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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Flowlogic Resource Report Resource Website 50+ mentions |
Flowlogic (RRID:SCR_020942) | data processing software, data analysis software, software resource, software application | Software tool for flow cytometry data analysis by Miltenyi Biotec. | Flow cytometry data, data analysis, flow cytometry, Miltenyi Biotec | is listed by: SoftCite | Restricted | SCR_020942 | Flowlogic TM Software, Flowlogic Software | 2026-08-12 10:52:15 | 81 | |||||||||
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ggraph Resource Report Resource Website 50+ mentions |
ggraph (RRID:SCR_021239) | data processing software, data visualization software, software resource, software application | Software tool as extension of ggplot2 aimed at supporting relational data structures such as networks, graphs, and trees. While it builds upon foundation of ggplot2 and its API it comes with its own self-contained set of geoms, facets, etc., as well as adding concept of layouts to grammar. | Relational data structures support, data networks, data graphs, data trees | is related to: ggplot2 | Free, Available for download, Freely available | https://CRAN.R-project.org/package=ggraph, https://github.com/thomasp85/ggraph/ | SCR_021239 | grammar of graphics for relational data | 2026-08-12 10:52:18 | 53 | ||||||||
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Bs-Seeker2 Resource Report Resource Website 1+ mentions |
Bs-Seeker2 (RRID:SCR_020948) | sequence analysis software, software application, data processing software, software resource, data analysis software | Software tool as versatile aligning pipeline for bisulfite sequencing data. Used for mapping bisulfite sequencing data and generating DNA methylomes. Improves mappability over existing aligners by using local alignment. Maps reads from RRBS library by building special indexes with improved efficiency and accuracy. Provides additional function for filtering out reads with incomplete bisulfite conversion, which is useful in minimizing overestimation of DNA methylation levels. | Versatile aligning pipeline, bisulfite sequencing data, mapping bisulfite sequencing data, generating DNA methylomes, DNA methylation level, reads mapping, Reduced Represented Bisulfite Sequencing library, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: BS Seeker has parent organization: University of California at Los Angeles; California; USA |
Institute of Genomics and Proteomics at UCLA ; NBRPC 2012CB316503; China Scholarship Council |
PMID:24206606 | Free, Available for download, Freely available | biotools:bs-seeker2 | http://pellegrini.mcdb.ucla.edu/BS_Seeker2/, https://bio.tools/bs-seeker2 | SCR_020948 | Bisulfite Sequencing Seeker2, BS Seeker2 | 2026-08-12 10:52:25 | 2 | |||||
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MITE-Hunter Resource Report Resource Website 1+ mentions |
MITE-Hunter (RRID:SCR_020946) | sequence analysis software, software application, data processing software, software resource, data analysis software | Software pipeline to identify MITEs as well as other small Class 2 non autonomous Transposable Elements from genomic DNA data sets. Used for discovering miniature inverted repeat transposable elements from genomic sequences. Can search large genomic data sets including whole genome sequences. | Class 2 non-autonomous transposable element, genes non-coding regions, genome evolution, coding sequence, genomic DNA data sets, | NSF 0607123 | PMID:20880995 | Free, Available for download, Freely available | https://github.com/jburnette/MITE-Hunter | SCR_020946 | Miniature Inverted repeat Transposable Elements Hunter | 2026-08-12 10:52:27 | 7 | |||||||
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Abricate Resource Report Resource Website 1000+ mentions |
Abricate (RRID:SCR_021093) | data processing software, data analysis software, software resource, software application | Software tool for mass screening of contigs for antimicrobial and virulence genes. Mass screening of contigs for antimicrobial resistance or virulence genes. It comes bundled with multiple databases: NCBI, CARD, ARG-ANNOT, Resfinder, MEGARES, EcOH, PlasmidFinder, Ecoli_VF and VFDB. | contigs mass screening, antimicrobial genes, virulence genes, antimicrobial genes contigs, virulence genes contigs, FASEB list | Free, Available for download, Freely available | SCR_021093 | ABRicate | 2026-08-12 10:52:16 | 1355 | ||||||||||
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xiNET Resource Report Resource Website 10+ mentions |
xiNET (RRID:SCR_021010) | data visualization software, software application, data processing software, data access protocol, software resource, web service | Open source web based visualization tool for exploring crosslinking mass spectrometry results. Displays residue resolution positional information including linkage sites and linked peptides, all types of crosslinking reaction product, ambiguous results and additional sequence information such as domains. | Crosslinking mass spectrometry data visualization, linkage sites, linked peptides, crosslinking reaction product display, crosslink network maps, maps with residue resolution | Wellcome Trust | PMID:25648531 | Free, Available for download, Freely available | http://github.com/colin-combe/crosslink-viewer | SCR_021010 | Crosslink Network Maps With Residue Resolution | 2026-08-12 10:52:27 | 20 | |||||||
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Biofactoid Resource Report Resource Website 1+ mentions |
Biofactoid (RRID:SCR_021011) | project portal, portal, data or information resource, data access protocol, software resource, knowledge environment resource, web service | Web tool for creating digital profile of scientific discoveries in article and connecting them to related research. Authors describe molecular interactions supported by their results, letting researchers explore first hand account of article findings and connect to related articles and knowledge. Web based system for scientists to compose structured representation of networks of interactions between genes, their products, and chemical compounds, represented using power of formal ontology. | Knowledge management, molecular interactions, pathway, compose network structured representation, digital profile, connect related articles, formal ontology |
is related to: Biological Pathways Exchange is related to: Biological Pathways Exchange has parent organization: University of Toronto; Ontario; Canada has parent organization: Harvard University; Cambridge; United States has parent organization: University of Oregon; Oregon; USA |
NHGRI U41HG006623; DARPA Big Mechanism |
Free, Freely available | SCR_021011 | 2026-08-12 10:52:28 | 1 | |||||||||
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Applied Biosystems QuantStudio 12K Flex RT PCR Software Resource Report Resource Website 1+ mentions |
Applied Biosystems QuantStudio 12K Flex RT PCR Software (RRID:SCR_021096) | data acquisition software, software application, data processing software, software resource, data analysis software | Software supports QuantStudio12K Flex Real Time PCR System to open and analyze experiments. Enables to set up experiments, send experiments to instrument, control thermal cycling process in instrument, collect data and analyze collected data. | control instrument thermal cycling process, data collection, data analysis, QuantStudio12K Flex Real Time PCR System support | is used by: Thermo Fisher: Applied Biosystems: QuantStudio 12K Flex RealTime PCR System | Restricted | SCR_021096 | QuantStudio 12K Flex Real Time PCR Software, Applied Biosystems QuantStudio 12K Flex RT PCR Software | 2026-08-12 10:52:16 | 5 | |||||||||
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Minhee Analysis Package Resource Report Resource Website 1+ mentions |
Minhee Analysis Package (RRID:SCR_021250) | software toolkit, software application, data processing software, software resource, standalone software, data analysis software | Software package for detection and measurement of spontaneous synaptic events. Integrated software package for detection and management of spontaneous synaptic events. Used in neurophysiology to detect spontaneous postsynaptic currents, search and visualize them in custom way, and perform hypothesis testing of retrieved data. | Spontaneous synaptic events, synaptic events detecting, synaptic events sorting, quantifying PSC data, spontaneous postsynaptic currents, neurophysiology | DOI:10.1186/s13041-021-00847-x | Free, Available for download, Freely available | SCR_021250 | 2026-08-12 10:52:32 | 7 | ||||||||||
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ExpressionSuite Resource Report Resource Website 10+ mentions |
ExpressionSuite (RRID:SCR_021095) | data processing software, data analysis software, software resource, software application | Software tool to quantify relative gene expression across large number of genes and samples. Allows to analyze gene expression data on any current Applied Biosystems real time PCR instrument. | QuantStudio Real-Time PCR analysis, quantify relative gene expression, genes large number, analyze gene expression data, Applied Biosystems RT PCR instrument | Free, Available for download, Freely available | SCR_021095 | ExpressionSuite Software, ExpressionSuite v1.3 | 2026-08-12 10:52:30 | 11 | ||||||||||
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cgmapotools Resource Report Resource Website 1+ mentions |
cgmapotools (RRID:SCR_020950) | data processing software, data analysis software, software resource, software application | Software package for DNA methylation analysis. Used for context-wise, gene-wise, bin-wise, region-wise and sample-wise analysis and visualizations. Used to improve precision of heterozygous SNV calls and supports allele-specific methylation detection and visualization in bisulfite-sequencing data. | DNA methylomes analysis, DNA methylomes, context-wise analysis, gene-wise analysis, bin-wise analysis, region-wise analysis, sample-wise analysis, bisulfite sequencing data, allele specific methylation detection | National Key Research and Development Program of China ; National Natural Science Foundation of China |
PMID:28968643 | Free, Available for download, Freely available | SCR_020950 | 2026-08-12 10:52:15 | 3 | |||||||||
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Scholia Resource Report Resource Website 1+ mentions |
Scholia (RRID:SCR_021248) | software resource, data access protocol, web service | Software Python package and webapp for interaction with scholarly information in Wikidata. Wikidata profiling service.Wikidata service generating scholarly profiles, e.g. for authors, journals, topics, and organisations. | Scientific bibliographic information, Wikidata, Wikidata profiling service |
is listed by: Wikidata is related to: Wikidata |
Free, Available for download, Freely available | Wikidata_Q45340488 | https://www.wikidata.org/wiki/Q45340488, https://github.com/fnielsen/scholia | SCR_021248 | 2026-08-12 10:52:33 | 2 | ||||||||
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immuneML Resource Report Resource Website 1+ mentions |
immuneML (RRID:SCR_021004) | portal, service resource, data or information resource, production service resource, analysis service resource | Open source Python platform for machine learning based analysis and classification of adaptive immune receptors and repertoires. Supported by ELIXIR Norway. | Immune receptor, machine learning, predicting immune status, predicting antigen specificity | DOI:10.1101/2021.03.08.433891 | Free, Available for download, Freely available | SCR_021007 | https://galaxy.immuneml.uio.no/, https://github.com/uio-bmi/immuneML | SCR_021004 | 2026-08-12 10:52:27 | 1 | ||||||||
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Hugging Face Resource Report Resource Website 100+ mentions |
Hugging Face (RRID:SCR_020958) | data or information resource, community building portal, portal, organization portal | Portal to build, train and deploy state of the art models powered by reference open source in natural language processing. | Hugging Face, Inc., NLP, Natural Language Processing, build art models, deploy art models, reference open source | Free, Freely available | https://github.com/huggingface | SCR_020958 | 2026-08-12 10:52:26 | 121 | ||||||||||
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MesKit Resource Report Resource Website 1+ mentions |
MesKit (RRID:SCR_020959) | sequence analysis software, data visualization software, software toolkit, software application, data processing software, software resource, data analysis software | Software R package for dissecting cancer evolution from multi region derived tumor biopsies via somatic mutations. Used for characterizing cancer genomic ITH and inferring history of tumor evolution via implementation of well established computational and statistical methods. | Dissecting cancer evolution, region derived tumor biopsies, somatic mutations, cancer genomic ITH, tumor evolution | has parent organization: Sun Yat-sen University; Guangdong; China | Free, Available for download, Freely available | https://bioconductor.org/packages/MesKit/ | SCR_020959 | Multi region exome sequencing analysis tool Kit | 2026-08-12 10:52:27 | 4 | ||||||||
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Mouse Brain Architecture Project Resource Report Resource Website 1+ mentions |
Mouse Brain Architecture Project (RRID:SCR_004683) | data or information resource, atlas, reference atlas, d spatial image | An atlas project whose goal is to enerate brainwide maps of inter-regional neural connectivity that specify the inputs and outputs of every brain region, at a "mesoscopic" level of analysis. A 3D injection viewer is used to view the mouse brain. To determine the outputs of a brain region, anterograde tracers are used which are taken up by neurons locally ("the input"), then transported actively down the axons to the "output regions." The whole brain is then sliced thinly, and each slice is digitally imaged. These 2-D images are reconstructed in 3D. The majority of the resulting 3-D brain image is unlabeled. Only the injected region and its output regions have tracer in them, allowing for identification of this small fraction of the connectivity map. This procedure is repeated identically, to account for individual variability. To determine the inputs to the same brain region as above, a retrograde tracer is injected in the same stereotaxic location ("the input"), and the process is repeated. In order to accumulate data from different mice (each of whom has a slightly different brain shape and size), 3-D spatial normalization is performed using registration algorithms. These gigapixel images of whole-brain sections can be zoomed to show individual neurons and their processes, providing a "virtual microscope." Each sampled brain is represented in about 500 images, each image showing an optical section through a 20 micron-thick slice of brain tissue. A multi-resolution viewer permits users to journey through each brain, following the pathways taken through three-dimensional brain space by tracer-labeled neuronal pathways. A key point is that at the mid-range "mesoscopic" scale, the team expects to assemble a picture of connections that are stereotypical and probably genetically determined in a species-specific manner. By dividing the volume of a hemisphere of the mouse brain into 250 equidistant, predefined grid-points, and administering four different kinds of tracer injections at each grid point -- in different animals of the same sex and age a complete wiring diagram that will be stitched together in "shotgun" fashion from the full dataset. | atlas, brain, brain architecture, connectivity, mouse brain architecture, neuroanatomy |
is related to: Brain Architecture Project has parent organization: Brain Architecture Project |
NIH Office of the Director ; NIMH RC1MH088659; NIMH R01MH087988 |
Fully accessible to the neuroscience community as well as interested members of the general public, Acknowledgement requested | nlx_146201 | http://www.brainarchitecture.org | http://www.brainarchitecture.org/mouse/about | SCR_004683 | MBA Project, Mouse Brain Architecture | 2026-08-12 10:49:01 | 5 | |||||
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Orthopaedic Surgery Resource Report Resource Website 1+ mentions |
Orthopaedic Surgery (RRID:SCR_004715) | data or information resource, narrative resource, wiki, book | Orthopaedic Surgery is a collaborative wikibook of orthopedic surgery. *Preface *Chapter 1: Basic Sciences *Chapter 2: Upper Limb *Chapter 3: Foot and Ankle *Chapter 4: Spine *Chapter 5: Hand and Microsurgery *Chapter 6: Pediatric Orthopedics *Chapter 7: Adult Reconstruction *Chapter 8: Sports Medicine *Chapter 9: Musculoskeletal Tumors *Chapter 10: Injury *Chapter 11: Surgical Procedures *Chapter 12: Rehabilitation *Chapter 13: Practice | has parent organization: Wikibooks | nlx_71236 | SCR_004715 | Orthopaedic Surgery (wikibook), Orthopedic Surgery | 2026-08-12 10:49:01 | 1 | ||||||||||
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CBLAST Resource Report Resource Website 1+ mentions |
CBLAST (RRID:SCR_004711) | production service resource, d spatial image, analysis service resource, service resource | The NCBI Related Structures tool allows you to find 3D structures from the Molecular Modeling Database (MMDB) that are similar in sequence to a query protein. Although the query protein may not yet have a resolved structure, the 3D shape of a similar protein sequence can shed light on the putative shape and biological function of the query protein. CBLAST is a tool that compares a query protein sequence against all protein sequences from resolved 3D structures by using protein BLAST against the PDB data set. The purpose is to find representative 3D structures for the query and/or its homologs, as available. Each record in the Entrez Protein database has been CBLAST''ed and the search results are available as Related Structures in the Links menu of Entrez Protein records. You can also enter a protein query sequence directly into the CBLAST search page in order to find its sequence-similar 3D structure records. The search results can be viewed in Cn3D (hence the name CBLAST), which displays an alignment of the query protein to the related structure''s sequence and allows you to interactively examine the sequence-structure relationship. | gold standard |
is related to: NCBI Structure has parent organization: NCBI |
PMID:17135201 | nlx_70506 | SCR_004711 | NCBI Related Structures, NCBI Related Structure Search | 2026-08-12 10:49:02 | 2 | ||||||||
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Systems Biology Graphical Notation Resource Report Resource Website 1+ mentions |
Systems Biology Graphical Notation (RRID:SCR_004671) | SBGN | portal, data or information resource, narrative resource, training resource, standard specification, topical portal, software resource, meeting resource, international standard specification | The Systems Biology Graphical Notation (SBGN) project aims to develop high quality, standard graphical languages for representing biological processes and interactions. Each SBGN language is based on the consensus of the broad international SBGN community of biologists, curators and software developers. Over the course of its development many individuals, organizations and companies made invaluable contributions to the SBGN through participating in discussions and meetings, providing feedback on the documentation and worked examples, adopting the standard and spreading the word. Circuit diagrams and Unified Modeling Language diagrams are just two examples of standard visual languages that help accelerate work by promoting regularity, removing ambiguity and enabling software tool support for communication of complex information. Ironically, despite having one of the highest ratios of graphical to textual information, biology still lacks standard graphical notations. The recent deluge of biological knowledge makes addressing this deficit a pressing concern. Toward this goal, we present the Systems Biology Graphical Notation (SBGN), a visual language developed by a community of biochemists, modelers and computer scientists. SBGN consists of three complementary languages: process diagram, entity relationship diagram and activity flow diagram. Together they enable scientists to represent networks of biochemical interactions in a standard, unambiguous way. We believe that SBGN will foster efficient and accurate representation, visualization, storage, exchange and reuse of information on all kinds of biological knowledge, from gene regulation, to metabolism, to cellular signaling. A list of software packages known to provide (or have started to develop) support for SBGN notations is available. | New Energy and Industrial Technology Development Organization ; Okinawa Institute of Science and Technology ; BBSRC ; National Institute of Advanced Industrial Science and Technology of Japan ; European Media Laboratory EML Research GmbH ; California Institute of Technology; California; USA ; NIGMS 1R01GM081070-01 |
PMID:19668183 | nlx_66628 | SCR_004671 | 2026-08-12 10:49:01 | 1 | |||||||||
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OpenAnesthesia.org Resource Report Resource Website 1+ mentions |
OpenAnesthesia.org (RRID:SCR_004547) | continuing medical education, data or information resource, podcast, narrative resource, training resource, radio, wiki, audio track | OpenAnesthesia.org is a wiki promoting evidence-based medicine in anesthesiology, critical care and pain management. It is divided into several, major Units (Anesthesia Text, Critical Care Manual, Practice-Changing Articles, Controversies in Anesthesia, ABA keywords, Audio/Video Archives, CME, GME, Pharmacology...), each of which is subdivided into Chapters (or in some cases, even smaller subdivisions, such as sections, individual key words, topics, points of interest, or bibliographic references). The goal of Anasthesia Text is to collect and distribute evidence-based information regarding all aspects of anesthesia. This section is similar to a traditional textbook in the broad range of topics covered, but different in that it will provide this information in the form of a wiki (i.e. anyone can edit, add, or subtract to it). OpenAneshesia.org provides anesthesia residents with GME credit and Program Directors with a tool to document core competency activities for Accreditation Council for Graduate Medical Education (ACGME)-mandated learning portfolios. Residents are invited invited to read the Anesthesia & Analgesia article of the month and listen to an interview with one of the article''s authors. During the interview, the author will discuss the specifics of the article as well as general topics geared towards improving each resident''s appreciation of basic or clinical research. After listening to the podcast and reading the article, residents can answer 5 questions in order to demonstrate their mastery of the topics discussed (similar to the Anesthesia & Analgesia Continuing Medical Education (CME) section). Like the CME section, after demonstrating proficiency, a resident will receive a printable certificate that will specify which ACGME core competencies were addressed in the article and interview. The certificates can be put in each resident''s ACGME-required learning portfolio. | graduate medical education | International Anesthesia Research Society | nlx_54007 | SCR_004547 | OpenAnesthesia Wiki, OA.org, OpenAnesthesia | 2026-08-12 10:49:00 | 8 |
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