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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Panaroo Resource Report Resource Website 10+ mentions |
Panaroo (RRID:SCR_021090) | data analysis software, data processing software, software resource, software application | Software pipeline for pangenome investigation. Shares information between genomes to correct errors. Can call large structural variants.Fast and scalable to over 10k bacterial genomes. | pangenome investigation, correct errors, genomes, large structural variants, bacterial genomes | Free, Available for download, Freely available | https://gtonkinhill.github.io/panaroo/#/gettingstarted/quickstart | SCR_021090 | Bacterial Pangenome Analysis Pipeline | 2026-08-11 09:44:01 | 32 | |||||||||
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Tandem Repeats Finder Resource Report Resource Website 100+ mentions |
Tandem Repeats Finder (RRID:SCR_022065) | data analysis software, software application, software resource, data processing software, sequence analysis software | Software tool to locate and display tandem repeats in DNA sequences. Used to analyze DNA sequences. | locate and display tandem repeats, analyze DNA sequences, tandem repeat, DNA sequence | PMID:9862982 | Free, Available for download, Freely available | SCR_022065 | 2026-08-11 09:44:16 | 443 | ||||||||||
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Brain Cell Methylation Viewer Resource Report Resource Website 1+ mentions |
Brain Cell Methylation Viewer (RRID:SCR_020954) | mC Viewer | service resource, analysis service resource, data or information resource, web service, software resource, production service resource, data access protocol | Viewer for DNA Methylation Atlas of Mouse Brain at Single Cell Resolution. Browser to interactively explore single cell methylome dataset including exploration of methylation diversity of one gene at single-cell or cell-type level, exploration of cell type composition of adult mouse brain dissection regions and anatomical structures, explorartion of spatial distribution and methylation signature genes of one cell type. | BRAIN Initiative Cell Census Network, mouse brain, cell types, epigenomes, single cell exploration, methylome dataset | has parent organization: Salk Institute for Biological Studies | DOI:10.1101/2020.04.30.069377 | Free, Freely available | SCR_020954 | Neomorph: Brain Cell Methylation Viewer | 2026-08-11 09:43:58 | 2 | |||||||
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CSpritz Resource Report Resource Website 1+ mentions |
CSpritz (RRID:SCR_021884) | web service, software resource, data access protocol | Web tool for prediction of intrinsic protein disorder segments with annotation for homology, secondary structure and linear motifs. | Intrinsic protein disorder segments prediction, homology, secondary structure, linear motifs, annotation | University of Padova ; Italian Ministry of Education |
DOI:10.1093/nar/gkr411 | Free, Freely available | SCR_021884 | 2026-08-11 09:44:14 | 2 | |||||||||
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SIGNOR Resource Report Resource Website 50+ mentions |
SIGNOR (RRID:SCR_018485) | service resource, data or information resource, storage service resource, database, data repository | Software application to organize and store in structured format signaling information published in scientific literature. Information is stored as binary causative relationships between biological entities and can be represented graphically as activity flow. Each relationship is linked to literature reporting experimental evidence. Each node is annotated with chemical inhibitors that modulate its activity. Signaling information is mapped to human proteome. SIGNOR 2.0 stores manually annotated causal relationships between proteins and other biologically relevant entities including chemicals, phenotypes, complexes, etc with compliance to FAIR data principles. | Signal transduction data, signaling information, published data collection, activity flow, chemical inhibitor, human proteome, manually annotated data, protein, protein relationship, FAIR data, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: REDIportal |
Italian Association for Cancer Research ; ELIXIR-IIB ; Italian Node of the European ELIXIR infrastructure ; EMBL-EBI |
PMID:31665520 | Free, Available for download, Freely available | biotools:signor | https://bio.tools/signor | SCR_018485 | SIGnaling Network Open Resource, SIGNOR 2.0 | 2026-08-11 09:43:57 | 61 | |||||
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University of Pennsylvania Perelman School of Medicine Tumor Tissue Biospecimen Bank Core Facility Resource Report Resource Website 1+ mentions |
University of Pennsylvania Perelman School of Medicine Tumor Tissue Biospecimen Bank Core Facility (RRID:SCR_022430) | TTAB | service resource, material storage repository, storage service resource, core facility, access service resource, biobank | Centralized biorepository of human biosamples. TTAB is responsible for the collection, processing, and storage of human blood, fluid, and tissue at the University of Pennsylvania Health System. TTAB has a collection bench within Surgical Pathology Suite at Hospital of University of Pennsylvania (HUP).� Our collection bench sits adjacent to frozen section teams managing clinical sample collection and allowing for tight integration of tissue sample collection with clinical pathology teams. | USEDit, ABRF, biorepository |
is listed by: ABRF CoreMarketplace is related to: USEDit has parent organization: University of Pennsylvania Perelman School of Medicine; Pennsylvania; USA |
ARBF_1435 | https://coremarketplace.org?citation=1&FacilityID=1435 | SCR_022430 | Tumor Tissue/Biospecimen Bank (TTAB), University of Pennsylvania Perelman School of Medicine Tumor Tissue/Biospecimen Bank (TTAB) | 2026-08-11 09:44:22 | 3 | |||||||
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PyFRAP Resource Report Resource Website 1+ mentions |
PyFRAP (RRID:SCR_022665) | data analysis software, data processing software, software resource, software application | Software Python package for FRAP analysis. Simulation based analysis software that makes use of PDE simulations to analyze FRAP experiments in 3D geometries. Used to assess molecular diffusion. | Fluorescence recovery after photobleaching, analyze FRAP experiments in 3D geometries, assess molecular diffusion, | Free, Available for download, Freely available | biotools:pyfrap | https://bio.tools/pyfrap | SCR_022665 | Python Fluorescence Recovery After Photobleaching | 2026-08-11 09:44:20 | 1 | ||||||||
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ANTS marking and analysis tools Resource Report Resource Website 1+ mentions |
ANTS marking and analysis tools (RRID:SCR_022543) | data analysis software, data processing software, software resource, software application | Software tool for marking ant motion trajectories dataset from video. Provided marking software, three data quality analysis scripts, and tracking performance evaluation tool. | marking ant motion trajectories, dataset from video, tracking performance evaluation | Free, Available for download, Freely available | SCR_022543 | ANTS_marking_and_analysis_tools | 2026-08-11 09:44:23 | 3 | ||||||||||
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PyFDAP Resource Report Resource Website 1+ mentions |
PyFDAP (RRID:SCR_022664) | data analysis software, data processing software, software resource, software application | Software tool as automated analysis of fluorescence decay after photoconversion (FDAP) experiments. | automated analysis of fluorescence decay, photoconversion experiments, FDAP | PMID:25380959 | Free, Available for download, Freely available | SCR_022664 | Python Fluorescence Decay After Photoconversion | 2026-08-11 09:44:24 | 1 | |||||||||
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Chemotaxis and Migration Tool Resource Report Resource Website 1+ mentions |
Chemotaxis and Migration Tool (RRID:SCR_022708) | data analysis software, data processing software, software resource, software application | Software tool for data analysis from time stack chemotaxis experiments. Based on NIH ImageJ image processing system. | time stack chemotaxis experiments data, time stack chemotaxis experiments analysis, chemotaxis experiments graphs, statistical analysis | Free, Available for download, Freely available | SCR_022708 | Chemotaxis and Migration Tool version 2.0 | 2026-08-11 09:44:25 | 7 | ||||||||||
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SwissDock Resource Report Resource Website 100+ mentions |
SwissDock (RRID:SCR_022564) | web service, software resource, data access protocol | Web service to predict molecular interactions that may occur between target protein and small molecule. Protein small molecule docking web service based on EADock DSS. | Protein small molecule docking, predict molecular interactions, target protein and small molecule interactions, | FNS 310030_130857; Swiss Institute of Bioinformatics |
PMID:21624888 | Free, Freely available | SCR_022564 | 2026-08-11 09:44:23 | 159 | |||||||||
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SpiecEasi Resource Report Resource Website 10+ mentions |
SpiecEasi (RRID:SCR_022712) | SpiecEasi | data analysis software, data processing software, software resource, software application | Software R package for microbiome network analysis. Used for inference of microbial ecological networks from amplicon sequencing datasets. Combines data transformations developed for compositional data analysis with graphical model inference framework that assumes underlying ecological association network is sparse. | microbiome network analysis, amplicon sequencing datasets, microbial ecological networks inference | NIAID AI007180; NIDDK DK103358; NIGMS GM63270; Simons Foundation |
PMID:25950956 | Free, Available for download, Freely available | SCR_022712 | SParse InversE Covariance Estimation for Ecological Association Inference | 2026-08-11 09:44:25 | 20 | |||||||
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CORAL Resource Report Resource Website 50+ mentions |
CORAL (RRID:SCR_022711) | CORAL | data analysis software, data processing software, software resource, software application | Software tool as framework for rigorous self validated data modeling and integrative, reproducible data analysis. | FAIR data, Contexton, Microtype, Data Management, Provenance, Data Analysis, Jupyter | has parent organization: University of California at Berkeley; Berkeley; USA | US Department of Energy | Free, Available for download, Freely available | SCR_022711 | Contextual Ontology based Repository Analysis Library | 2026-08-11 09:44:27 | 95 | |||||||
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SNPRelate Resource Report Resource Website 10+ mentions |
SNPRelate (RRID:SCR_022719) | data analysis software, data processing software, software resource, software application | Software R package as parallel computing toolset for relatedness and principal component analysis of SNP data. | parallel computing, relatedness and principal component analysis, SNP data analysis | NHGRI U01 HG 004446 | PMID:23060615 | Free, Available for download, Freely available | https://github.com/zhengxwen/SNPRelate | SCR_022719 | 2026-08-11 09:44:21 | 13 | ||||||||
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University of Pennsylvania Perelman School of Medicine IFI CyTOF Service Center Core Facility Resource Report Resource Website 10+ mentions |
University of Pennsylvania Perelman School of Medicine IFI CyTOF Service Center Core Facility (RRID:SCR_022410) | CyTOF | service resource, material storage repository, storage service resource, access service resource, core facility | CyTOF�enables multi-parametric high-dimensional single�cell analysis�of more than 40 markers per cell, with�minimal background and compensation�issues.�Core�offers variety of�CyTOF-related services including�reagent distribution, consultation,�antibody conjugation, and data acquisition.� | USEDit, ABRF, stockroom | is listed by: ABRF CoreMarketplace | ARBF_1419 | https://coremarketplace.org?citation=1&FacilityID=1419 | SCR_022410 | University of Pennsylvania Perelman School of Medicine IFI CyTOF Service Center, IFI CyTOF Service Center | 2026-08-11 09:44:18 | 39 | |||||||
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AxonDeepSeg Resource Report Resource Website 1+ mentions |
AxonDeepSeg (RRID:SCR_022531) | software application, image analysis software, software resource, segmentation software, data processing software | Open source software tool for automatic axon and myelin segmentation from microscopy data using convolutional neural networks. | automatically segmenting axons and myelin sheaths, microscopy images | Canada Research Chair in Quantitative Magnetic Resonance Imaging ; Canadian Institute of Health Research ; Canada Foundation for Innovation ; Natural Sciences and Engineering Research Council of Canada ; TransMedTech ; Quebec BioImaging Network |
PMID:29491478 | Free, Available for download, Freely available | SCR_022531 | 2026-08-11 09:44:24 | 1 | |||||||||
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Bandage Resource Report Resource Website 10+ mentions |
Bandage (RRID:SCR_022772) | data analysis software, data processing software, software resource, software application | Software tool for visualising de novo assembly graphs. By displaying connections which are not present in contigs file, opens up new possibilities for analysing de novo assemblies. Used for interactive visualization of de novo genome assemblies. | interactive visualization, de novo genome assemblies, visualising de novo assembly graphs, analysing de novo assemblies |
is listed by: Debian is listed by: OMICtools |
PMID:26099265 | Free, Available for download, Freely available | OMICS_09013 | https://github.com/rrwick/Bandage, https://sources.debian.org/src/bandage/ | SCR_022772 | Bioinformatics Application for Navigating De novo Assembly Graphs Easily | 2026-08-11 09:44:28 | 27 | ||||||
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hifiasm-meta Resource Report Resource Website 1+ mentions |
hifiasm-meta (RRID:SCR_022771) | data analysis software, data processing software, software resource, software application | Software tool as metagenome assembler that exploits high accuracy of recent data. De novo metagenome assembler, based on haplotype resolved de novo assembler for PacBio Hifi reads. Workflow consists of optional read selection, sequencing error correction, read overlapping, string graph construction and graph cleaning. | Error correction, read overlapping, hifiasm, haplotype resolved de novo assembler, PacBio Hifi reads | NHGRI R01HG010040; NHGRI U01HG010971 |
PMID:35534630 | Free, Available for download, Freely available | SCR_022771 | hifiasm_meta | 2026-08-11 09:44:21 | 2 | ||||||||
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Cell Morphology Labelling Tool Resource Report Resource Website 1+ mentions |
Cell Morphology Labelling Tool (RRID:SCR_022770) | software application, data or information resource, data management software, image, software resource, 3d spatial image | Software tool for image quality. Used for labeling quality of images and labeling center point of 3D RI images. Used to mange 3D RI cell images taken from holotomography. | LabelingTool, holotomography, 3D RI cell image, image quality, mange 3D RI cell images | has parent organization: Yonsei University; Seoul; South Korea | Free, Available for download, Freely available | https://github.com/DigitalHealthcareLab/22CellMorphologyLabelingTool | https://github.com/DigitalHealthcareLab/22CellMorphologyLabelingTool | SCR_022770 | 22CellMorphologyLabelingTool | 2026-08-11 09:44:26 | 1 | |||||||
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Knowledge based Identification of Pathway Enzymes Resource Report Resource Website 1+ mentions |
Knowledge based Identification of Pathway Enzymes (RRID:SCR_022370) | KIPEs | data analysis software, data processing software, software resource, software application | Software tool as automatic approach for identification of players in biosynthesis pathway. Used for automatic annotation of flavonoid biosynthesis steps in new transcriptome of genome sequence assembly. Various enzymes of entire metabolic networks can be identified if sufficient knowledge about functionally relevant amino acids is available.Combines comprehensive sequence similarity analyses with inspection of functionally relevant amino acid residues and domains in subjected peptide sequences. | Automatic annotation, biosynthesis steps, new transcriptome of genome sequence assembly annotation, biosynthesis pathway, sequence similarity analyses, inspection of functionally relevant amino acid residues, peptide sequences | PMID:32867203 | Free, Available for download, Freely available | SCR_022370 | 2026-08-11 09:44:20 | 2 |
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