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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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purge dups Resource Report Resource Website 500+ mentions |
purge dups (RRID:SCR_021173) | data analysis software, data processing software, software application, software resource | Software tool to purge haplotigs and overlaps in assembly based on read depth.Used for haplotypic duplication identification. Designed to remove haplotigs and contig overlaps in a de novo assembly based on read depth. | haplotypic duplication identification, remove haplotigs overlap, remove contig overlaps, de novo assembly, read depth | Free, Available for download, Freely available | SCR_021173 | purge_dups | 2026-08-29 11:27:49 | 503 | ||||||||||
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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) | consortium, data or information resource, organization portal, 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 | 2026-08-29 11:27:47 | 0 | |||||||
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UCLA Diffraction Anisotropy Server Resource Report Resource Website 1+ mentions |
UCLA Diffraction Anisotropy Server (RRID:SCR_018722) | analysis service resource, data access protocol, production service resource, service resource, software resource, web service | Web server to indicate severity of anisotropy in data set. Degree of anisotropy is indicated by anisotropic delta B statistic. | Anisotropy, anisotropy severity, anisotropy severity indication, anisotropy degree, anisotropic delta B statistic | has parent organization: University of California at Los Angeles; California; USA | Free, Freely available | SCR_018722 | 2026-08-29 11:27:48 | 8 | ||||||||||
|
UMI4Cats Resource Report Resource Website 1+ mentions |
UMI4Cats (RRID:SCR_021780) | data analysis software, data processing software, data visualization software, software application, software resource | Software R package for analyzing UMI-4C chromatin contact data. Used to analyze chromatin contact profiles obtained by UMI-4C. | Profile and quantitatively compare, targeted chromosomal contact profiles, unique molecular identifiers, combines chromosome conformation capture | DOI:10.1093/bioinformatics/btab392 | Free, Available for download, Freely available | https://bioconductor.org/packages/UMI4Cats/, https://github.com/Pasquali-lab/UMI4Cats | SCR_021780 | Unique Molecular Identifiers combines chromosome conformation capture | 2026-08-29 11:28:16 | 2 | ||||||||
|
Computational Analysis of gene Family Evolution Resource Report Resource Website 10+ mentions |
Computational Analysis of gene Family Evolution (RRID:SCR_018924) | CAFE | data analysis software, data processing software, software application, software resource | Software tool for computational analysis of gene family evolution. Used for statistical analysis of evolution gene family sizes. Models evolution of gene family sizes over phylogeny. | Computational analysis, gene family evolution, evolution statistical analysis, gene family size, gene evolution, phylogeny | has parent organization: Indiana University; Indiana; USA | Lilly Endowment ; Inc ; METACyt Initiative of Indiana University ; NHGRI R33 HG003070; NSF MCB 0528465 |
PMID:16543274 | SCR_018924 | CAFE v2.0, CAFE v4.0, CAFE v3.0, CAFE v5.0, Computational Analysis of gene Family Evolution | 2026-08-29 11:27:48 | 17 | |||||||
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Creative Peptides PNA Modification by C Replacement Service Resource Resource Report Resource Website |
Creative Peptides PNA Modification by C Replacement Service Resource (RRID:SCR_022230) | service resource | PNA modification service provides replacement of backbone C. | Creative Peptides, PNA Biotech, biomedical service, replacement of backbone C, peptide nucleic acid |
is related to: Creative Peptides PNA Modification Service Resource has parent organization: Creative Peptides |
Restricted | SCR_022230 | Modification by C Replacement | 2026-08-29 11:27:44 | 0 | |||||||||
|
SuperSegger Resource Report Resource Website 1+ mentions |
SuperSegger (RRID:SCR_018532) | data processing software, image analysis software, software application, software resource, software toolkit | Software package as automated MATLAB based trainable image cell segmentation, fluorescence quantification and analysis suite. Used for high throughput time lapse fluorescence microscopy of in vivo bacterial cells. Robust image segmentation, analysis and lineage tracking of bacterial cells. | Image cell segmentation, fluorescence quantification, data analysis, high throughput, time lapse, fluorescence microscopy, bacteria cell, image segmentation |
is related to: MATLAB has parent organization: University of Washington; Seattle; USA |
Danish National Research Foundation ; NSF MCB‐1151043‐CAREER; NSF PHY‐084845; Sloan BR2011‐110; University of Washington Royalty Research Fund |
PMID:27569113 | Free, Available for download, Freely available | https://github.com/wiggins-lab/SuperSegger | SCR_018532 | 2026-08-29 11:27:47 | 3 | |||||||
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Creative Peptides PNA N/C Terminal Modification Service Resource Resource Report Resource Website |
Creative Peptides PNA N/C Terminal Modification Service Resource (RRID:SCR_022229) | service resource | Service to modify monomer backbone, including chemically active sites at both ends. Monomer N-terminal and C-terminal modification. | Creative Peptides, PNA Biotech, biomedical service, N-terminal and C-terminal modification, peptide nucleic acid, PNA |
is related to: Creative Peptides PNA Modification Service Resource has parent organization: Creative Peptides |
Restricted | SCR_022229 | N/C Terminal Modification | 2026-08-29 11:28:18 | 0 | |||||||||
|
Simple Behavior Analysis Resource Report Resource Website 10+ mentions |
Simple Behavior Analysis (RRID:SCR_021413) | data analysis software, data processing software, software application, software resource, software toolkit | Open source software toolkit for computer classification of complex social behaviors in experimental animals. | Complex social behaviors classifications, supervised behavioral classifiers development, score behaviors across different background settings, OpenBehavior |
is listed by: OpenBehavior is related to: Simple Behavior Analysis project |
DOI:10.1101/2020.04.19.049452 | Free, Available for download, Freely Available | https://edspace.american.edu/openbehavior/project/simba/ | SCR_021413 | SimBA | 2026-08-29 11:27:50 | 16 | |||||||
|
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 | 2026-08-29 11:27:46 | 256 | |||||
|
NCBI Virus Resource Report Resource Website 50+ mentions |
NCBI Virus (RRID:SCR_018253) | data access protocol, data or information resource, portal, software resource, topical portal, web service | 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 | 2026-08-29 11:27:46 | 76 | ||||||||
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Creative Biogene Mitochondrial Biomarkers and Therapeutic Targets Service Resource Resource Report Resource Website 1+ mentions |
Creative Biogene Mitochondrial Biomarkers and Therapeutic Targets Service Resource (RRID:SCR_022240) | service resource | Creative Biogene service for discovery of disease specific proteins associated with mitochondrial epigenetic products, which can be used as molecular targets for new drug design and provide molecular markers for early diagnosis of diseases. | Creative Biogene, biomedical service, disease specific proteins discovery, mitochondrial epigenetic product, molecular targets, new drug design, molecular markers | has parent organization: Creative Biogene | Restricted | SCR_022240 | Mitochondrial Biomarkers and Therapeutic Targets | 2026-08-29 11:28:18 | 6 | |||||||||
|
triku Resource Report Resource Website 1+ mentions |
triku (RRID:SCR_020977) | data analysis software, data processing software, software application, software resource | Software tool as feature selection method based on nearest neighbors for single-cell data. | Selection method, nearest neighbors, single cell data, data analysis | uses: scanpy | Free, Available for download, Freely available | https://triku.readthedocs.io/en/latest/ | SCR_020977 | 2026-08-29 11:27:43 | 2 | |||||||||
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3DOC Resource Report Resource Website |
3DOC (RRID:SCR_021547) | data or information resource, instrument resource, portal, project portal | Project related to animals learned perform action in order to achieve reward. Fully 3D printable chamber able to perform operant conditioning using off-the-shelf, low-cost optical and electronic components, that can be reproduced rigorously in any laboratory equipped with 3D printer. | Instrument, operant conditioning, 3D printable chamber, OpenBehavior | is listed by: OpenBehavior | DOI:10.1523/eneuro.0502-19.2020 | Commercially available | SCR_021547 | 2026-08-29 11:27:50 | 0 | |||||||||
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Creative Biogene Mitochondrial Physiological and Pathological Modifications Service Resource Resource Report Resource Website |
Creative Biogene Mitochondrial Physiological and Pathological Modifications Service Resource (RRID:SCR_022239) | service resource | Provides multi species mitochondrial epigenetic analysis and customizes appropriate research route. Providies services on epigenetic characteristics of mitochondria under different physiological and pathological conditions. | Creative Biogene, biomedical service, multi species mitochondrial epigenetic analysis, epigenetic characteristics, different physiological and pathological conditions | has parent organization: Creative Biogene | Restricted | SCR_022239 | Mitochondrial Physiological and Pathological Modifications | 2026-08-29 11:27:53 | 0 | |||||||||
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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 | 2026-08-29 11:27:46 | 112 | |||||||
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DrivAER Resource Report Resource Website 1+ mentions |
DrivAER (RRID:SCR_019076) | data analysis software, data processing software, software application, software resource | 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 | 2026-08-29 11:27:48 | 1 | |||||||
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STENCIL Resource Report Resource Website 1+ mentions |
STENCIL (RRID:SCR_021878) | data processing software, data visualization software, software application, software resource | Web engine for visualizing and sharing life science datasets.Designed to organize, visualize, and enable sharing of interactive genomic data visualizations. Provides ability to inspect and interpret sequencing data, without requiring programming expertise. | Visualizing genomic data, sharing genomic data, interactive genomic data visualizations, interpret sequencing data | NIEHS ES013768; NIGMS GM125722 |
DOI:10.1101/2021.06.04.447108 | Free, Available for download, Freely available | SCR_021878 | 2026-08-29 11:28:16 | 4 | |||||||||
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IMGT HighV-QUEST Resource Report Resource Website 10+ mentions |
IMGT HighV-QUEST (RRID:SCR_018196) | alignment software, analysis service resource, data or information resource, data processing software, image analysis software, portal, production service resource, service resource, software application, software resource | Next generation B and T cell sequence alignment and characterization online surface by IMGT. Web portal for immunoglobulin (IG) or antibody and T cell receptor (TR) analysis from NGS high throughput and deep sequencing. | Next generation sequencing, B cell, T cell, sequence alignment, immunoglobulin, antibody, T cell receptor, analysis, sequence, bio.tools |
is listed by: bio.tools is listed by: Debian |
CNRS ; GENCI ; MESR ; NHMRC ; Université Montpellier 2 ; France |
PMID:22647994 PMID:23995877 PMID:22665256 |
Restricted | biotools:IMGt_HighV-QUESt | https://bio.tools/IMGT_HighV-QUEST | SCR_018196 | IMGT/HighV QUEST, IMGT/HighV-QUEST, IMGT web portal | 2026-08-29 11:27:46 | 15 | |||||
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Genomic Association Tester Resource Report Resource Website 10+ mentions |
Genomic Association Tester (RRID:SCR_020949) | GAT | data analysis software, data processing software, simulation software, software application, software resource | Software tool as simulation framework for testing association of genomic intervals. Used for estimating significance of overlap between multiple sets of genomic intervals. Estimates statistical significance based on simulation and controls for multiple tests using false discovery rate. | Genomic intervals, genomic intervals association testing, overlap significance estimation, genomic intervals sets, segment length distribution, chromosomal location, isochores | UK Medical Research Council | PMID:23782611 | Free, Available for download, Freely available | https://github.com/AndreasHeger/gat | http://code.google.com/p/genomic-association-tester | SCR_020949 | 2026-08-29 11:27:49 | 31 |
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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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