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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.

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Resource Name Proper Citation Abbreviations Resource Type Description Keywords Resource Relationships Related Condition Funding Defining Citation Availability Specification URL Alternate IDs Alternate URLs Old URLs Parent Organization Resource ID Synonyms Record Last Update Mentions Count
hms
 
Resource Report
Resource Website
hms (RRID:SCR_024294) software toolkit, software resource Software R package implements S3 class for storing and formatting time-of-day values, based on the 'difftime' class. storing and formatting time-of-day values, is listed by: Debian Free, Available for download, Freely available, https://sources.debian.org/src/r-cran-hms/ SCR_024294 2026-08-09 09:08:51 0
Thermo Scientific Maps Software
 
Resource Report
Resource Website
1+ mentions
Thermo Scientific Maps Software (RRID:SCR_024446) software toolkit, software resource Correlative electron microscopy and cross-platform imaging automation software. Imaging and correlative workflow software suite compatible with full line of Thermo Scientific SEM, DualBeam (FIB SEM) and TEM platforms. Correlative electron microscopy, cross-platform imaging automation, imaging and correlative workflow, Restricted SCR_024446 Maps Software 2026-08-09 09:09:03 5
sambamba
 
Resource Report
Resource Website
50+ mentions
sambamba (RRID:SCR_024328) software toolkit, software resource Software tools for working with SAM/BAM data working with SAM/BAM data, is listed by: Debian PMID:25697820 Free, Available for download, Freely available, OMICS_07586 https://sources.debian.org/src/sambamba/ SCR_024328 2026-08-09 09:08:26 59
seq-seq-pan
 
Resource Report
Resource Website
seq-seq-pan (RRID:SCR_024343) software toolkit, software resource Software workflow for SEQuential alignment of SEQuences to build PAN-genome data structure and whole-genome-alignment. SEQuential alignment, SEQuences, build PAN-genome data structure, is listed by: Debian PMID:29334898 Free, Available for download, Freely available, https://sources.debian.org/src/seq-seq-pan/ SCR_024343 2026-08-09 09:08:52 0
SIMA
 
Resource Report
Resource Website
1+ mentions
SIMA (RRID:SCR_024466) software toolkit, software resource Software Python package for analysis of dynamic fluorescence microscopy data. fluorescence microscopy data, microscopy data analysis, Free, Available for download, Freely available SCR_024466 2026-08-09 09:09:04 2
microbiome
 
Resource Report
Resource Website
10+ mentions
microbiome (RRID:SCR_024699) software toolkit, software resource Software R package for use in microbiome analysis. Used to provide comprehensive collection of tools and tutorials, with particular focus on amplicon sequencing data. amplicon sequencing data, microbiome analysis, is listed by: Bioconductor Free, Available for download, Freely available https://microbiome.github.io/tutorials/, https://github.com/microbiome/microbiome/, SCR_024699 2026-08-09 09:09:05 22
genetics
 
Resource Report
Resource Website
1+ mentions
genetics (RRID:SCR_024279) software toolkit, software resource Software R package for handling genetic data. Includes classes to represent genotypes and haplotypes at single markers up to multiple markers on multiple chromosomes. Function include allele frequencies, flagging homo/heterozygotes, flagging carriers of certain alleles, estimating and testing for Hardy-Weinberg disequilibrium, estimating and testing for linkage disequilibrium. handling genetic data, allele frequencies, flagging homo/heterozygotes, flagging carriers of certain alleles, estimating and testing for Hardy-Weinberg disequilibrium, estimating and testing for linkage disequilibrium, is listed by: Debian Free, Available for download, Freely available, https://sources.debian.org/src/r-cran-genetics/ SCR_024279 2026-08-09 09:08:50 3
scCustomize
 
Resource Report
Resource Website
100+ mentions
scCustomize (RRID:SCR_024675) software toolkit, software resource Software R package for custom visualizations and functions for streamlined analyses of single cell sequencing. custom visualizations, single cell sequencing, single cell sequencing analysis, is listed by: CRAN Free, Available for download, Freely available https://CRAN.R-project.org/package=scCustomize, https://github.com/samuel-marsh/scCustomize, https://doi.org/10.5281/zenodo.5706430 SCR_024675 2026-08-09 09:08:58 100
readseq
 
Resource Report
Resource Website
1+ mentions
readseq (RRID:SCR_024313) software toolkit, software resource Software package as Java based common sequence file format reader and sequence file manipulation. Java, common sequence file format reader, sequence file manipulation, is listed by: Debian Free, Available for download, Freely available, https://sources.debian.org/src/rdp-readseq/ SCR_024313 2026-08-09 09:08:26 6
rsvd
 
Resource Report
Resource Website
rsvd (RRID:SCR_024303) software toolkit, software resource Software R package used to compute near optimal low-rank singular value decomposition of massive data sets with high accuracy. Provides several randomized matrix algorithms such as randomized singular value decomposition (rsvd), randomized principal component analysis (rpca), randomized robust principal component analysis (rrpca), randomized interpolative decomposition (rid), and the randomized CUR decomposition (rcur). In addition several plot functions are provided. randomized singular value decomposition, singular value decomposition, compute optimal low-rank singular value decomposition, massive data sets, is listed by: Debian DOI:10.18637/jss.v089.i11 Free, Available for download, Freely available, https://sources.debian.org/src/r-cran-rsvd/ SCR_024303 randomized singular value decomposition 2026-08-09 09:08:51 0
riskRegression
 
Resource Report
Resource Website
10+ mentions
riskRegression (RRID:SCR_024424) software toolkit, software resource Software R package provides risk regression models and prediction scores for survival analysis with competing risks. risk prediction, risk regression models, prediction scores, survival analysis, competing risks, is listed by: SoftCite Free, Available for download, Freely available https://github.com/tagteam/riskRegression SCR_024424 2026-08-09 09:08:54 15
surveillance
 
Resource Report
Resource Website
surveillance (RRID:SCR_024304) software toolkit, software resource Software R package for modeling and monitoring of time series of counts, proportions and categorical data, as well as for modeling of continuous-time point processes of epidemic phenomena. modeling and monitoring of time series of counts, proportions and categorical data, modeling of continuous-time point processes, is listed by: Debian DOI:10.1007/s00180-007-0074-8 Free, Available for download, Freely available, https://sources.debian.org/src/r-cran-surveillance/ SCR_024304 2026-08-09 09:08:26 0
tsne
 
Resource Report
Resource Website
1+ mentions
tsne (RRID:SCR_024305) software toolkit, software resource Softare R package as implementation of the t-SNE algorithm. t-SNE algorithm implementation, R is listed by: Debian Free, Available for download, Freely available, https://sources.debian.org/src/r-cran-tsne/ SCR_024305 2026-08-09 09:09:02 6
RapGreen
 
Resource Report
Resource Website
1+ mentions
RapGreen (RRID:SCR_024426) PMID:34568824 software toolkit, software resource Software phylogenetic tree analysis package. Phylogenetic tree management, exploration and display package. Phylogenetic tree management, phylogenetic tree analysis, is listed by: SoftCite Free, Available for download, Freely available https://github.com/SouthGreenPlatform/rap-green/wiki, http://southgreenplatform.github.io/rap-green/ SCR_024426 2026-08-09 09:09:03 1
rotl
 
Resource Report
Resource Website
rotl (RRID:SCR_024306) software toolkit, software resource Software R package provides interface to the 'Open Tree of Life' API to retrieve phylogenetic trees, information about studies used to assemble the synthetic tree, and utilities to match taxonomic names to 'Open Tree identifiers'. The 'Open Tree of Life' aims at assembling comprehensive phylogenetic tree for all named species. interface to 'Open Tree of Life' API, retrieve phylogenetic trees, retrieve information about studies used to assemble synthetic tree, retrieve utilities to match taxonomic names, is listed by: Debian Free, Available for download, Freely available, OMICS_28401 https://sources.debian.org/src/r-cran-rotl/ SCR_024306 2026-08-09 09:08:51 0
snowfall
 
Resource Report
Resource Website
snowfall (RRID:SCR_024309) software toolkit, software resource Software R package usability wrapper around snow for easier development of parallel R programs. This package offers e.g. extended error checks, and additional functions. All functions work in sequential mode if no cluster is present or wished. Package is also designed as connector to the cluster management tool sfCluster, but can also used without it. usability wrapper around snow, development of parallel R programs, extended error checks, is listed by: Debian Free, Available for download, Freely available, https://sources.debian.org/src/r-cran-snowfall/ SCR_024309 2026-08-09 09:08:51 0
parmigene
 
Resource Report
Resource Website
1+ mentions
parmigene (RRID:SCR_024285) software toolkit, software resource Software R package for parallel estimation of mutual information based on entropy estimates from k-nearest neighbors distances and algorithms for reconstruction of gene regulatory networks. parallel estimation, mutual information, entropy estimates from k-nearest neighbors distances, reconstruction of gene regulatory networks, is listed by: Debian PMID:21531770 Free, Available for download, Freely available, OMICS_16887 https://sources.debian.org/src/r-cran-parmigene/ SCR_024285 Parallel Mutual Information Estimation for Gene Network Reconstruction 2026-08-09 09:08:51 1
pcapp
 
Resource Report
Resource Website
1+ mentions
pcapp (RRID:SCR_024287) software toolkit, software resource Software R package provides functions for principal component analysis by projection pursuit. principal component analysis, projection pursuit, is listed by: Debian Free, Available for download, Freely available, https://sources.debian.org/src/r-cran-pcapp/ SCR_024287 2026-08-09 09:09:02 1
psychotree
 
Resource Report
Resource Website
psychotree (RRID:SCR_024288) software toolkit, software resource Software R package for recursive partitioning based on psychometric models, employing general MOB algorithm to obtain Bradley-Terry trees, Rasch trees, rating scale and partial credit trees, and MPT trees, trees for 1PL, 2PL, 3PL and 4PL models and generalized partial credit models. recursive partitioning based on psychometric models, recursive partitioning, psychometric models, is listed by: Debian Free, Available for download, Freely available, https://sources.debian.org/src/r-cran-psychotree/ SCR_024288 2026-08-09 09:08:51 0
saint
 
Resource Report
Resource Website
100+ mentions
saint (RRID:SCR_024324) SAINT software toolkit, software resource Software package for assigning confidence scores to protein-protein interactions based on quantitative proteomics data in AP-MS experiments. assigning confidence scores, protein-protein interactions, quantitative proteomics data, AP-MS experiments, is listed by: Debian Free, Available for download, Freely available, OMICS_16243 https://sources.debian.org/src/saint/ SCR_024324 Significance Analysis of INTeractome 2026-08-09 09:08:52 231

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