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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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OrthoFinder Resource Report Resource Website 1000+ mentions |
OrthoFinder (RRID:SCR_017118) | data analysis software, data processing software, software resource, software application | Software Python application for comparative genomics analysis. Finds orthogroups and orthologs, infers rooted gene trees for all orthogroups and identifies all of gene duplcation events in those gene trees, infers rooted species tree for species being analysed and maps gene duplication events from gene trees to branches in species tree, improves orthogroup inference accuracy. Runs set of protein sequence files, one per species, in FASTA format. | comparative, genomic, analysis, find, orthogroup, ortholog, infer, gene, tree, duplicate, accuracy, protein, sequence, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
Bill and Melinda Gates Foundation ; UKAID |
PMID:26243257 DOI:10.1101/466201 |
Free, Available for download, Freely available | biotools:OrthoFinder, OMICS_09733, BioTools:OrthoFinder | https://bio.tools/OrthoFinder, https://bio.tools/OrthoFinder, https://bio.tools/OrthoFinder | SCR_017118 | OrthoFinder2, OrthoFinder | 2026-08-11 09:43:25 | 3413 | |||||
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Phaff Yeast Culture Collection Resource Report Resource Website 1+ mentions |
Phaff Yeast Culture Collection (RRID:SCR_016781) | portal, service resource, data or information resource, database, organization portal | 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 | 2026-08-11 09:43:31 | 6 | ||||||||||
|
tximport Resource Report Resource Website 100+ mentions |
tximport (RRID:SCR_016752) | data analysis software, data processing software, software resource, software application | 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 |
SNSF 143883; European Commission ; NCI T32 CA009337 |
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 | 2026-08-11 09:43:22 | 100 | ||||
|
Nephele Resource Report Resource Website 10+ mentions |
Nephele (RRID:SCR_016595) | service resource, web application, analysis service resource, software resource, data analysis service, production 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 | 2026-08-11 09:43:22 | 36 | ||||||
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scanpy Resource Report Resource Website 100+ mentions |
scanpy (RRID:SCR_018139) | data analysis software, data processing software, software resource, software application | 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 |
Helmholtz Postdoc Programme ; German Research Foundation |
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 | 2026-08-11 09:43:56 | 256 | |||||
|
Pixelink Image Capture Software Resource Report Resource Website 1+ mentions |
Pixelink Image Capture Software (RRID:SCR_016197) | software application, image acquisition software, data processing software, software resource, data acquisition software | 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 | 2026-08-11 09:43:16 | 4 | |||||||||
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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 | service resource, core facility, access service resource, data or information 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 | 2026-08-11 09:43:26 | 3 | ||||||
|
NCBI Virus Resource Report Resource Website 50+ mentions |
NCBI Virus (RRID:SCR_018253) | portal, topical portal, data or information resource, web service, software resource, data access protocol | Community portal for viral sequence data from RefSeq, GenBank and other NCBI repositories. Integrative, value added resource designed to support retrieval, display and analysis of curated collection of virus sequences and large sequence datasets. Used to increase usability of data archived in GenBank and other NCBI repositories. | Viral sequence data, viral data retrival, viral data analysis, viral data display, curated virus sequence, data set |
is related to: RefSeq is related to: GenBank |
PMID:27899678 | Free, Freely available | SCR_018253 | National Center for Biotechnology Information Virus | 2026-08-11 09:43:42 | 76 | ||||||||
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NEB Tm calculator Resource Report Resource Website 1+ mentions |
NEB Tm calculator (RRID:SCR_017969) | service resource, web service, software resource, data access protocol | 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 | 2026-08-11 09:43:49 | 3 | ||||||||||||
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PASC Resource Report Resource Website 1+ mentions |
PASC (RRID:SCR_016642) | PASC | service resource, analysis service resource, data or information resource, database, web service, software resource, production service resource, data access protocol | 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 | 2026-08-11 09:43:23 | 6 | ||||||
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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 resource, software application | 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 | Autism Speaks 7657; UCLA ; 5T32HC00722834 ; NIMH RO1MH081754; NICHD P50 HD055784; NIMH R01 MH081754; NIMH R01 MH070712 |
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 | 2026-08-11 09:43:11 | 2 | |||||||
|
Singularity Registry Resource Report Resource Website 1+ mentions |
Singularity Registry (RRID:SCR_016249) | sregistry | software application, web application, application programming interface, software resource, data storage software, data processing software, data distribution software, data access protocol | 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 | 2026-08-11 09:43:16 | 2 | |||||||
|
SNP2TFBS Resource Report Resource Website 1+ mentions |
SNP2TFBS (RRID:SCR_016885) | SNP2TFBS | data or information resource, database, web service, software resource, data access protocol | 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 | 2026-08-11 09:43:23 | 8 | |||||||
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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 | service resource, analysis service resource, core facility, access service resource, production 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 | 2026-08-11 09:43:38 | 1 | |||||||||
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Stress Mice Portal Resource Report Resource Website 1+ mentions |
Stress Mice Portal (RRID:SCR_017572) | portal, project portal, data or information resource, database, data set | 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 | 2026-08-11 09:43:38 | 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 resource, software application | 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 |
Stanley Center for Psychiatric Research ; MGH Psychiatry Residency Research Program ; Stanley-MGH Fellowship in Psychiatric Neuroscience ; Stewart Trust Fellows Award ; Simons Foundation ; NHGRI P50 HG006193; Klarman Cell Observatory ; NIMH U01 MH105960; NIMH R25 MH094612; NICHD F32 HD075541; NSF ECS 0335765; NSF DMR 1310266; NSF DMR 1420570 |
PMID:26000488 | https://sources.debian.org/src/drop-seq-tools/ | SCR_018142 | Droplet sequencing tools, Droplet sequencing data analysis software tools | 2026-08-11 09:43:41 | 112 | |||||||
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MetaNeighbor Resource Report Resource Website 50+ mentions |
MetaNeighbor (RRID:SCR_016727) | data analysis software, data processing software, software resource, software application | 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 | 2026-08-11 09:43:24 | 58 | |||||||||
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OMiCC Resource Report Resource Website 1+ mentions |
OMiCC (RRID:SCR_016604) | OMiCC | service resource, web application, analysis service resource, data or information resource, software resource, data analysis service, production 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 | 2026-08-11 09:43:20 | 3 | |||||||
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ASaiM Resource Report Resource Website 1+ mentions |
ASaiM (RRID:SCR_015878) | data analysis software, data processing software, software resource, software application | Software that analyzes intestinal microbiota data. This environment is composed of a framework to process and analyze microbiota data from raw sequences to taxonomic and functional assignations. | metagenomic, galaxy, microbiota, metatranscriptomic, metataxonomic, | Open source, Free, Available for download, Tutorial available | https://github.com/asaim | SCR_015878 | ASaiM: Auvergne Sequence analysis of intestinal Microbiota, Auvergne Sequence analysis of intestinal Microbiota, ASaiM (Auvergne Sequence analysis of intestinal Microbiota) | 2026-08-11 09:43:09 | 2 | |||||||||
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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, software application, data or information resource, workflow, narrative resource, training material, software resource, data processing software | 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 | 2026-08-11 09:43:31 | 2 |
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