Epigenomics Workflow on Galaxy and Jupyter Resource Report Resource Website 1+ mentions |
Epigenomics Workflow on Galaxy and Jupyter (RRID:SCR_017544) | software application, narrative resource, data analysis software, data or information resource, data processing software, software resource, workflow, training material | Software tool as epigenomics analysis pipeline for analysis of ChIP-Seq and RNA-Seq data using Docker images containing Galaxy and Jupyter. | Epigenomic, analysis, pipeline, ChIP-Seq, RNA-Seq, data, Galaxy, Jupyter, bio.tools |
is listed by: bio.tools is listed by: Debian |
Agencia Estatal de Investigación of Spain SEV-2016-0672 (2017-2021) | Free, Available for download, Freely available | biotools:Epigenomics_Workflow_on_Galaxy_and_Jupyter | https://zenodo.org/record/3298029, https://bio.tools/Epigenomics_Workflow_on_Galaxy_and_Jupyter | SCR_017544 | REA pipeline | 2026-07-28 09:44:37 | 2 | ||||||
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OpticalMapping.info Resource Report Resource Website |
OpticalMapping.info (RRID:SCR_017146) | data or information resource, topical portal, portal, software resource | Platform to provide tutorials and resources in experimental design and data analysis to researchers interested in using optical mapping data. | platform, tutorial, experimental, design, data, analysis, optical, mapping, structural, labelling, pattern, long, DNA, molecule, fluorescent, signal, capture | Free, Freely available | SCR_017146 | 2026-07-28 09:44:31 | 0 | |||||||||||
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factoextra Resource Report Resource Website 50+ mentions |
factoextra (RRID:SCR_016692) | software application, data analysis software, software resource, data processing software, data visualization software | R package from CRAN to extract and visualize the results of multivariate data analysis. | extract, visualize, multivariate, data, analysis |
is affiliated with: R Project for Statistical Computing is affiliated with: CRAN |
Free, Available for download, Freely available | https://rpkgs.datanovia.com/factoextra/index.html | SCR_016692 | 2026-07-28 09:44:23 | 89 | |||||||||
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Shannon Resource Report Resource Website 1+ mentions |
Shannon (RRID:SCR_017037) | software application, software resource, data analysis software, data processing software | Software tool for de novo transcriptome assembly from RNA-Seq data. | de novo, transcriptome, assembly, RNAseq, data |
has parent organization: University of Washington; Seattle; USA has parent organization: University of California at Berkeley; Berkeley; USA has parent organization: Stanford University; Stanford; California |
NSF Center for Science of Information ; NHGRI ; University of Washington |
Free, Available for download, Freely available | http://sreeramkannan.github.io/Shannon/ | SCR_017037 | 2026-07-28 09:44:26 | 1 | ||||||||
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NiMARE Resource Report Resource Website 10+ mentions |
NiMARE (RRID:SCR_017398) | NiMARE | software application, software resource, data analysis software, data processing software | Software Python package for coordinate and image based meta analysis of neuroimaging data. | Coordinate, image, based, meta, analysis, neuroimaging, data |
uses: PyMARE is used by: Neurosynth Compose |
Free, Available for download, Freely available | https://nimare.readthedocs.io/en/latest/ | SCR_017398 | Neuroimaging Meta Analysis Research Environment, Neuroimaging Meta-Analysis Research Environment | 2026-07-28 09:44:29 | 13 |
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