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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Phaff Yeast Culture Collection Resource Report Resource Website 1+ mentions |
Phaff Yeast Culture Collection (RRID:SCR_016781) | data or information resource, database, organization portal, portal, service resource | Collection of wild yeast in the world. Academic and industrial resarchers utilize this collection for a variety of research and applications, including pigments, enzymes, food ingredients, and hosts for protein expression. Provides contract screening and strain selection services. | yeast, strain, wild, screening, selection, service | has parent organization: University of California at Davis; California; USA | Commercially available | SCR_016781 | 2026-09-05 06:30:08 | 6 | ||||||||||
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tximport Resource Report Resource Website 100+ mentions |
tximport (RRID:SCR_016752) | data analysis software, data processing software, software application, software resource | Software R package for importing pseudoaligned reads into R for use with downstream differential expression analysis. Used for import and summarize transcript level estimates for transcript and gene level analysis. | pseudoaligned, reads, R, differential, expression, analysis, gene, transcript, bio.tools |
is listed by: Bioconductor is listed by: Debian is listed by: bio.tools works with: edgeR works with: DESeq2 |
European Commission ; NCI T32 CA009337; SNSF 143883 |
DOI:10.12688/f1000research.7563.1 | Free, Available for download, Freely available | biotools:tximport | https://bioconductor.org/packages/tximport/, https://bioconductor.org/packages/devel/bioc/vignettes/tximport/inst/doc/tximport.html, https://github.com/F1000Research/tximport, https://bio.tools/tximport | https://zenodo.org/record/35123#.W_w3behKiM8 | SCR_016752 | tximport v1.4.0 | 2026-09-05 06:30:08 | 100 | ||||
|
Nephele Resource Report Resource Website 10+ mentions |
Nephele (RRID:SCR_016595) | analysis service resource, data analysis service, production service resource, service resource, software resource, web application | 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 | 2026-09-05 06:30:07 | 36 | ||||||
|
Cyflogic Resource Report Resource Website 10+ mentions |
Cyflogic (RRID:SCR_016635) | data analysis software, data processing software, software application, software resource, 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 | 2026-09-05 06:30:08 | 27 | ||||||||||
|
scanpy Resource Report Resource Website 100+ mentions |
scanpy (RRID:SCR_018139) | data analysis software, data processing software, software application, software resource | Software Python tool for large scale single cell gene expression data analysis. Integrates analysis possibilities of established R-based frameworks, provides pre processing, visualization, graph-drawing and diffusion maps, clustering, identification of marker genes for clusters via differential expression tests and pseudo temporal ordering via diffusion pseudo time. | Large scale, single cell, gene expression, data analysis, R, pre processing, visualization, graph drawing, diffusion map, clustering, marker gene, differential expression test, bio.tools |
uses: BBKNN is used by: triku is used by: MUON is listed by: Debian is listed by: bio.tools is related to: Anndata has plug in: infercnvpy |
German Research Foundation ; Helmholtz Postdoc Programme |
PMID:29409532 | Free, Available for download, Freely available | biotools:scanpy, BioTools:scanpy | https://icb-scanpy.readthedocs-hosted.com/en/stable/, https://bio.tools/scanpy, https://bio.tools/scanpy, https://bio.tools/scanpy | SCR_018139 | Single Cell Analysis in Python | 2026-09-05 06:30:09 | 256 | |||||
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Pixelink Image Capture Software Resource Report Resource Website 1+ mentions |
Pixelink Image Capture Software (RRID:SCR_016197) | data acquisition software, data processing software, image acquisition software, software application, software resource | Software application for real-time, interactive, multi-camera recording. It is compatible with all Pixelink PL-B and PL-D line of cameras. | microscopy, microscope, image, camera, video, industrial | Commercially available, Account required | http://pixelink.com/wp-content/uploads/Pixelink-Capture-Jan-2018.pdf | SCR_016197 | Pixelink Capture, Image Capture Software | 2026-09-05 06:30:07 | 4 | |||||||||
|
Indiana University Center for Genomics and Bioinformatics Core Facility Resource Report Resource Website 1+ mentions |
Indiana University Center for Genomics and Bioinformatics Core Facility (RRID:SCR_017165) | CGB | access service resource, core facility, data or information resource, service resource | CGB offers range of genomic services, including high-throughput DNA/RNA extraction, library preparation, next-generation sequencing, and bioinformatic analysis. | ABRF, genomic services, DNA/RNA extraction, library preparation, next-generation sequencing, bioinformatic analysis, |
is listed by: ABRF CoreMarketplace has parent organization: Indiana University Bloomington; Indiana; USA |
Restricted | SCR_025534, ABRF_2841 | https://indianactsi.org/servicecores/core/20/, https://coremarketplace.org/?FacilityID=2841&citation=1 | SCR_017165 | Indiana University Bloomington Center for Genomics and Bioinformatics | 2026-09-05 06:30:08 | 3 | ||||||
|
NEB Tm calculator Resource Report Resource Website 1+ mentions |
NEB Tm calculator (RRID:SCR_017969) | data access protocol, service resource, software resource, web service | Calculator to estimate appropriate annealing temperature when using NEB PCR products.Tm calculator provided by New England Biolabs. | Calculate, estimate, annealing, temperature, PCR, product, New England Biolabs Inc., NEBtool | SCR_017969 | 2026-09-05 06:30:09 | 3 | ||||||||||||
|
PASC Resource Report Resource Website 1+ mentions |
PASC (RRID:SCR_016642) | PASC | analysis service resource, data access protocol, data or information resource, database, production service resource, service resource, software resource, web service | 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 | 2026-09-05 06:30:08 | 6 | ||||||
|
Vocal Inventory Clustering Engine (VoICE) Resource Report Resource Website 1+ mentions |
Vocal Inventory Clustering Engine (VoICE) (RRID:SCR_016004) | VoICE | data analysis software, data processing software, software application, software resource | Software that groups vocal elements of birdsong by creating a high dimensionality dataset through scoring spectral similarity between vocalizations. | bird, song, birdsong, vocal, audio, analysis, vocalization, spectral similarity, avian, matlab | uses: MATLAB | 5T32HC00722834 ; Autism Speaks 7657; NICHD P50 HD055784; NIMH R01 MH070712; NIMH R01 MH081754; NIMH RO1MH081754; UCLA |
Free, Available for download | SCR_016004 | VoICE (Vocal Inventory Clustering Engine), Vocal Inventory Clustering Engine (VoICE), VoICE: Vocal Inventory Clustering Engine, VoICE: A semi-automated pipeline for standardizing vocal analysis across models | 2026-09-05 06:30:07 | 2 | |||||||
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Singularity Registry Resource Report Resource Website 1+ mentions |
Singularity Registry (RRID:SCR_016249) | sregistry | application programming interface, data access protocol, data distribution software, data processing software, data storage software, software application, software resource, web application | Web application and registry for institutional deployment of Singularity containers. | containers, singularity, containers, linux, python, django, storage | is related to: Singularity Hub | PMID:28494014 | Open source, Freely available | SCR_016249 | Singularity Registry Server | 2026-09-05 06:30:07 | 2 | |||||||
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CMMT Mouse Animal Production Service Resource Report Resource Website |
CMMT Mouse Animal Production Service (RRID:SCR_016403) | EMS, MAPS, CMMT MAPS, CMMT EMS | biomaterial supply resource, material resource, organism supplier | Supplier of mice for research purposes. The service is run by Dr. Elizabeth M. Simpson, Ph.D. and is affiliated with her lab. | mouse, strain, supply, research, repository, subject, genetic engineering, knockout, mice, gene, model | SCR_016403 | Mouse Animal Production Service (MAPS), Centre for Molecular Medicine and Therapeutics MAPS, Dr. Elizabeth M. Simpson PhD, Elizabeth M. Simpson, Mouse Animal Production Service, Centre for Molecular Medicine and Therapeutics Mouse Animal Production Service | 2026-09-05 06:30:07 | 0 | ||||||||||
|
SNP2TFBS Resource Report Resource Website 1+ mentions |
SNP2TFBS (RRID:SCR_016885) | SNP2TFBS | data access protocol, data or information resource, database, 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 Institute of Bioinformatics ; Swiss National Science Foundation |
PMID:27899579 | Free, Freely available | SCR_016885 | Single Nucleotide Polymorphisms 2 Transcription Factor Binding Site, SNP2TFBS | 2026-09-05 06:30:08 | 8 | |||||||
|
Johns Hopkins Medicine Institute for Basic Biomedical Sciences Single Cell and Transcriptomics Core Facility Resource Report Resource Website 1+ mentions |
Johns Hopkins Medicine Institute for Basic Biomedical Sciences Single Cell and Transcriptomics Core Facility (RRID:SCR_017172) | SCTC, JHMI, JHU | access service resource, analysis service resource, core facility, production service resource, service resource | Core provides assistance with Single Cell RNA and DNA Sequencing, Spatial Transcriptomics, Next-Generation Sequencing libraries. | single, cell, spatial, omics, next, generation, sequencing, DNA, RNA | Restricted | SCR_017172 | , Institute for Basic Biomedical Sciences Single Cell and Transcriptomics Core | 2026-09-05 06:30:08 | 1 | |||||||||
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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 | access service resource, analysis service resource, core facility, data analysis service, data or information resource, production service resource, service resource, software resource | 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 | 2026-09-05 06:30:08 | 0 | |||||||||
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Stress Mice Portal Resource Report Resource Website 1+ mentions |
Stress Mice Portal (RRID:SCR_017572) | data or information resource, data set, database, portal, project 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 | 2026-09-05 06:30:09 | 1 | |||||||||||
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Drop-seq tools Resource Report Resource Website 100+ mentions |
Drop-seq tools (RRID:SCR_018142) | data analysis software, data processing software, software application, software resource | Software Java tools for analyzing Drop-seq data. Used to analyze gene expression from thousands of individual cells simultaneously. Analyzes mRNA transcripts while remembering origin cell transcript. | Simultaneous analysis, Drop-seq data, gene expression, thousands individual cells |
is listed by: Debian has parent organization: Broad Institute |
Klarman Cell Observatory ; MGH Psychiatry Residency Research Program ; NHGRI P50 HG006193; NICHD F32 HD075541; NIMH R25 MH094612; NIMH U01 MH105960; NSF DMR 1310266; NSF DMR 1420570; NSF ECS 0335765; Simons Foundation ; Stanley Center for Psychiatric Research ; Stanley-MGH Fellowship in Psychiatric Neuroscience ; Stewart Trust Fellows Award |
PMID:26000488 | https://sources.debian.org/src/drop-seq-tools/ | SCR_018142 | Droplet sequencing tools, Droplet sequencing data analysis software tools | 2026-09-05 06:30:09 | 112 | |||||||
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MetaNeighbor Resource Report Resource Website 50+ mentions |
MetaNeighbor (RRID:SCR_016727) | data analysis software, data processing software, software application, software resource | Software package to assess cell type identity using both functional and random gene sets. Used for single cell replicability analysis to quantify cell type replicability across datasets using neighbor voting. | quantify, cell, type, replicability, dataset, access, cell, type, identity, functional, random, gene |
is used by: BICCN is listed by: Bioconductor is listed by: OMICtools |
Free, Available for download, Freely available | https://github.com/maggiecrow/MetaNeighbor, https://github.com/gillislab/MetaNeighbor | SCR_016727 | 2026-09-05 06:30:08 | 58 | |||||||||
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OMiCC Resource Report Resource Website 1+ mentions |
OMiCC (RRID:SCR_016604) | OMiCC | analysis service resource, data analysis service, data or information resource, production service resource, service resource, software resource, web application | 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 | 2026-09-05 06:30:07 | 3 | |||||||
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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) | data analysis software, data or information resource, data processing software, narrative resource, software application, software resource, training material, workflow | 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 | 2026-09-05 06:30:09 | 2 |
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