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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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ClusPro Resource Report Resource Website 500+ mentions |
ClusPro (RRID:SCR_018248) | data access protocol, software resource, web service, service resource | Web tool for protein-protein docking. Server provides removal of unstructured protein regions, application of attraction or repulsion, accounting for pairwise distance restraints, construction of homo-multimers, consideration of small-angle X-ray scattering data, and location of heparin-binding sites. Six different energy functions can be used, depending on protein type.This protocol describes use of various options, construction of auxiliary restraints files, selection of energy parameters, and analysis of results. | Protein-protein docking, protein structure, energy function, energy parameter selection, analysis, data |
has parent organization: Boston University; Massachusetts; USA has parent organization: Stony Brook University; New York; USA |
NIGMS R35 GM118078; NIGMS R01 GM061867 |
PMID:28079879 | Free, Freely available | SCR_018248 | ClusPro 2.0 | 2026-02-14 02:04:58 | 858 | |||||||
|
Neutron Scattering Length and Cross Sections Resource Report Resource Website 1+ mentions |
Neutron Scattering Length and Cross Sections (RRID:SCR_019140) | data or information resource, service resource | Web tool for thermal neutron cross sections. Data of scattering lengths and corresponding scattering and absorption cross sections of elements. Data go through element number 96Cm. Used for study of condensed matter structure and dynamics. | NIST Center for Neutron Research, thermal neutron cross sections, scattering lengths, condensed matter, condensed matter structure, condensed matter dynamics, absorption cross sections, scattering cross sections, data | DOI:10.1080/10448639208218770 | Free, Freely available | SCR_019140 | 2026-02-14 02:03:46 | 4 | ||||||||||
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Neural Module Resource Report Resource Website 1+ mentions |
Neural Module (RRID:SCR_019270) | data analysis software, software resource, data processing software, software application | Neural Module by Axion BioSystems Inc, provides simplified approach to set up, execution and analysis of neural experiments. Enables Maestro Pro and Edge to record and analyze key parameters of neural network function, including activity, synchrony, and network oscillations. | Axion BioSystems Inc, neural data, neural network function, neural activity, neural synchrony, network oscillation, data analysis, neural experiment, data | Restricted | SCR_019270 | Neural Software Module, NeuralMetricTool | 2026-02-14 02:03:30 | 5 | ||||||||||
|
SoftWoRx software Resource Report Resource Website 10+ mentions |
SoftWoRx software (RRID:SCR_019157) | data visualization software, data processing software, data acquisition software, image acquisition software, software application, image processing software, software resource, image analysis software | Software for acquisition, deconvolution, processing, analysis, and display of DeltaVision images. Used in DeltaVision OMX SR imaging system., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | GE Healthcare, DeltaVision OMX SR, imaging system, image, data | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_019157 | softWoRx 7.0, softWoRx 6.5.2 | 2026-02-14 02:03:29 | 34 | ||||||||||
|
SC2diseases Resource Report Resource Website 1+ mentions |
SC2diseases (RRID:SCR_019093) | analysis service resource, data or information resource, production service resource, service resource, database | Manually curated database of single cell transcriptome for human diseases. scRNA-seq database derived from numerous human studies. Provides researchers with encyclopedia of biomarkers at level of genes, cells, and diseases. | Human disease, single cell transcriptome, data, manually curated data, biomarker | National Natural Science Foundation of China | PMID:33010177 | Free, Freely available | SCR_019093 | 2026-02-14 02:03:45 | 5 | |||||||||
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Deep Collaborative Learning Resource Report Resource Website |
Deep Collaborative Learning (RRID:SCR_019258) | DCL | data analysis software, software resource, data processing software, software application | Software tool as deep collaborative learning with application to study of multimodal brain development. Uses deep network to represent original data and then seeks their correlations, while also linking data representation with phenotypical information. | Data fusion method, nonlinear predictive relationship, functional magnetic resonance imaging, brain research, data, data correlation, phenotypical information | has parent organization: Tulane University; Louisiana; USA | Free, Available for download, Freely available | SCR_019258 | dcl_model | 2026-02-14 02:03:48 | 0 | ||||||||
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SoupX Resource Report Resource Website 50+ mentions |
SoupX (RRID:SCR_019193) | data processing software, data analysis software, software toolkit, software application, software resource | Software R package for estimation and removal of cell free mRNA contamination in droplet based single cell RNA-seq data. | Estimation, removal, cell free mRNA contamination, droplet based, single cell RNA-seq data, RNA-seq data, data, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Available for download, Freely available | biotools:soupx | https://bio.tools/soupx | SCR_019193 | 2026-02-14 02:03:47 | 77 | ||||||||
|
DatA Tag Suite Resource Report Resource Website |
DatA Tag Suite (RRID:SCR_019236) | DATS | data or information resource, software toolkit, software resource, narrative resource, standard specification | Software suite to enable discoverability of datasets. Enables submission of metadata on datasets to DataMed. Has core set of elements, which are generic and applicable to any type of dataset, and extended set that can accommodate more specialized data types. Platform independent model developed by NIH BD2K bioCADDIE project for DataMed Data Discovery Index prototype being developed. Also available as annotated serialization in schema.org, which in turn is widely used by major search engines like Google, Microsoft, Yahoo and Yandex. | Data processing, data discovery, metadata submission, DataMed, data, discovery | NIAID U24 AI117966; ELIXIR EXCELERATE ; ELIXIR-UK |
PMID:28585923 | Free, Freely available | SCR_019236 | 2026-02-14 02:03:48 | 0 | ||||||||
|
NSW BioNet Resource Report Resource Website 10+ mentions |
NSW BioNet (RRID:SCR_019162) | data repository, storage service resource, portal, data or information resource, service resource | Repository for biodiversity data products managed by Department of Planning, Industry and Environment, New South Wales, Australia. It stores species sightings, systematic surveys, threatened biodiversity records and species names. | Species sightings, systematic surveys, threatened biodiversity records, species names, data | Restricted | SCR_019162 | New South Wales BioNet | 2026-02-14 02:03:46 | 33 | ||||||||||
|
Phantom Camera Control Resource Report Resource Website 1+ mentions |
Phantom Camera Control (RRID:SCR_021080) | PCC | data analysis software, software resource, data processing software, software application | Software application for Phantom cameras. Controls every camera function on every Phantom camera model. Fine-tune resolution, frame rate, exposure, memory segmentation, trigger modes and automatic functions prior to recording. PCC also makes it easy to work with synchronized cameras, manage Phantom Cine raw files and convert files to format for final project.Software is compatible with Windows 7 Pro and Windows 8.1 and Windows 10, for both 32 and 64-bit operating systems. | Phantom, Phantom camera, image, data, processing, raw files, convert files | Free, Available for download, Freely available | SCR_021080 | 2026-02-14 02:04:10 | 1 | ||||||||||
|
miRDeep Resource Report Resource Website 100+ mentions |
miRDeep (RRID:SCR_010829) | miRDeep2 | sequence analysis software, data processing software, data analysis software, software application, software resource | Software tool to identify known and novel miRNA genes in seven animal clades by analyzing sequenced RNAs. Used for discovering known and novel miRNAs from small RNA sequencing data. | miRNA, gene, animal, clade, analysis, sequence, RNA, data | is listed by: OMICtools | Helmholtz-Alliance on Systems Biology ; Helmholtz Association ; German Ministry of Education and Research ; Senate of Berlin ; China Scholarship Council ; Max Delbrück Centrum Systems Biology Network |
PMID:18392026 PMID:21911355 |
Free, Available for download, Freely available | OMICS_00373 | https://github.com/rajewsky-lab/mirdeep2 | SCR_010829 | 2026-02-14 02:02:04 | 163 | |||||
|
Mainz Institute of Molecular Biology Bioinformatics Core Facility Resource Report Resource Website 1+ mentions |
Mainz Institute of Molecular Biology Bioinformatics Core Facility (RRID:SCR_011244) | Fraunhofer IME, IMB | institution | Provides assistance with consulting on experimental design, training on bioinformatics tools and databases, data quality assessment, data processing, data visualization, data interpretation, data mining of published datasets, and assistance with preparation of manuscripts and grant proposals. | bioinformatics, data, quality assessment, processing, visualization, interpretation, mining, consulting |
is related to: Pharma-Planta Consortium has parent organization: Fraunhofer-Gesellschaft is parent organization of: Pharma-Planta Consortium is parent organization of: European ScreeningPort |
open | ISNI: 0000 0004 0573 9904, grid.418010.c, nlx_158283, Wikidata: Q1452021 | https://ror.org/03j85fc72 | SCR_011244 | Fraunhofer-Institut f�r Molekularbiologie und Angewandte Oekologie IME, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Fraunhofer-Institut fur Molekularbiologie und Angewandte Oekologie IME, Fraunhofer Institute for Molecular Biology and Applied Ecology | 2026-02-14 02:02:14 | 1 | ||||||
|
Nextstrain Resource Report Resource Website 100+ mentions |
Nextstrain (RRID:SCR_018223) | data set, data or information resource, portal, project portal | Open source project to harness scientific and public health potential of pathogen genome data. Provides continually updated view of publicly available data alongside powerful analytic and visualization tools for use by community. Used to aid epidemiological understanding and improve outbreak response. Open source SARS-CoV-2 genome data and analytic and visualization tools. | Pathogen genome data, data, analytic tool, visualization tool, epidemiology, outbreak response |
is listed by: Data and Computational Resources to Address COVID-19 is related to: SARS-CoV-2 mutation effects and 3D structure prediction from sequence covariation works with: Global Initiative on Sharing All Influenza Data |
COVID-19 | Free, Freely available | https://nextstrain.org/ncov/global | SCR_018223 | nextstrain.org | 2026-02-14 02:03:35 | 273 | |||||||
|
Allen Software Development Kit Resource Report Resource Website 10+ mentions |
Allen Software Development Kit (RRID:SCR_018183) | AllenSDK | data analysis software, software resource, data processing software, software application | Software tool as code for processing and analyzing data in Allen Brain Atlas. Source code for reading and processing Allen Brain Atlas data. Allen SDK focuses on Allen Brain Observatory, Cell Types Database, and Mouse Brain Connectivity Atlas. | Data analysis, data processing, Allen Brain Atlas, data, brain |
is related to: Allen Brain Atlas is organization facet of: BICCN |
Free, Freely available | SCR_018192 | https://allensdk.readthedocs.io/en/latest/ | SCR_018183 | 2026-02-14 02:03:34 | 28 | |||||||
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NetMHCpan Server Resource Report Resource Website 100+ mentions |
NetMHCpan Server (RRID:SCR_018182) | data access protocol, software resource, web service | Web server for quantitative prediction of peptide binding to any MHC molecule of known sequence using artificial neural networks. Characterizes binding specificity of given major histocompatibility complex molecule and predicts peptide length profile and peptide binding affinity. NetMHCpan 3.0 is improved prediction of binding to MHC class I molecules integrating information from multiple receptor and peptide length data sets. NetMHCpan 4.0 is trained on naturally eluted ligands and on peptide binding affinity data. NetMHCpan-4.1 server predicts binding of peptides to any MHC molecule of known sequence using artificial neural networks (ANNs). | Quantitative prediction, peptide binding, MHC molecule, artificial neural network, Major Histocompatibilty Complex, peptide length, peptide binding affinity, data, bio.tools |
is listed by: bio.tools is listed by: Debian |
Agencia Nacional de Promoción Científica y Tecnológica ; Argentina ; NIAID |
PMID:19002680 PMID:28978689 |
Free, Available for download, Freely Available | biotools:netmhcpan | https://bio.tools/netmhcpan https://services.healthtech.dtu.dk/services/NetMHCpan-4.1/ |
SCR_018182 | NetMHCpan 1.0, NetMHCpan 3.0, NetMHCpan 2.0, NetMHCpan 4.1, NetMHCpan 4.0, NetMHCpan | 2026-02-14 02:03:28 | 138 | |||||
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IMGT Repertoire Resource Report Resource Website 10+ mentions |
IMGT Repertoire (RRID:SCR_018220) | data or information resource | Web resource for immunoglobulins (IG), T cell receptors (TR) and major histocompatibility (MH) and related proteins of immune system (RPI). Comprises LIGM expertized data on immunoglobulins (IG), T cell receptors (TR) and major histocompatibility (MH) and related proteins of immune system. | LIGM data, immunoglobulins, T cell receptor, histocompatibility, protein, immune system, data | is related to: IMGT - the international ImMunoGeneTics information system | Free, Freely available | SCR_018220 | IMGT Repertoire (MH), Repertoire (IG and TR), IMGT Repertoire (RPI), ImMunoGeneTics Repertoire | 2026-02-14 02:03:18 | 10 | |||||||||
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Velocyto Resource Report Resource Website 100+ mentions |
Velocyto (RRID:SCR_018167) | data analysis software, software resource, data processing software, software application | Software package for analysis of expression dynamics in single cell RNA seq data. Enables estimations of RNA velocities of single cells by distinguishing unspliced and spliced mRNAs in standard single-cell RNA sequencing protocols. Estimates RNA velocity in single cell RNA sequencing datasets. RNA velocity estimation in Python or R. | Expression dynamic, single cell RNAseq data, data, RNAseq, RNA velocity, mRNA, RNAseq dataset, estimation RNA velocity | Free, Available for download, Freely available | https://github.com/velocyto-team/velocyto.py https://github.com/velocyto-team/velocyto.R |
SCR_018167 | velocyto.py, velocyto, velocyto.R | 2026-02-14 02:03:17 | 137 | |||||||||
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astroML Resource Report Resource Website |
astroML (RRID:SCR_018138) | data visualization software, data processing software, data set, data or information resource, data analysis software, software toolkit, software application, software resource | Software Python package for machine learning, statistics and data mining. Contains library of statistical and machine learning routines for analyzing astronomical data in Python, loaders for several open astronomical data sets, and examples of analyzing and visualizing astronomical data sets. Repository of common tools and routines used for statistical data analysis in astronomy and astrophysics. | Machine learning, statistics, data mining, data, astronomy, astrophysics, data analysis | DOI:10.1109/CIDU.2012.6382200 | Free, Available for download, Freely available | https://github.com/astroML/astroML/blob/master/doc/index.rst | SCR_018138 | 2026-02-14 02:03:31 | 0 | |||||||||
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SnapTools Resource Report Resource Website 10+ mentions |
SnapTools (RRID:SCR_018097) | SnapTools | data processing software, alignment software, software application, software resource, image analysis software | Software tool as module for working with snap files in Python. Snap files are designed for storing single nucleus ATAC-seq datasets. | Sequence, snap file, single nucleus, ATACseq dataset, data | is used by: scATAC Pipeline | Free, Available for download, Freely available | SCR_018097 | Single Nucleus Accessibility Profile Tools, Single nucleus accessibility profile Tools | 2026-02-14 02:03:33 | 14 | ||||||||
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astropy Resource Report Resource Website 10+ mentions |
astropy (RRID:SCR_018148) | software library, portal, data or information resource, software toolkit, software resource, project portal | Community software Pyton library for astronomy. Collection of software packages written in Python programming language for use in astronomy. Package contains key functionality and common tools needed for performing astronomy and astrophysics with Python. Core of Astropy Project, which aims to enable community to develop ecosystem of Affiliated Packages covering broad range of needs for astronomical research, data processing, and data analysis. | Astronomy, domain specific file format, flexible image transport system file, virtual observatory table, physical quantity conversion, unit conversion, celestial coordinate, data, cosmological transformation framework, cosmological conversion framework | DOI:10.3847/1538-3881/aabc4f DOI:10.1051/0004-6361/201322068 |
Free, Available for download, Freely available | SCR_018148 | 2026-02-14 02:03:31 | 12 |
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