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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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GALA Resource Report Resource Website 1+ mentions |
GALA (RRID:SCR_026184) | GALA | source code, software resource | Softawer framework for de novo chromosome-by-chromosome assembly with long reads. Long-reads gap-free chromosome-scale assembler. | long-reads gap-free chromosome-scale assembler | PMID:36639368 | Free, Available for download, Freely available | SCR_026184 | GAp-free Long-read Assembler | 2026-08-09 09:09:24 | 1 | ||||||||
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optmatch Resource Report Resource Website 1+ mentions |
optmatch (RRID:SCR_026185) | software toolkit, software resource | Software package for optimal matching in R. Distance based bipartite matching using minimum cost flow, oriented to matching of treatment and control groups in observational studies. Routines are provided to generate distances from generalised linear models (propensity score matching), formulas giving variables on which to limit matched distances, stratified or exact matching directives, or calipers, alone or in combination. | Distance based bipartite matching, optimal matching in R, matching of treatment and control groups in observational studies, | DOI:10.1198/106186006X137047 | Free, Available for download, Freely available | https://github.com/markmfredrickson/optmatch | SCR_026185 | 2026-08-09 09:09:23 | 3 | |||||||||
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ENVI Resource Report Resource Website 1+ mentions |
ENVI (RRID:SCR_026160) | source code, software resource | Deep learnining based variational inference method to integrate scRNA-seq with spatial transcriptomics data. ENVI learns to reconstruct spatial onto for dissociated scRNA-seq data and impute unimagd genes onto spatial data. | integrate scRNA-seq with spatial transcriptomics data, integrate, scRNA-seq data, unimagd genes, | Free, Available for download, Freely available | SCR_026160 | 2026-08-09 09:09:24 | 1 | |||||||||||
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DropletUtils Resource Report Resource Website 100+ mentions |
DropletUtils (RRID:SCR_026136) | software toolkit, software resource | Software R package provides number of utility functions for handling single-cell (RNA-seq) data from droplet technologies such as 10X Genomics. This includes data loading from count matrices or molecule information files, identification of cells from empty droplets, removal of barcode-swapped pseudo-cells, and downsampling of the count matrix. | handling single-cell data, RNA-seq data, 10X Genomics, | Free, Available for download, Freely available | SCR_026136 | 2026-08-09 09:08:58 | 184 | |||||||||||
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Illustrator for Biological Sequences Resource Report Resource Website 10+ mentions |
Illustrator for Biological Sequences (RRID:SCR_026149) | IBS | software toolkit, software resource | Software package called illustrator of biological sequences. Can be used for representing organization of either protein or nucleotide sequences. Multiple options are provided, and biological sequences can be manipulated, recolored or rescaled in user-defined mode. Final representational artwork can be directly exported into publication-quality figure. Used as illustrator for presentation and visualization of biological sequences. Standalone package was implemented in JAVA, while the online service was implemented in HTML5 and JavaScript. Both the standalone package and online service are freely available | Illustrator, presentation, visualization, biological sequences, protein or nucleotide sequences, | PMID:26069263 | Free, Freely available | SCR_026149 | 2026-08-09 09:08:58 | 15 | |||||||||
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aactr Resource Report Resource Website 1+ mentions |
aactr (RRID:SCR_026245) | source code, software resource | Software R client for the Aggregate Content of ClinicalTrials.gov (AACT) database API. | R client, Aggregate Content of ClinicalTrials.gov, database API, | Free, Available for download, Freely available | SCR_026245 | 2026-08-09 09:09:01 | 1 | |||||||||||
|
gfastats Resource Report Resource Website 50+ mentions |
gfastats (RRID:SCR_026368) | source code, software resource | Standalone tool to compute assembly summary statistics and manipulate assembly sequences in FASTA, FASTQ or GFA [.gz] format. Gfastats stores assembly sequences internally in a GFA-like format. This feature allows gfastats to seamlessly convert FAST* to and from GFA [.gz] files. Gfastats can also build an assembly graph that can in turn be used to manipulate the underlying sequences following instructions provided by the user, while simultaneously generating key metrics for the new sequences. | summary statistics, genome assembly file manipulation, fasta, fastq, gfa, file conversion, | Rockefeller University ; German National Research Data Initiative |
PMID:35799367 | Free, Available for download, Freely available | SCR_026368 | 2026-08-09 09:09:04 | 55 | |||||||||
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FCS-GX Resource Report Resource Website 1+ mentions |
FCS-GX (RRID:SCR_026367) | source code, software resource | Software Foreign Contamination Screening - GX source code. Part of NCBI’s Foreign Contamination Screen (FCS) tool suite, optimized to identify and remove contaminant sequences in new genomes. | Foreign contamination screening, identify and remove contaminant sequences, sequences in new genomes, | National Center for Biotechnology Information of the National Library of Medicine | PMID:38409096 | Free, Available for download, Freely available | https://zenodo.org/records/10651084 | SCR_026367 | Foreign Contamination Screening - GX | 2026-08-09 09:09:27 | 6 | |||||||
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openMINDS chemicals metadata model Resource Report Resource Website |
openMINDS chemicals metadata model (RRID:SCR_026248) | openMINDS_chemicals, openMINDS chemicals | source code, software resource | Software repository hosts one of the metadata models of the openMINDS metadata framework. It defines modular metadata schemas for describing chemical substances and mixtures. | metadata schema, graph metadata model, descriptions, chemical substances, mixtures, |
is related to: EBRAINS is related to: openMINDS metadata framework |
European Union’s Horizon 2020 Framework Programme for Research and Innovation - Human Brain Project SGA1 720270; European Union’s Horizon 2020 Framework Programme for Research and Innovation - Human Brain Project SGA2 785907; European Union’s Horizon 2020 Framework Programme for Research and Innovation - Human Brain Project SGA3 945539; Helmholtz International BigBrain Analytics and Learning Laboratory (HIBALL) ; European Union’s Research and Innovation Program Horizon Europe - EBRAINS 2.0 101147319 |
Free, Available for download, Freely available | https://openminds-documentation.readthedocs.io/en/latest/schema_specifications/chemicals.html | SCR_026248 | 2026-08-09 09:09:24 | 0 | |||||||
|
BayesSpace Resource Report Resource Website 1+ mentions |
BayesSpace (RRID:SCR_026309) | software toolkit, software resource | Software R package for clustering and enhancing resolution of spatial gene expression experiments. Clusters low-dimensional representation of gene expression matrix, incorporating spatial prior to encourage neighboring spots to cluster together. The method can enhance the resolution of the low-dimensional representation into "sub-spots", for which features such as gene expression or cell type composition can be imputed. | Clusters low-dimensional representation of gene expression matrix, spatial transcriptomics, clustering and enhancing resolution of spatial gene expression, spacial gene expression, spacial gene expression resolution, | DOI:10.1038/s41587-021-00935-2 | Free, Available for download, Freely available | SCR_026309 | 2026-08-09 09:09:26 | 1 | ||||||||||
|
Qualimap 2 Resource Report Resource Website 10+ mentions |
Qualimap 2 (RRID:SCR_026258) | software application, software resource | Software platform-independent application written in Java and R that provides both Graphical User Inteface and command-line interface to facilitate quality control of alignment sequencing data and its derivatives like feature counts. Used for advanced multi-sample quality control for high-throughput sequencing data. | ChIP-seq, RNA-seq, quality control of alignment, advanced multi-sample quality control, high-throughput sequencing data, | DOI:10.1093/bioinformatics/btv566 | Free, Available for download, Freely available | SCR_026258 | 2026-08-09 09:09:24 | 14 | ||||||||||
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GreedyFHist Resource Report Resource Website 1+ mentions |
GreedyFHist (RRID:SCR_026477) | source code, software resource | Algorithm for registration of stained fresh frozen serial images. Used for registration of stained histology images. | Registration of stained histology images, stained fresh frozen serial images, images, histology images, images registration, | Free, Available for download, Freely available | SCR_026477 | 2026-08-09 09:09:08 | 1 | |||||||||||
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ggtext Resource Report Resource Website 1+ mentions |
ggtext (RRID:SCR_026470) | source code, software resource | Software R package that enhances text rendering in ggplot2 by allowing the use of Markdown, HTML, and rich text formatting for annotations, labels, and titles in plots. | Improved text rendering support, ggplot2, annotations, labels, titles, plots | works with: ggplot2 | Free, Available for download, Freely available | https://CRAN.R-project.org/package=ggtext, https://wilkelab.org/ggtext/ | SCR_026470 | 2026-08-09 09:09:08 | 3 | |||||||||
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ecodist Resource Report Resource Website 1+ mentions |
ecodist (RRID:SCR_026509) | software toolkit, software resource | Software R package as dissimilarity-based functions for ecological analysis. Used for analyzing ecological data. | dissimilarity-based functions, ecological analysis, analyzing ecological data, | Free, Available for download, Freely available | SCR_026509 | 2026-08-09 09:09:10 | 1 | |||||||||||
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chopper Resource Report Resource Website 10+ mentions |
chopper (RRID:SCR_026486) | source code, software resource | Software tool that combines the utility of NanoFilt and NanoLyse, for filtering sequencing reads based on quality, length, and contaminating sequences, delivers 7-fold speed up compared to the Python implementation, making use of the Rust-Bio library and Rust bindings to minimap2. | filtering sequencing reads, quality, length, contaminating sequences, | Flanders Institute for Biotechnology ; Belgium ; University of Antwerp |
PMID:37171891 | Free, Available for download, Freely available | SCR_026486 | 2026-08-09 09:09:29 | 14 | |||||||||
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AutoDockTools Resource Report Resource Website 1000+ mentions |
AutoDockTools (RRID:SCR_026401) | ADT | software application, software resource | Software graphical user interface to help to set up which bonds will treated as rotatable in the ligand and to analyze dockings. Used for automated docking with selective receptor flexibility. Designed to predict how small molecules, such as substrates or drug candidates, bind to receptor of known 3D structure. | automated docking, selective receptor flexibility, predict binding, bind to receptor of known 3D structure, ligand, analyze dockings | NIGMS RO1 GM069832 | PMID:19399780 | Free, Available for download, Freely available | https://autodock.scripps.edu/ | SCR_026401 | AutoDockTools: the Graphical User Interface for AutoDock | 2026-08-09 09:09:05 | 2063 | ||||||
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hgu133plus2 Resource Report Resource Website |
hgu133plus2 (RRID:SCR_026448) | software toolkit, software resource | Software R package for Affymetrix Affymetrix HG-U133_Plus_2 Array annotation data assembled using data from public repositories. | annotation data assembled package, | Free, Free available, | SCR_026448 | 2026-08-09 09:09:07 | 0 | |||||||||||
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NucleAIzer Resource Report Resource Website 1+ mentions |
NucleAIzer (RRID:SCR_026500) | source code, software resource | Software tool as parameter-free deep learning framework for nucleus segmentation using image style transfer. Cell segmentation tool. | nucleus segmentation, image style transfer, | NIGMS R35 GM122547; European Regional Development Funds ; Academy of Finland ; Swedish Research Council |
DOI:10.1016/j.cels.2020.04.003 | Free, Available for download, Freely available | SCR_026500 | 2026-08-09 09:09:09 | 4 | |||||||||
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NC4gate Resource Report Resource Website |
NC4gate (RRID:SCR_026445) | source code, software resource | Code for testing and operating NC4gate modules of modular gate system for autonomous control of rodent behavior. Fully customizable gate system that can be used in behavioral experiments involving rodent mazes (T-maze, Y-maze, radial arm, etc.). | OpenBehavior, modular gate system, autonomous control of rodent behavior, behavioral experiments, rodent mazes, | is listed by: OpenBehavior | DOI:10.1101/2024.11.22.624912 | Free, Available for download, Freely available | https://osf.io/uy7ez/, https://edspace.american.edu/openbehavior/project/nc4gate/ | SCR_026445 | 2026-08-09 09:09:07 | 0 | ||||||||
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timeROC Resource Report Resource Website 10+ mentions |
timeROC (RRID:SCR_026444) | software toolkit, software resource | Software R package for estimation of time-dependent ROC curve and area under time dependent ROC curve in the presence of censored data, with or without competing risks. Confidence intervals of AUCs and tests for comparing AUCs of two rival markers measured on the same subjects can be computed, using the iid-representation of the AUC estimator. | estimation of time-dependent ROC curve and area, presence of censored data, | Free, Available for download, Freely available | SCR_026444 | 2026-08-09 09:09:07 | 19 |
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