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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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ReMM score Resource Report Resource Website 1+ mentions |
ReMM score (RRID:SCR_023095) | ReMM score | software resource, software application | Software tool that scores positions in human genome in terms of their regulatory probability. Regulatory Mendelian Mutation score was created for relevance prediction of non-coding variations (SNVs and small InDels) in human genome (hg19) in terms of Mendelian diseases. | positions in human genome scoring, regulatory probability, relevance prediction, non-coding variations, SNVs and small InDels, Mendelian diseases, human genome | DOI:10.1101/2022.03.14.484240 | Free, Available for download, Freely available | https://charite.github.io/software-remm-score.html, https://search.datacite.org/works/10.5281/zenodo.1197579 | SCR_023095 | Regulatory Mendelian Mutation score | 2026-08-12 10:52:58 | 6 | |||||||
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eido Resource Report Resource Website 1+ mentions |
eido (RRID:SCR_021076) | software resource, software application | Software validation tool for Portable Encapsulated Projects or PEPs in python. | validation tool, Portable Encapsulated Projects, PEPs, python | is related to: peppy | DOI:10.1101/2020.10.08.331322 | Free, Available for download, Freely available | https://github.com/pepkit/eido/ | SCR_021076 | 2026-08-12 10:52:29 | 1 | ||||||||
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insane.py Resource Report Resource Website 1+ mentions |
insane.py (RRID:SCR_022317) | software resource, software application | Software tool for generating custom membranes for molecular simulations. Software Python script to setup Martini bilayer systems. | Generating custom membranes, molecular simulations, Martini bilayer system | DOI:10.1021/acs.jctc.5b00209 | Free, Available for download, Freely available | SCR_022317 | 2026-08-12 10:52:42 | 1 | ||||||||||
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ACD/ChemSketch Resource Report Resource Website 10+ mentions |
ACD/ChemSketch (RRID:SCR_019272) | software resource, software application | Software tool as molecular structure drawing application by ACD Labs. Allows user to Draw chemical structures, reactions, and schema, and access variety of graphical tools and templates, Generate names from molecular structure and vice versa, Calculate molecular properties from chemical structure, Create professional reports, presentations, and publication ready figures, Communicate scientific information with clarity and ease. | Chemical structure, molecular structure, drawing application, generate molecular structure names, calculate molecular properties, create professional reports, ACD Labs | Restricted | SCR_019272 | ChemSketch | 2026-08-12 10:52:24 | 22 | ||||||||||
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dandi-cli Resource Report Resource Website 1+ mentions |
dandi-cli (RRID:SCR_019009) | software resource, software application | Command line client to facilitate common operations. | Command line client, facilite common operations, neurophysiology data integration, distributed archives, client | Free, Freely available | SCR_019009 | Distributed Archives for Neurophysiology Data Integration client, DANDI client | 2026-08-12 10:52:17 | 1 | ||||||||||
|
ATLAS.ti Resource Report Resource Website 500+ mentions |
ATLAS.ti (RRID:SCR_022920) | data analytics software, software resource, software application | Software qualitative analysis tool. Used by researchers and practitioners to uncover and systematically analyze complex phenomena hidden in unstructured data including text, multimedia, geospatial. Provides tools that let the user locate, code, and annotate findings in primary data material, to weigh and evaluate their importance, and to visualize relations between them. Consolidates documents and keeps track of all notes, annotations, codes and memos in all fields that require close study and analysis of primary material consisting of text, images, audio, video, and geo data. Provides analytical and visualization tools designed to open new interpretative views on material. | ATLAS.ti Scientific Software Development GmbH, unstructured data analysis, text, images, audio, video, geo data, analytical and visualization tools, locate, code, and annotate findings in primary data material | Restricted | SCR_022920 | ATLAS.ti version no. 5. 2 | 2026-08-12 10:52:57 | 581 | ||||||||||
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BioConda Resource Report Resource Website 50+ mentions |
BioConda (RRID:SCR_018316) | software resource, software application | Software distribution management for life sciences. Channel for Conda package manager specializing in bioinformatics software. Consists of repository of recipes hosted on GitHub, build system turning these recipes into conda packages, repository of packages containing bioinformatics packages ready to use with conda install. | Software distribution management, bioinformatic software, package repository, GitHub, conda, bio.tools |
lists: CCS is listed by: bio.tools is listed by: Debian is related to: Conda is related to: RNAProt |
Intramural Program of the National Institute of Diabetes and Digestive and Kidney Diseases ; Netherlands Organisation for Scientific Research ; German Research Foundation ; NYU Abu Dhabi Research Institute |
PMID:29967506 | Free, Available for download, Freely available | biotools:bioconda | https://bio.tools/bioconda | SCR_018316 | Bioconda | 2026-08-12 10:52:06 | 73 | |||||
|
BBKNN Resource Report Resource Website 10+ mentions |
BBKNN (RRID:SCR_022807) | software resource, software application | Software to identify each cell’s top neighbours in each batch separately instead of entire cell pool with no accounting for batch. Nearest neighbours for each batch are then merged to create final list of neighbours for cell. Aligns batches in a quick and lightweight manner. | Aligns batches, nearest neighbours for each batch, identify each cell’s top neighbours, each batch separately, | is used by: scanpy | Free, Available for download, Freely available | https://github.com/Teichlab/bbknn/blob/master/docs/index.rst, https://github.com/Teichlab/bbknn | SCR_022807 | Batch Balanced KNN | 2026-08-12 10:52:38 | 20 | ||||||||
|
PretextView Resource Report Resource Website 100+ mentions |
PretextView (RRID:SCR_022024) | software resource, software application | Software tool to enable visualization from PretextMap output. Desktop application for viewing pretext contact maps. OpenGL Powered Pretext Contact Map Viewer. | visualization from PretextMap output, viewing pretext contact maps, map viewer | works with: PretextMap | Free, Available for download, Freely available | SCR_022024 | Wellcome Sanger Institute's High-Performance Assembly Group's Paired REad TEXTure Viewer, REad TEXTure Viewer | 2026-08-12 10:52:26 | 448 | |||||||||
|
FreeCAD Resource Report Resource Website 100+ mentions |
FreeCAD (RRID:SCR_022535) | software resource, software application | Open source parametric 3D modeler to design real life objects of any size. Parametric modeling allows modify your design by going back into your model history and changing its parameters. | parametric 3D modeler, design real life objects, changing model parameters | Free, Available for download, Freely available | https://github.com/FreeCAD/FreeCAD | SCR_022535 | 2026-08-12 10:52:33 | 126 | ||||||||||
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Galactic Circos Resource Report Resource Website 1+ mentions |
Galactic Circos (RRID:SCR_018207) | software resource, software application | Software tool as Galaxy wrapper providing GUI for Circos tool. Circos allows visualizing data in circular format. | Galaxy wrapper, GUI for circos tool, visualizing data, circular format |
is listed by: ELIXIR Tools and Data Services Registry is related to: Galaxy |
Free, Available for download, Freely available | https://toolshed.g2.bx.psu.edu/repository?repository_id=5e3c8169d70360fa | SCR_018207 | 2026-08-12 10:52:04 | 1 | |||||||||
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d-StructMAn Resource Report Resource Website 1+ mentions |
d-StructMAn (RRID:SCR_022534) | d-StructMAn | software resource, software application | Software tool provides annotation of non-synonymous single nucleotide variants in context of structural properties of resulting amino acid changes in corresponding proteins. Improved implementation of StructMAn, shipped in container form and extended to annotation of short in-frame indels and alterations arising as consequence of alternative splicing events. Produces range of structural features by combining information from experimentally resolved structures of many related proteins, which is unique feature of StructMAn family tools. Can also harness all protein structure models stored in AlphaFold Protein Structure Database. | Structural mutation annotation, non-synonymous single nucleotide variants annotation, non-synonymous single nucleotide variants, structural properties, amino acid changes, protein structure | Free, Available for download, Freely available | SCR_022534 | d-Structural Mutation Annotation | 2026-08-12 10:52:44 | 1 | |||||||||
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NutriSurvey Resource Report Resource Website 10+ mentions |
NutriSurvey (RRID:SCR_022655) | data analytics software, software resource, software application | Software tool for nutrition calculations and surveys. | Nutrition calculation, nutrition surveys | Free, Available for download, Freely available | SCR_022655 | 2026-08-12 10:52:46 | 17 | |||||||||||
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CorrDrugTumorMSI Resource Report Resource Website 1+ mentions |
CorrDrugTumorMSI (RRID:SCR_018962) | software resource, software application | Software R pipeline to correlate drug distribution with tumor tissue types in mass spectrometry imaging data. | Drug, tumor heterogeneity, mass spectrometry imaging, spatial methods, drug distribution correlation, tumor tissue types, MSI, imaging data, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Freely available | biotools:corrdrugtumormsi | https://bio.tools/corrdrugtumormsi | SCR_018962 | 2026-08-12 10:52:16 | 1 | ||||||||
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calN50 Resource Report Resource Website 1+ mentions |
calN50 (RRID:SCR_022015) | data analytics software, software resource, software application | Software tool as simple script to calculate N50/NG50 and auN/auNG. | calculate N50/NG50, calculate auN/auNG | Free, Available for download, Freely available | SCR_022015 | 2026-08-12 10:52:26 | 8 | |||||||||||
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Hi5App Resource Report Resource Website |
Hi5App (RRID:SCR_022819) | software resource, software application | Software cross platform mobile application that supports 2D/3D/4D image visualization, multi-morphometry annotation, proofreading, interactive imaging system controlling, and distributed collaboration. | 2D/3D/4D image visualization, multi-morphometry annotation, proofreading, interactive imaging system controlling, distributed collaboration | is used by: BICCN | Free, Available for download, Freely available | SCR_022819 | 2026-08-12 10:52:47 | 0 | ||||||||||
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draw.io Resource Report Resource Website 1+ mentions |
draw.io (RRID:SCR_022939) | software resource, software application | Software tool as diagramming application that enables collaboration in real time. | diagramming, secure diagrams, collaboration in real-time | Restricted | SCR_022939 | 2026-08-12 10:52:40 | 1 | |||||||||||
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Sapporo service Resource Report Resource Website 1+ mentions |
Sapporo service (RRID:SCR_023202) | software resource, software application | Software for standard implementation conforming to Global Alliance for Genomics and Health Workflow Execution Service API specification. | GA4GH, Global Alliance for Genomics and Health, Workflow Execution Service, API specification | is related to: Sapporo web | Free, Available for download, Freely available | SCR_023202 | Sapporo-service | 2026-08-12 10:52:43 | 1 | |||||||||
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SAS JMP Pro Resource Report Resource Website 500+ mentions |
SAS JMP Pro (RRID:SCR_022199) | JMP Pro | data analytics software, software resource, software application | Statistical software tool. Predictive analytics software. Offers all tools in JMP plus advanced features for more sophisticated analyses. | Predictive analytics, statistics, visualizing data, building graphs, JMP | Restricted | SCR_022199 | JMP Pro from SAS | 2026-08-12 10:52:28 | 569 | |||||||||
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Jupyter-client Resource Report Resource Website 1+ mentions |
Jupyter-client (RRID:SCR_018413) | software resource, software application | Jupyter protocol implementation and client libraries. Part of Project Jupyter which exists to develop open-source software, open-standards, and services for interactive computing across dozens of programming languages. Jupyter-client contains reference implementation of Jupyter protocol and provides client and kernel management APIs for working with kernels. | Jupyter protocol implementation, Jupyter client library, kernel management API, kernel |
is related to: Jupyter Notebook is related to: Jupyter-core is related to: Jupyter-console |
Free, Freely available | https://github.com/jupyter/jupyter_client/, https://jupyter-client.readthedocs.io/en/stable/ | SCR_018413 | 2026-08-12 10:52:08 | 6 |
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