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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Machine Learning Made Easy Resource Report Resource Website 1+ mentions |
Machine Learning Made Easy (RRID:SCR_024439) | MLme | software resource, software toolkit | Software toolkit for Machine Learning Driven Data Analysis. Simplifies machine learning for data exploration, visualization and analysis. | Machine Learning Driven Data Analysis, | Federal Ministry of Education and Research of Germany ; NIDDK R01 DK127673; Swiss National Science Foundation ; Wings for Life Spinal Cord Research Foundation |
PMID:37461685 | Free, Available for download, Freely available | SCR_024439 | SciCrunch Registry | 2026-11-07 12:01:52 | 1 | ||||||||
|
stringi Resource Report Resource Website |
stringi (RRID:SCR_024319) | software resource, software toolkit | 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 | SciCrunch Registry | 2026-11-07 12:01:51 | 0 | |||||||||
|
VARNA Resource Report Resource Website 10+ mentions |
VARNA (RRID:SCR_024373) | software resource, software toolkit | 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 | SciCrunch Registry | , Visualization Applet for RNA, varna | 2026-11-07 12:01:59 | 12 | ||||||
|
variation graph Resource Report Resource Website |
variation graph (RRID:SCR_024369) | vg | software resource, software toolkit | 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 | SciCrunch Registry | variationgraph | 2026-11-07 12:02:09 | 0 | ||||||
|
bedr Resource Report Resource Website 1+ mentions |
bedr (RRID:SCR_024526) | software resource, software toolkit | 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 | SciCrunch Registry | 2026-11-07 12:02:00 | 1 | ||||||||||
|
Trinculo Resource Report Resource Website |
Trinculo (RRID:SCR_024384) | software resource, software toolkit | 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 | SciCrunch Registry | trinculo | 2026-11-07 12:02:09 | 0 | ||||||||
|
ROCit Resource Report Resource Website 1+ mentions |
ROCit (RRID:SCR_024420) | software resource, software toolkit | 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 | SciCrunch Registry | Receiver Operating Characteristic it | 2026-11-07 12:01:59 | 1 | |||||||||
|
Luna Resource Report Resource Website 1+ mentions |
Luna (RRID:SCR_024541) | software resource, software toolkit | 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 | SciCrunch Registry | 2026-11-07 12:01:52 | 8 | ||||||||||
|
Rgdal Resource Report Resource Website 1+ mentions |
Rgdal (RRID:SCR_024422) | software resource, software toolkit | 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 | SciCrunch Registry | , R geospatial data abstraction library, rgdal | 2026-11-07 12:01:51 | 6 | ||||||||
|
Mouse Single Nucleotide Polymorphism Database Resource Report Resource Website 1+ mentions |
Mouse Single Nucleotide Polymorphism Database (RRID:SCR_000033) | Mouse SNP | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. This website contains a database of the mouse SNP. DNA sequencing was performed along with genotyping. There is information on genotyping, mouse strain, and haplotype map. | dna sequence, genotype, mouse snp, nucleotide | NHGRI | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-20984 | SCR_000033 | SciCrunch Registry | Mouse Single Nucleotide Polymorphism, Mouse Single Nucleotide Polymorphism Database | 2026-11-07 12:01:53 | 3 | |||||||
|
rwave Resource Report Resource Website |
rwave (RRID:SCR_024302) | software resource, software toolkit | 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 | SciCrunch Registry | 2026-11-07 12:01:58 | 0 | |||||||||
|
umis Resource Report Resource Website 1+ mentions |
umis (RRID:SCR_024381) | software resource, software toolkit | 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 | SciCrunch Registry | 2026-11-07 12:01:52 | 3 | |||||||
|
survivalROC Resource Report Resource Website 10+ mentions |
survivalROC (RRID:SCR_024415) | software resource, software toolkit | 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 | SciCrunch Registry | survival Receiver Operating Characteristic | 2026-11-07 12:01:51 | 23 | |||||||||
|
sra-toolkit Resource Report Resource Website 100+ mentions |
sra-toolkit (RRID:SCR_024350) | software resource, software toolkit | 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 | SciCrunch Registry | NCBI SRA Toolkit | 2026-11-07 12:01:52 | 271 | ||||||
|
sumaclust Resource Report Resource Website 1+ mentions |
sumaclust (RRID:SCR_024352) | software library, software resource, software toolkit | Software tool aims to cluster sequences in a way that is fast and exact at the same time. | cluster sequences, fast and exact clustering, | is listed by: Debian | Free, Available for download, Freely available, | OMICS_19112 | https://sources.debian.org/src/sumaclust/ | SCR_024352 | SciCrunch Registry | 2026-11-07 12:02:09 | 2 | ||||||||
|
windrose Resource Report Resource Website |
windrose (RRID:SCR_024594) | software library, software resource, software toolkit | Software Python library to manage wind data, draw windroses also known as polar rose plots, and fit Weibull probability density functions. | manage wind data, draw windroses, polar rose plots, fit Weibull probability density functions, | Free, Available for download, Freely available | https://zenodo.org/records/8029782, https://github.com/python-windrose/windrose/tree/v1.9.0 | SCR_024594 | SciCrunch Registry | 2026-11-07 12:01:52 | 0 | ||||||||||
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MMV Im2Im Resource Report Resource Website 1+ mentions |
MMV Im2Im (RRID:SCR_024630) | software resource, software toolkit | 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 | SciCrunch Registry | MMV_Im2Im | 2026-11-07 12:01:52 | 1 | |||||||||
|
libswiss-perl Resource Report Resource Website |
libswiss-perl (RRID:SCR_024356) | software library, software resource, software toolkit | Software object oriented Perl library to handle Swiss-Prot entries | object oriented Perl library, handle Swiss-Prot entries, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/libswiss-perl/ | SCR_024356 | SciCrunch Registry | 2026-11-07 12:01:59 | 0 | |||||||||
|
ggridges Resource Report Resource Website 1+ mentions |
ggridges (RRID:SCR_024511) | software resource, software toolkit | 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 | SciCrunch Registry | 2026-11-07 12:01:52 | 8 | |||||||||
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gamm4 Resource Report Resource Website 1+ mentions |
gamm4 (RRID:SCR_024507) | software resource, software toolkit | 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 | SciCrunch Registry | 2026-11-07 12:01:52 | 4 |
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