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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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readucks Resource Report Resource Website |
readucks (RRID:SCR_024315) | software toolkit, software resource | Software package as Nanopore read de-multiplexer. | Nanopore, read de-multiplexer, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/readucks/ | SCR_024315 | 2026-08-15 11:28:14 | 0 | |||||||||
|
Machine Learning Made Easy Resource Report Resource Website 1+ mentions |
Machine Learning Made Easy (RRID:SCR_024439) | MLme | software toolkit, software resource | Software toolkit for Machine Learning Driven Data Analysis. Simplifies machine learning for data exploration, visualization and analysis. | Machine Learning Driven Data Analysis, | Wings for Life Spinal Cord Research Foundation ; NIDDK R01 DK127673; Federal Ministry of Education and Research of Germany ; Swiss National Science Foundation |
PMID:37461685 | Free, Available for download, Freely available | SCR_024439 | 2026-08-15 11:28:21 | 1 | ||||||||
|
stringi Resource Report Resource Website |
stringi (RRID:SCR_024319) | software toolkit, software resource | Software R package as collection of character string/text/natural language processing tools for pattern searching, random string generation, case mapping, string transliteration, concatenation, sorting, padding, wrapping, Unicode normalisation, date time formatting and parsing. | pattern searching, random string generation, case mapping, string transliteration, concatenation, sorting, padding, wrapping, Unicode normalisation, date time formatting and parsing, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/r-cran-stringi/ | SCR_024319 | 2026-08-15 11:28:14 | 0 | |||||||||
|
VARNA Resource Report Resource Website 10+ mentions |
VARNA (RRID:SCR_024373) | software toolkit, software resource | Software tool for automated drawing, visualization and annotation of secondary structure of RNA, designed as companion software for web servers and databases.Allows manual modification and structural annotation of resulting drawing using either interactive point and click approach, within web server or through command-line arguments. | Java, secondary structure of RNA drawing, secondary structure of RNA visualization, secondary structure of RNA annotation, | is listed by: Debian | PMID:19398448 | Free, Available for download, Freely available, | OMICS_04455 | https://sources.debian.org/src/varna/ | SCR_024373 | , Visualization Applet for RNA, varna | 2026-08-15 11:28:14 | 12 | ||||||
|
variation graph Resource Report Resource Website |
variation graph (RRID:SCR_024369) | vg | software toolkit, software resource | Software toolkit to improve read mapping by representing genetic variation in reference.Provides succinct encoding of sequences of many genomes. | read mapping, representing genetic variation in reference, encoding of sequences, genome | is listed by: Debian | PMID:30125266 | Free, Available for download, Freely available, | https://sources.debian.org/src/vg/ | SCR_024369 | variationgraph | 2026-08-15 11:28:14 | 0 | ||||||
|
bedr Resource Report Resource Website 1+ mentions |
bedr (RRID:SCR_024526) | software toolkit, software resource | Software R package for genomic interval processing.Genomic regions processing using open-source command line tools to perform genome arithmetic e.g indexing, formatting and merging. | genomic regions processing | Free, Available for download, Freely available | https://CRAN.R-project.org/package=bedr | SCR_024526 | 2026-08-15 11:28:15 | 1 | ||||||||||
|
Trinculo Resource Report Resource Website |
Trinculo (RRID:SCR_024384) | software toolkit, software resource | Software toolkit for carrying out genetic association for multi-catagory phenotypes. Implements multinomial and ordinal association incorporating covariates, conditional analysis, empirical and non-emperical priors and fine-mapping. | carrying out genetic association for multi-catagory phenotypes, incorporating covariates, conditional analysis, mapping | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/trinculo/ | SCR_024384 | trinculo | 2026-08-15 11:28:15 | 0 | ||||||||
|
ROCit Resource Report Resource Website 1+ mentions |
ROCit (RRID:SCR_024420) | software toolkit, software resource | Software R package for assessing overall diagnostic ability of binary classifier. Used to evaluate threshold bound metrics, construct confidence interval of ROC curve and AUC, construct empirical gains table, visualize ROC curve, visualize KS plot, visualize lift plot. | assessing overall diagnostic ability of binary classifier, evaluate threshold bound metrics, construct confidence interval of ROC curve and AUC, construct empirical gains table, visualize ROC curve, visualize KS plot, visualize lift plot, | is listed by: SoftCite | Free, Available for download, Freely available | SCR_024420 | Receiver Operating Characteristic it | 2026-08-15 11:28:23 | 1 | |||||||||
|
Luna Resource Report Resource Website 1+ mentions |
Luna (RRID:SCR_024541) | software toolkit, software resource | Software package for analysis of sleep signal data. Open source C/C++ software for manipulating and analyzing polysomnographic recordings, with focus on sleep EEG. | sleep signal data analysis, polysomnographic recordings manipulating and analysis, sleep EEG, | is related to: Moonlight | Free, Available for download, Freely available | SCR_024541 | 2026-08-15 11:28:15 | 8 | ||||||||||
|
Rgdal Resource Report Resource Website 1+ mentions |
Rgdal (RRID:SCR_024422) | software toolkit, software resource | Software R package provides bindings for the Geospatial Data Abstraction Library. Translator library for raster and vector geospatial data formats. | Translator library, geospatial data formats, Geospatial Data Abstraction Library bindings, | is listed by: SoftCite | Free, Available for download, Freely available | https://r-forge.r-project.org/projects/rgdal/ | SCR_024422 | , R geospatial data abstraction library, rgdal | 2026-08-15 11:28:15 | 6 | ||||||||
|
rwave Resource Report Resource Website |
rwave (RRID:SCR_024302) | software toolkit, software resource | Software R package provides environment for Time-Frequency analysis of 1-D signals. | Time-Frequency analysis of 1-D signals, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/r-cran-rwave/ | SCR_024302 | 2026-08-15 11:28:20 | 0 | |||||||||
|
umis Resource Report Resource Website 1+ mentions |
umis (RRID:SCR_024381) | software toolkit, software resource | Software tools for estimating expression in RNA-Seq data which performs sequencing of end tags of transcript, and incorporate molecular tags to correct for amplification bias. | estimating expression in RNA-Seq data, sequencing of end tags of transcript, incorporate molecular tags, correct for amplification bias, | is listed by: Debian | PMID:28263961 | Free, Available for download, Freely available, | OMICS_12783 | https://sources.debian.org/src/umis/ | SCR_024381 | 2026-08-15 11:28:21 | 3 | |||||||
|
survivalROC Resource Report Resource Website 10+ mentions |
survivalROC (RRID:SCR_024415) | software toolkit, software resource | Software R package to compute time dependent Receiver Operating Characteristic curve from censored survival data. | compute time dependent Receiver Operating Characteristic curve, censored survival data, | is listed by: SoftCite | Free, Available for download, Freely available | SCR_024415 | survival Receiver Operating Characteristic | 2026-08-15 11:28:23 | 23 | |||||||||
|
sra-toolkit Resource Report Resource Website 100+ mentions |
sra-toolkit (RRID:SCR_024350) | software toolkit, software resource | Software collection of tools and libraries for using data in the INSDC Sequence Read Archives.Used for long term storage of the next-generation sequence traces. | using data in the INSDC Sequence Read Archives, long term storage of the next-generation sequence traces, | is listed by: Debian | PMID:19906712 | Free, Available for download, Freely available, | OMICS_03771 | https://sources.debian.org/src/sra-toolkit/ | SCR_024350 | NCBI SRA Toolkit | 2026-08-15 11:28:14 | 271 | ||||||
|
MMV Im2Im Resource Report Resource Website 1+ mentions |
MMV Im2Im (RRID:SCR_024630) | software toolkit, software resource | Software Python package for image to image transformation in bioimaging applications. Can be used for semantic segmentation, instance segmentation, image restoration, image generation, and more. | image to image transformation, semantic segmentation, instance segmentation, image restoration, image generation, | DOI:10.48550/arXiv.2209.02498 | Free, Available for download, Freely available | SCR_024630 | MMV_Im2Im | 2026-08-15 11:28:15 | 1 | |||||||||
|
ggridges Resource Report Resource Website 1+ mentions |
ggridges (RRID:SCR_024511) | software toolkit, software resource | Software R package enables creation of Ridgeline plots in 'ggplot2' | creation of Ridgeline plots in 'ggplot2', | is listed by: SoftCite | Free, Available for download, Freely available | https://github.com/wilkelab/ggridges | SCR_024511 | 2026-08-15 11:28:15 | 8 | |||||||||
|
gamm4 Resource Report Resource Website 1+ mentions |
gamm4 (RRID:SCR_024507) | software toolkit, software resource | Software R package to estimate generalized additive mixed models. | estimate generalized additive mixed models, | is listed by: SoftCite | Free, Available for download, Freely available | SCR_024507 | 2026-08-15 11:28:21 | 4 | ||||||||||
|
Optimization Toolbox Resource Report Resource Website 1+ mentions |
Optimization Toolbox (RRID:SCR_024486) | software toolkit, software resource | Software package provides functions for finding parameters that minimize or maximize objectives while satisfying constraints. Toolbox includes solvers for linear programming, mixed integer linear programming, quadratic programming, second order cone programming, nonlinear programming, constrained linear least squares, nonlinear least squares, nonlinear equations. | Mathworks, finding parameters, minimize or maximize objectives, linear programming solver, mixed integer linear programming solver, quadratic programming solver, second order cone programming solver, nonlinear programming solver, constrained linear least squares solver, nonlinear least squares solver, nonlinear equations solver, | is listed by: SoftCite | Restricted | SCR_024486 | 2026-08-15 11:28:24 | 1 | ||||||||||
|
Lightning Pose Resource Report Resource Website |
Lightning Pose (RRID:SCR_024480) | software toolkit, software resource | Software video centric package for direct video manipulation. Semi supervised animal pose estimation algorithm, Bayesian post processing approach and deep learning package. Improved animal pose estimation via semi-supervised learning, Bayesian ensembling, and cloud-native open-source tools. | OpenBehavior, animal pose estimation algorithm, Bayesian post processing approach, direct video manipulation, | is listed by: OpenBehavior | Gatsby Charitable Foundation ; NINDS K99NS128075; Irma T Hirschl Trust ; NINDS NS075023; NINDS U19NS123716; NSF ; Simons Foundation |
PMID:37162966 | Free, Available for download, Freely available | https://edspace.american.edu/openbehavior/project/lightningpose/ | SCR_024480 | 2026-08-15 11:28:21 | 0 | |||||||
|
CopyKAT Resource Report Resource Website 50+ mentions |
CopyKAT (RRID:SCR_024512) | software toolkit, software resource | Software R package to estimate genomic copy number profiles at average genomic resolution of 5 Mb from read depth in high throughput single cell RNA sequencing data.Used for inference of genomic copy number and subclonal structure of human tumors from high-throughput single cell RNAseq data. | Inference of genomic copy number and subclonal structure of human tumors, high throughput single cell RNAseq data, | is listed by: SoftCite | PMID:33462507 | Free, Available for download, Freely available | SCR_024512 | , Copynumber Karyotyping of Aneuploid Tumors | 2026-08-15 11:28:15 | 84 |
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
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