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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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Plastimatch Resource Report Resource Website 1+ mentions |
Plastimatch (RRID:SCR_024168) | software resource, software library, software toolkit | Open source software for image computation with main focus on high performance volumetric registration, segmentation, and image processing of volumetric medical images. | image computation, volumetric registration, segmentation, image processing, volumetric medical images, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/plastimatch/, https://gitlab.com/plastimatch/plastimatch | SCR_024168 | 2026-08-01 12:08:47 | 4 | |||||||||
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pngquant Resource Report Resource Website |
pngquant (RRID:SCR_024169) | software resource, software library, software toolkit | Software command line utility and library for lossy compression of PNG images. The conversion reduces file sizes significantly and preserves full alpha transparency. Generated images are compatible with all web browsers and operating systems. | lossy compression of PNG images, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/pngquant/, https://github.com/kornelski/pngquant | SCR_024169 | 2026-08-01 12:08:58 | 0 | |||||||||
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qcumber Resource Report Resource Website |
qcumber (RRID:SCR_024203) | software resource, software library, software toolkit | Software for quality control, quality trimming, adapter removal and sequence content check of NGS data. | quality control, quality trimming, adapter removal, sequence content check, NGS data, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/qcumber/ | SCR_024203 | 2026-08-01 12:08:54 | 0 | |||||||||
|
PiGx-RNAseq Resource Report Resource Website |
PiGx-RNAseq (RRID:SCR_024160) | software resource, software toolkit | Software reproducible genomics analysis pipelines with GNU Guix. Used for analysis of RNA sequencing, chromatin immunoprecipitation sequencing, bisulfite-treated DNA sequencing, and single-cell resolution RNA sequencing. All pipelines process raw experimental data and generate reports containing publication-ready plots and figures, with interactive report elements and standard observables. | reproducible genomics analysis pipelines, GNU Guix, RNA sequencing analysis, chromatin immunoprecipitation sequencing analysis, bisulfite-treated DNA sequencing analysis, single cell resolution RNA sequencing analysis, | is listed by: Debian | PMID:30277498 | Free, Available for download, Freely available, | OMICS_33677 | https://sources.debian.org/src/pigx-rnaseq/ | SCR_024160 | pigx-rnaseq | 2026-08-01 12:08:53 | 0 | ||||||
|
mediana Resource Report Resource Website |
mediana (RRID:SCR_024281) | software resource, software toolkit | Software R package for clinical trial simulations based on Clinical Scenario Evaluation approach. The package supports broad class of data models, analysis strategies and commonly used evaluation criteria. | clinical trial simulations, Clinical Scenario Evaluation approach, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/r-cran-mediana/ | SCR_024281 | 2026-08-01 12:09:01 | 0 | |||||||||
|
picopore Resource Report Resource Website |
picopore (RRID:SCR_024161) | software resource, software library, software toolkit | Software tool for reducing the storage size of Oxford Nanopore Technologies datasets without loss of functionality. | reducing storage size, Oxford Nanopore Technologies datasets, without functionality loss, | is listed by: Debian | PMID:28413619 | Free, Available for download, Freely available, | https://sources.debian.org/src/picopore/ | SCR_024161 | 2026-08-01 12:08:58 | 0 | ||||||||
|
itertools Resource Report Resource Website |
itertools (RRID:SCR_024282) | software resource, software toolkit | Software R package for creating iterators, many patterned after functions in the Python itertools module, and others patterned after functions in the 'snow' package. | creating iterators, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/r-cran-itertools/ | SCR_024282 | 2026-08-01 12:08:49 | 0 | |||||||||
|
PHYLOViZ Resource Report Resource Website 50+ mentions |
PHYLOViZ (RRID:SCR_024162) | software resource, software library, software toolkit | Platform independent JAVA software for analysis of sequence based typing methods that generate allelic profiles and their associated epidemiological data.Phylogenetic inference and data visualization for sequence based typing methods. | JAVA, phylogenetic inference, data visualization, sequence based typing methods, generate allelic profiles and their associated epidemiological data, | is listed by: Debian | PMID:22568821 | Free, Available for download, Freely available, | https://sources.debian.org/src/phyloviz-core/ | SCR_024162 | 2026-08-01 12:08:47 | 74 | ||||||||
|
rbgl Resource Report Resource Website |
rbgl (RRID:SCR_024251) | software resource, software toolkit | Software R package as interface to the graph algorithms contained in the BOOST library. | interface to the graph algorithm, BOOST library, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/r-bioc-rbgl/ | SCR_024251 | 2026-08-01 12:09:00 | 0 | |||||||||
|
pcaMethods Resource Report Resource Website 10+ mentions |
pcaMethods (RRID:SCR_024252) | software resource, software toolkit | Software R package providing PCA methods for incomplete data. Provides Bayesian PCA, Probabilistic PCA, Nipals PCA, Inverse Non-Linear PCA and conventional SVD PCA. Cluster based method for missing value estimation is included for comparison. BPCA, PPCA and NipalsPCA may be used to perform PCA on incomplete data as well as for accurate missing value estimation. | PCA methods for incomplete data, missing value estimation, | is listed by: Debian | PMID:17344241 | Free, Available for download, Freely available, | OMICS_14344 | https://sources.debian.org/src/r-bioc-pcamethods/ | SCR_024252 | pcamethods | 2026-08-01 12:08:55 | 11 | ||||||
|
rcpi Resource Report Resource Website |
rcpi (RRID:SCR_024253) | software resource, software toolkit | Software R package as molecular informatics toolkit with integration of bioinformatics and chemoinformatics tools for drug discovery. | drug discovery, bioinformatics and chemoinformatics integration, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/r-bioc-rcpi/ | SCR_024253 | 2026-08-01 12:09:00 | 0 | |||||||||
|
rgsepd Resource Report Resource Website |
rgsepd (RRID:SCR_024256) | software resource, software toolkit | Software R package to help disambiguate transcriptome samples by automating differential expression, then gene set enrichment, and finally N-dimensional projection to quantify in which ways each sample is like either treatment group. | disambiguate transcriptome samples, automating differential expression, gene set enrichment, N-dimensional projection, treatment group, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/r-bioc-rgsepd/ | SCR_024256 | 2026-08-01 12:09:00 | 0 | |||||||||
|
makecdfenv Resource Report Resource Website 1+ mentions |
makecdfenv (RRID:SCR_024248) | software resource, software toolkit | Software R package has two functions. One reads Affymetrix chip description file and creates hash table environment containing location/probe set membership mapping. The other creates package that automatically loads that environment. | read Affymetrix chip description file, create hash table environment, location, probe, set membership mapping, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/r-bioc-makecdfenv/ | SCR_024248 | 2026-08-01 12:08:55 | 1 | |||||||||
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beeswarm Resource Report Resource Website |
beeswarm (RRID:SCR_024262) | software resource, software toolkit | Software R package implementing bee swarm plots. Bee swarm plot is one-dimensional scatter plot like "stripchart", but with closely packed, non overlapping points. | bee swarm plots, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/r-cran-beeswarm/ | SCR_024262 | an Alternative to Stripchart, r-cran-beeswarm, The Bee Swarm Plot, beeswarm: The Bee Swarm Plot | 2026-08-01 12:08:55 | 0 | ||||||||
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adephylo Resource Report Resource Website 1+ mentions |
adephylo (RRID:SCR_024267) | software resource, software toolkit | Software R package provides multivariate tools to analyze comparative data. Analysis of comparative evolutionary data. Used for investigating phylogenetic signal in biological traits. | analyze comparative data, investigating phylogenetic signal, biological traits, investigating phylogenetic signal in biological traits, comparative evolutionary data analysis, | is listed by: Debian | PMID:20525823 | Free, Available for download, Freely available, | OMICS_08682 | https://sources.debian.org/src/r-cran-adephylo/ | SCR_024267 | 2026-08-01 12:09:00 | 3 | |||||||
|
tfbstools Resource Report Resource Website 10+ mentions |
tfbstools (RRID:SCR_024260) | software resource, software toolkit | Software R package for analysis and manipulation of transcription factor binding sites. It includes matrices conversion between Position Frequency Matirx (PFM), Position Weight Matirx (PWM) and Information Content Matrix (ICM). It can also scan putative TFBS from sequence/alignment, query JASPAR database and provides a wrapper of de novo motif discovery software. | analysis and manipulation of transcription factor binding sites, transcription factor binding sites analysis, transcription factor binding sites manipulation, | is listed by: Debian | PMID:26794315 | Free, Available for download, Freely available, | OMICS_11082 | https://sources.debian.org/src/r-bioc-tfbstools/ | SCR_024260 | TFBSTools | 2026-08-01 12:09:00 | 16 | ||||||
|
DendroPy Resource Report Resource Website 10+ mentions |
DendroPy (RRID:SCR_024197) | software resource, software library, software toolkit | Software Python library for phylogenetic computing. Provides classes and functions for simulation, processing, and manipulation of phylogenetic trees and character matrices, and supports the reading and writing of phylogenetic data in range of formats, such as NEXUS, NEWICK, NeXML, Phylip, FASTA., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | phylogenetic computing, manipulation of phylogenetic trees, reading and writing of phylogenetic data, | is listed by: Debian | PMID:20421198 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_08877 | https://sources.debian.org/src/python3-dendropy/ | SCR_024197 | python-dendropy | 2026-08-01 12:08:59 | 15 | ||||||
|
bsgenome Resource Report Resource Website 10+ mentions |
bsgenome (RRID:SCR_024230) | software resource, software toolkit | Software R package provides infrastructure shared by all the Biostrings-based genome data packages. | infrastructure shared, Biostrings-based genome data packages, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/r-bioc-bsgenome/ | SCR_024230 | 2026-08-01 12:08:59 | 10 | |||||||||
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ctc Resource Report Resource Website |
ctc (RRID:SCR_024232) | software resource, software toolkit | Software R package for export and import classification trees and clusters to other programs. | export and import classification trees and clusters, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/r-bioc-ctc/ | SCR_024232 | 2026-08-01 12:08:59 | 0 | |||||||||
|
geneplotter Resource Report Resource Website |
geneplotter (RRID:SCR_024234) | software resource, software toolkit | Software R package provides functions for plotting genomic data | functions for plotting genomic data | is listed by: Debian | Free, Available for download, Freely available, | OMICS_15854 | https://sources.debian.org/src/r-bioc-geneplotter/ | SCR_024234 | 2026-08-01 12:08:54 | 0 |
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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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