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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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PERFect Resource Report Resource Website |
PERFect (RRID:SCR_024682) | software application, software resource, data processing software | Software R package as filtering test for microbiome data. Permutation filtering approach to address two unsolved problems in microbiome data processing: (i) define and quantify loss due to filtering by implementing thresholds and (ii) introduce and evaluate a permutation test for filtering loss to provide a measure of excessive filtering. | filtering test, microbiome data, microbiome data processing, | NSF ; NIGMS 1U54GM104944 |
PMID:29917060 | Free, Available for download, Freely available | SCR_024682 | Permutation Filtering Package in R | 2026-07-27 09:37:11 | 0 | ||||||||
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NIGMS Human Genetic Cell Repository Resource Report Resource Website 1+ mentions |
NIGMS Human Genetic Cell Repository (RRID:SCR_004517) | NIGMS Repository | cell repository, biomaterial supply resource, material resource | Highly characterized cell lines and high quality DNA for cell and genetic research representing a variety of disease states, chromosomal abnormalities, apparently healthy individuals and many distinct human populations. The NIGMS Repository contains more than 10,600 cell lines, primarily fibroblasts and transformed lymphoblasts, and over 5,500 DNA samples. The NIGMS Repository has a major emphasis on heritable diseases and chromosomally aberrant cell lines. In addition, it contains a large collection dedicated to understanding human variation that includes samples from populations around the world, the CEPH collection, the Polymorphism Discovery Resource, and many apparently healthy controls. Human induced pluripotent stem cell lines, many of which were derived from NIGMS Repository fibroblasts, have recently become available through the NIGMS Repository. Sample donation facilitates all areas of research by making available well-characterized materials to any qualified researcher who might have otherwise been unable to invest the time and resources to collect needed samples independently. Donations to the Repository have created a resource of unparalleled scope. Samples from the collection have been used in more than 5,500 publications and are distributed to scientists in more than 50 countries. This resource is continuously expanding to support new directions in human genetics. | cell, gene, cell line, dna, fibroblast, transformed lymphoblast, lymphoblast, induced pluripotent stem cell line, chromosomal abnormality, healthy, single-gene disorder, complex polygenic disorder, multifactorial birth defect, unaffected first-degree relatives of individuals with genetic disease, heritable disease, genetic disease, human variation, control, clinical data, blood |
is used by: NIF Data Federation is listed by: One Mind Biospecimen Bank Listing is related to: Integrated Cell Lines has parent organization: Coriell Cell Repositories |
Chromosomal abnormality, Healthy, Single-gene disorder, Complex polygenic disorder, Multifactorial birth defect, Unaffected first-degree relatives of individuals with genetic disease, Heritable disease, Genetic disease, Control | NIGMS ; NIH Blueprint for Neuroscience Research |
Public / non-commercial: Cell cultures and DNA samples are distributed only to qualified professional persons who are associated with recognized research, Medical, Educational, Or industrial organizations engaged in biomedical research with Statement of Research Intent and a MTA. Samples obtained from the Repository, And material derived from the samples, May not be used for commercial purposes, Although knowledge gained from their use may be used. | nlx_143798 | SCR_004517 | Human Genetic Cell Repository | 2026-07-27 09:32:03 | 4 | |||||
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plusTipTracker Resource Report Resource Website 10+ mentions |
plusTipTracker (RRID:SCR_021890) | software application, image analysis software, software resource, data processing software | Software package as quantitative image analysis software for measurement of microtubule dynamics. MATLAB software for tracking full dynamics of microtubules based on plusTIP marker live cell image sequences. | microtubule tracking, microtubule dynamics, microtubule dynamics measurement, plusTIP marker, live cell image sequences | NIGMS U01 GM67230 | PMID:21821130 | Free, Available for download, Freely available | SCR_021890 | 2026-07-27 09:36:29 | 10 | |||||||||
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bioPIXIE Resource Report Resource Website 1+ mentions |
bioPIXIE (RRID:SCR_004182) | bioPIXIE | analysis service resource, service resource, data analysis service, production service resource | bioPIXIE is a general system for discovery of biological networks through integration of diverse genome-wide functional data. This novel system for biological data integration and visualization, allows you to discover interaction networks and pathways in which your gene(s) (e.g. BNI1, YFL039C) of interest participate. The system is based on a Bayesian algorithm for identification of biological networks based on integrated diverse genomic data. To start using bioPIXIE, enter your genes of interest into the search box. You can use ORF names or aliases. If you enter multiple genes, they can be separated by commas or returns. Press ''submit''. bioPIXIE uses a probabilistic Bayesian algorithm to identify genes that are most likely to be in the same pathway/functional neighborhood as your genes of interest. It then displays biological network for the resulting genes as a graph. The nodes in the graph are genes (clicking on each node will bring up SGD page for that gene) and edges are interactions (clicking on each edge will show evidence used to predict this interaction). Most likely, the first results to load on the results page will be a list of significant Gene Ontology terms. This list is calculated for the genes in the biological network created by the bioPIXIE algorithm. If a gene ontology term appears on this list with a low p-value, it is statistically significantly overrepresented in this biological network. As you move the mouse over genes in the network, interactions involving these genes are highlighted. If you click on any of the highlighted interactions graph, evidence pop-up window will appear. The Evidence pop-up lists all evidence for this interaction, with links to the papers that produced this evidence - clicking these links will bring up the relevant source citation(s) in PubMed. You may need to download the Adobe Scalable Vector Graphic (SVG) plugin to utilize the visualization tool (you will be prompted if you need it). | prediction, bayesian network, probabilistic, interaction, network | has parent organization: Princeton University; New Jersey; USA | NHGRI T32 HG003284; NIGMS R01 GM071966; NHGRI R01 HG003471; NIGMS P50 GM071508; NSF DGE-9972930; NSF IIS-0513552 |
PMID:16420673 | nlx_20893 | SCR_004182 | biological Process Inference from eXperimental Interaction Evidence | 2026-07-27 09:31:57 | 1 | ||||||
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ProFunc Resource Report Resource Website 50+ mentions |
ProFunc (RRID:SCR_004450) | ProFunc | analysis service resource, service resource, data analysis service, production service resource | The ProFunc server had been developed to help identify the likely biochemical function of a protein from its three-dimensional structure. It uses both sequence- and structure-based methods including fold matching, residue conservation, surface cleft analysis, and functional 3D templates, to identify both the protein''''s likely active site and possible homologues in the PDB. Often, where one method fails to provide any functional insight another may be more helpful. You can submit your own structure, analyze an existing PDB entry, or retrieve the results of a previously submitted run. The files are usually stored for about 6 months before being deleted. However, they are stored on a partition that is not backed up; so, in principle, they could disappear at any time. | gold standard |
is related to: PDBsum has parent organization: European Bioinformatics Institute |
DOE contract W-31-109-Eng-38; NIGMS GM62414; European Union FP6 contract LHSG-CT-2003-503265 |
PMID:15980588 PMID:16019027 |
nlx_44430 | SCR_004450 | ProFunc - prediction of protein function from 3D structure, ProFunc: Analysis of a protein''''s 3D structure to help identify its likely biochemical function | 2026-07-27 09:32:02 | 63 | ||||||
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iPOP Resource Report Resource Website 10+ mentions |
iPOP (RRID:SCR_008991) | iPOP | data or information resource, data set | Data set generated by personal omics profiling of Dr. Michael Snyder at Stanford University. It combines genomic, transcriptomic, proteomic, metabolomic, and autoantibody profiles from a single individual over a 14 month period. The analysis revealed various medical risks, including type II diabetes. It also uncovered extensive, dynamic changes in diverse molecular components and biological pathways across healthy and diseased conditions. | genomics, proteomics, transcriptional profiling, saliva, blood, maternal data, metabolomics, personalized medicine, adult human, genetics, transcriptome, male | has parent organization: Stanford University; Stanford; California | Healthy | Breetwor Family Foundation ; Korber Foundation ; Fundacion Marcelino Botin ; Fundacion Lilly ; NLM T15-LM007033; NIGMS R24-GM61374; NHLBI T32 HL094274; NHLBI KO8 HL083914; NIH New Investigator DP2 award OD004613; Spanish Ministry of Science and Innovation Projects ; Spanish Ministry of Science and Innovation Projects ; European Union FP7 Genica ; European Union FP7 TELOMARKER ; European Research Council Advanced Grant |
PMID:22424236 | Free for personal, Non-exclusive, Non-transferable, Non-commercial access., Please cite. | nlx_152492 | SCR_008991 | Snyderome, Integrated Personal Omics Profiling | 2026-07-27 09:33:13 | 12 | ||||
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Systems Biology Graphical Notation Resource Report Resource Website 1+ mentions |
Systems Biology Graphical Notation (RRID:SCR_004671) | SBGN | narrative resource, training resource, data or information resource, standard specification, software resource, meeting resource, international standard specification, topical portal, portal | 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 | 2026-07-28 09:41:03 | 1 | |||||||||
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PR Resource Report Resource Website |
PR (RRID:SCR_004964) | PR | controlled vocabulary, data or information resource, ontology | An ontological representation of protein-related entities by explicitly defining them and showing the relationships between them. Each PRO term represents a distinct class of entities (including specific modified forms, orthologous isoforms, and protein complexes) ranging from the taxon-neutral to the taxon-specific. The ontology has a meta-structure encompassing three areas: proteins based on evolutionary relatedness (ProEvo); protein forms produced from a given gene locus (ProForm); and protein-containing complexes (ProComp). NOTICE: The PRO ID format has changed from PRO: to PR: (e.g. PRO:000000563 is now PR:000000563). | database, obo, protein |
is listed by: BioPortal has parent organization: Protein Information Resource has parent organization: Georgetown University; Washington D.C.; USA |
NIH ; NIGMS GM080646-01 |
nlx_92849 | SCR_004964 | PRO, Protein Ontology | 2026-07-28 09:41:13 | 0 | |||||||
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Protein Data Bank Markup Language Resource Report Resource Website 1+ mentions |
Protein Data Bank Markup Language (RRID:SCR_005085) | PDBML | narrative resource, markup language, data or information resource, standard specification, interchange format | Markup Language that provides a representation of PDB data in XML format. The description of this format is provided in XML schema of the PDB Exchange Data Dictionary. This schema is produced by direct translation of the mmCIF format PDB Exchange Data Dictionary Other data dictionaries used by the PDB have been electronically translated into XML/XSD schemas and these are also presented in the list below. * PDBML data files are provided in three forms: ** fully marked-up files, ** files without atom records ** files with a more space efficient encoding of atom records * Data files in PDBML format can be downloaded from the RCSB PDB website or by ftp. * Software tools for manipulating PDB data in XML format are available. | xml |
is related to: RCSB PDB Software Tools has parent organization: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) |
NSF ; NIGMS ; DOE ; NLM ; NCI ; NCRR ; NIBIB ; NINDS |
PMID:15509603 | nlx_144096 | SCR_005085 | PDBML: Protein Data Bank Markup Language | 2026-07-28 09:41:09 | 2 | ||||||
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SOURCE Resource Report Resource Website 50+ mentions |
SOURCE (RRID:SCR_005799) | SOURCE | service resource, data or information resource, data analysis service, database, production service resource, analysis service resource | SOURCE compiles information from several publicly accessible databases, including UniGene, dbEST, UniProt Knowledgebase, GeneMap99, RHdb, GeneCards and LocusLink. GO terms associated with LocusLink entries appear in SOURCE. The mission of SOURCE is to provide a unique scientific resource that pools publicly available data commonly sought after for any clone, GenBank accession number, or gene. SOURCE is specifically designed to facilitate the analysis of large sets of data that biologists can now produce using genome-scale experimental approaches Platform: Online tool | genomic, functional annotation, ontology, gene expression, gene, genome, statistical analysis, bio.tools, FASEB list |
is listed by: Gene Ontology Tools is listed by: Debian is listed by: bio.tools is related to: Gene Ontology has parent organization: SMD |
NIGMS ; NCI CA85129-04; NIGMS GM07365 |
PMID:12519986 | Restricted | biotools:source, nlx_149287 | https://login.stanford.edu/idp/profile/SAML2/Redirect/SSO?execution=e1s1, https://bio.tools/source | SCR_005799 | 2026-07-28 09:41:21 | 69 | |||||
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SBO Resource Report Resource Website 1+ mentions |
SBO (RRID:SCR_006753) | SBO | controlled vocabulary, data or information resource, database, ontology | A set of controlled, relational vocabularies of terms commonly used in Systems Biology, and in particular in computational modeling. The ontology consists of seven orthogonal vocabularies defining: the roles of reaction participants (eg. substrate), quantitative parameters (eg. Michaelis constant), a precise classification of mathematical expressions that describe the system (eg. mass action rate law), the modeling framework used (eg. logical framework), and a branch each to describe entity (eg. macromolecule) and interaction (eg. process) types, and a branch to define the different types of metadata that may be present within a model. SBO terms can be used to introduce a layer of semantic information into the standard description of a model, or to annotate the results of biochemical experiments in order to facilitate their efficient reuse. SBO is an Open Biomedical Ontologies (OBO) candidate ontology, and is free for use. A programmatic access to the content of the Systems Biology Ontology is provided by Web Services. | systems biology, computational modeling, web service, obo, gold standard |
is listed by: BioPortal is related to: BioModels.net is related to: OBO has parent organization: European Bioinformatics Institute |
NIGMS | PMID:17118155 | Free, The community can contribute to this resource | nlx_66206 | SCR_006753 | Systems Biology Ontology | 2026-07-28 09:41:37 | 4 | |||||
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iBioSeminars Resource Report Resource Website |
iBioSeminars (RRID:SCR_005848) | iBioSeminars | data or information resource, narrative resource, video resource, training material | iBioSeminars offers: * Free, on-demand lectures: Many universities/colleges have limited access to high profile leaders in biological research. Our goal is to add 15-20 seminars per year, of similar quality to outstanding lectures that are currently in this library. Access, through web streaming or download, is completely free-of-charge. * Targeting a broad audience: iBioSeminars start with an extended introduction, making them accessible to non-specialists and students, and then progress to cover current research. Senior scientists and students can view and enjoy these lectures. * Education: iBioSeminars are being used by undergraduate and graduate teachers to augment their classroom material. We have now added an education component to this web site (including lecture notes, questions/answers and short video clips for teaching). * International communication: iBioSeminars have viewers in 115 countries and they are being internally promoted in several countries as an educational tool and scientific resource. * Goodwill: Lecturers generously donate their time to prepare these lectures. The project, largely funded by HHMI, is a grass roots efforts with time invested by several individuals at UCSF, HHMI and ASCB. | biological research, biology, lecture, seminar, education, undergraduate, graduate |
has parent organization: University of California at San Francisco; California; USA has parent organization: American Society for Cell Biology has parent organization: Howard Hughes Medical Institute |
NSF ; NIGMS ; Howard Hughes Medical Institute |
Licensed under a Creative Commons Attribution-NonCommercial-NoDerivs v3 Unported License. | nlx_149380 | SCR_005848 | iBioSeminars - Bringing the World''s Best Biology to You, iBioSeminars - Bringing the Worlds Best Biology to You, iBioSeminars.org | 2026-07-28 09:41:30 | 0 | ||||||
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Biomedical Informatics Research Network Resource Report Resource Website 10+ mentions |
Biomedical Informatics Research Network (RRID:SCR_005163) | BIRN | service resource, data or information resource, data repository, database, software resource, atlas, storage service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 22, 2023. National initiative to advance biomedical research through data sharing and online collaboration that provides data sharing infrastructure, software tools, strategies and advisory services. Groups may choose whether to share data internally or with external audiences. Hardware and data remain under control of individual user groups. | dti, fmri, alzheimer's disease, cognitive impairment, collaborative environment, cyberinfrastructure, data sharing, depressive disorder, information technology, infrastructure, memory dysfunction, microarray, mri, neurodegenerative disease, neuroinformatics, neuroimaging, genetics, biomedical material, neurobiology, electrophysiology, collaboration, biomedical, imaging, imaging system, biomedical engineering, brain, health |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps is listed by: re3data.org is listed by: DataCite has parent organization: University of Southern California; Los Angeles; USA is parent organization of: Morphometry BIRN is parent organization of: Knowledge Engineering from Experimental Design is parent organization of: Mouse Biomedical Informatics Research Network is parent organization of: NIH Topic Maps - A Topic Database of NIH Funded Grants is parent organization of: Human Imaging Database is parent organization of: Function BIRN is parent organization of: B0 and eddy current correction for DTI is parent organization of: BrainSuite is parent organization of: Open Access Series of Imaging Studies |
NIH Blueprint for Neuroscience Research ; NCRR 1U24-RR025736; NCRR U24-RR021992; NCRR U24-RR021760; NCRR 1U24-RR026057-01; NIGMS U24 GM104203 |
PMID:21515543 PMID:18348946 PMID:17238407 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-00027, r3d100010770 | http://www.nitrc.org/projects/birn, https://doi.org/10.17616/R3F02K | http://www.birncommunity.org/, https://neuroscienceblueprint.nih.gov/factSheet/birn.htm | SCR_005163 | BIRN - The Conduit for Biomedical Research, Biomedical Informatics Research Network - The Conduit for Biomedical Research | 2026-07-28 09:41:17 | 12 | |||
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PhysioNet Resource Report Resource Website 500+ mentions |
PhysioNet (RRID:SCR_007345) | PhysioNet | service resource, data or information resource, data repository, data analysis service, storage service resource, database, production service resource, analysis service resource | Collection of dissemination and exchange recorded biomedical signals and open-source software for analyzing them. Provides facilities for cooperative analysis of data and evaluation of proposed new algorithm. Providies free electronic access to PhysioBank data and PhysioToolkit software. Offers service and training via on-line tutorials to assist users at entry and more advanced levels. In cooperation with annual Computing in Cardiology conference, PhysioNet hosts series of challenges, in which researchers and students address unsolved problems of clinical or basic scientific interest using data and software provided by PhysioNet. All data included in PhysioBank, and all software included in PhysioToolkit, are carefully reviewed. Researchers are further invited to contribute data and software for review and possible inclusion in PhysioBank and PhysioToolkit. Please review guidelines before submitting material. | physiologic, physiology, signal, software, research, biomedical, cardiopulmonary, neural, healthy, patient, cardiac, death, congestive heart failure, epilepsy, gait, disorder, sleep apnea, cardioogy, computation, physiologic signal, workspace, time series, FASEB list, DRKB |
is recommended by: National Library of Medicine is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: DataCite is listed by: re3data.org is listed by: FAIRsharing has parent organization: Massachusetts Institute of Technology; Massachusetts; USA; is parent organization of: CHB-MIT Scalp EEG Database is parent organization of: EEG Motor Movement/Imagery Dataset is parent organization of: Sleep-EDF Database |
Aging | NIBIB ; NIGMS ; NIH EB037545 |
PMID:22256277 PMID:14716615 PMID:14632011 PMID:11446213 PMID:10851218 |
Free, Freely available | r3d100011561, nif-0000-00250, DOI:10.17616/R3D06S, DOI:10.25504/FAIRsharing.bemzxg, DOI:10.13026 | https://doi.org/10.17616/R3D06S, https://doi.org/10.17616/r3d06s, https://doi.org/10.13026/, https://dx.doi.org/10.13026/, https://fairsharing.org/10.25504/FAIRsharing.bemzxg, https://doi.org/10.17616/R3D06S | SCR_007345 | Physionet: The Research Resource for Complex Physiologic Signals, PhysioNet, PhysioNet: The Research Resource for Complex Physiologic Signals | 2026-07-28 09:41:45 | 618 | |||
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GLIMMPSE Resource Report Resource Website 1+ mentions |
GLIMMPSE (RRID:SCR_016297) | software application, software resource, data analysis software, data processing software | Web based software tool that calculates power and sample size for study designs with normally distributed outcomes. Permits power calculations for clinical trials, randomized experiments, and observational studies with clustering, repeated measures, and both, and almost any testable hypothesis. GLIMMPSE Version 3 release back end has been refactored in Python, interface has been simplified, requiring user decisions about only one topic per screen, new menu improves specification of both between-participant and within-participant hypothese, recursive algorithm permits computing covariances for up to ten levels of clustering., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | power, multivariate, linear, models, Gaussian, error, Java, web, calculate | NIGMS R01 GM121081; NIGMS R25 GM111901; NLM G13 LM011879 |
PMID:24403868 PMID:40901910 |
THIS RESOURCE IS NO LONGER IN SERVICE | SCR_016297 | , GLIMMPSE Version 3 | 2026-07-28 09:44:10 | 8 | ||||||||
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CytoMAP Resource Report Resource Website 10+ mentions |
CytoMAP (RRID:SCR_021227) | software application, data analysis software, software resource, data processing software, data analytics software, software toolkit | Software tool as spatial analysis software for whole tissue sections.Utilizes information on cell type and position to phenotype local neighborhoods and reveal how their spatial distribution leads to generation of global tissue architecture.Used to make advanced data analytic techniques accessible for single cell data with position information. | Histo cytometric multidimensional, analysis pipeline, whole tissue sections, spatial analysis, single cell data with position information, phenotype local neighborhoods, global tissue architecture | has parent organization: Washington University School of Medicine in St. Louis; Missouri; USA | NIAID R01 AI134713; NIAID R21 AI142667; NIAID R01 AI134246; NIAID R01 AI076327; NIAID U19 AI135976; NIAID T32 AI10667; NIGMS T32 GM007270; NICHD T32 HD007233; NSF DGE 1762114 |
PMID:32320656 | Free, Available for download, Freely available | SCR_021227 | Histo-Cytometric Multidimensional Analysis Pipeline | 2026-07-28 09:45:08 | 22 | |||||||
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STENCIL Resource Report Resource Website 1+ mentions |
STENCIL (RRID:SCR_021878) | data visualization software, software resource, software application, data processing software | 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 | 2026-07-28 09:45:20 | 4 | |||||||||
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SpiecEasi Resource Report Resource Website 10+ mentions |
SpiecEasi (RRID:SCR_022712) | SpiecEasi | software application, software resource, data analysis software, data processing software | 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 | 2026-07-28 09:45:45 | 15 | |||||||
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Megadepth Resource Report Resource Website 1+ mentions |
Megadepth (RRID:SCR_022779) | software application, software resource, data analysis software, data processing software | Software tool for quantifying alignments and coverage for BigWig and BAM/CRAM input files.Quantifies number of RNA-seq reads assigned to gene in BAM file, successor of bamcounts. | quantifying alignments, BigWig and BAM/CRAM input files, RNA-seq reads assigned to gene in BAM file quantification, | NIGMS R01GM118568; NIGMS R01GM121459; UK Medical Research Council |
PMID:33693500 | Free, Available for download, Freely available | https://bioconductor.org/packages/megadepth | SCR_022779 | 2026-07-28 09:45:46 | 2 | ||||||||
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ZDOCK Server Resource Report Resource Website 50+ mentions |
ZDOCK Server (RRID:SCR_022518) | software resource, data access protocol, web service | Web tool as protein docking server, based on rigid body docking programs ZDOCK and M-ZDOCK, to predict structures of protein-protein complexes and symmetric multimers. | Protein docking server, ZDOCK, M-ZDOCK, predict structures, protein-protein complexes, symmetric multimers | NIGMS GM084884 | PMID:24532726 | Free, Freely available | SCR_022518 | 2026-07-28 09:45:35 | 75 |
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