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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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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 | ||||||||||
|
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 | |||||||||
|
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 | |||||||||
|
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 | |||||||||||
|
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 | ||||||||
|
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 | |||||||||||
|
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 | ||||||||||
|
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 | |||||||||||
|
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 | |||||||||
|
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 | |||||||||
|
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 | |||||||||
|
Chromosome Scale Assembler Resource Report Resource Website 1+ mentions |
Chromosome Scale Assembler (RRID:SCR_017960) | CSA | software resource, software application | Software pipeline for high-throughput chromosome level vertebrate genome assembly. Pipeline, which after contig assembly performs post assembly improvements by ordering assembly and closing gaps, as well as splitting of low supported regions. | Assembly, chromosome, vertebrate, genome, contig, closing, gap, splitting, low, supported, region, bio.tools |
is listed by: bio.tools is listed by: Debian |
German Research foundation | Free, Available for download, Freely available | biotools:csa2.6 | https://bio.tools/CSA2.6 | SCR_017960 | Chromosome Scale Assembler | 2026-08-12 10:52:00 | 5 | |||||
|
xAtlas Resource Report Resource Website 1+ mentions |
xAtlas (RRID:SCR_022987) | software resource, software application | Software tool as variant caller for SNVs and small indels. Implemented as software application written in C++ . | Single nucleotide variants, variant caller, SNVs, small indels | has parent organization: Baylor College of Medicine Human Genome Sequencing Center | Free, Available for download, Freely available | SCR_022987 | 2026-08-12 10:52:40 | 3 | ||||||||||
|
Starr Life Sciences MouseOx Plus Resource Report Resource Website 10+ mentions |
Starr Life Sciences MouseOx Plus (RRID:SCR_022984) | software resource, software application | Software is part of MouseOx Plus pulse oximeter system. | Starr Life Sciences Corp., MouseOx Plus oximeter system, pulse oximeter | Free, Available to download | https://www.starrlifesciences.com/product/pulse-oximetry-software/ | SCR_022984 | MouseOx Plus, MOUSEOX PLUS 2.0 | 2026-08-12 10:52:49 | 11 | |||||||||
|
Jupyter-console Resource Report Resource Website 1+ mentions |
Jupyter-console (RRID:SCR_018414) | software resource, software application | Terminal based console frontend for Jupyter kernels. This code is based on single process IPython terminal. | Terminal based console, Jupyter kernel, single process IPython terminal, Jupyter Project | is related to: Jupyter-client | Free, Available for download, Freely available | SCR_018414 | Jupyter Terminal Console | 2026-08-12 10:52:08 | 2 | |||||||||
|
Golddigger Resource Report Resource Website |
Golddigger (RRID:SCR_020960) | data analytics software, software resource, software application | ImageJ macro to detect, mark and count electron dense markers like goldgrains or quantum dots in electron micrographs. | Electron dense markers, detect electron dense markers, mark electron dense markers, count electron dense markers, goldgrains, goldgrains marker, quantum dots, electron micrographs |
is related to: Nanotomy is related to: ImageJ is related to: Fiji has parent organization: University of Groningen; Groningen; Netherlands |
Free, Freely available | SCR_020960 | 2026-08-12 10:52:15 | 0 | ||||||||||
|
Python Nose Resource Report Resource Website 1+ mentions |
Python Nose (RRID:SCR_018418) | software resource, software application | Software tool to extend unittest to make testing easier. Python unit test framework. Note, Nose has been in maintenance mode for the past several years and will likely cease without a new person/team to take over maintainership. New projects should consider using Nose2, py.test, or just plain unittest/unittest2. | Testing, extend unittest | Free, Available for download, Freely available | https://github.com/nose-devs/nose/ | SCR_018418 | 2026-08-12 10:52:08 | 1 |
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