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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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germline flow Resource Report Resource Website |
germline flow (RRID:SCR_021906) | software resource | High performance of GPU accelerated variant calling tool in genome data analysis. | variant calling, acceleration tool, GPU-based acceleration, GATK pipeline | Free, Freely available | SCR_021907 | SCR_021906 | SciCrunch Registry | germline_flow | 2026-10-31 12:18:16 | 0 | |||||||||
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Motif Mutation Analysis for Regulatory Genomic Elements Resource Report Resource Website 500+ mentions |
Motif Mutation Analysis for Regulatory Genomic Elements (RRID:SCR_021902) | MMARGE | data analysis software, data processing software, software application, software resource, software toolkit | Software package that integrates genome wide genetic variation with epigenetic data to identify collaborative transcription factor pairs. Optimized to work with chromatin accessibility assays such as ATAC-seq or DNase I hypersensitivity, as well as transcription factor binding data collected by ChIP-seq. Used to identify combinations of cell type specific transcription factors while simultaneously interpreting functional effects of non-coding genetic variation. | genome wide genetic variation, epigenetic data, identify collaborative transcription factor pairs, interpreting functional effects, non-coding genetic variation | NCI CA173903; NHLBI R00 123485; NIDDK DK091183; NIGMS GM085764 |
PMID:29893919 | Free, Available for download, Freely available | SCR_021902 | SciCrunch Registry | 2026-10-31 12:18:18 | 608 | ||||||||
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CancerMIRNome Resource Report Resource Website 10+ mentions |
CancerMIRNome (RRID:SCR_022092) | data access protocol, data or information resource, database, software resource, web service | Web server for cancer miRNome interactive analysis and visualization based on human miRNome data of cancer types from The Cancer Genome Atlas, and public cancer circulating miRNome profiling datasets from NCBI Gene Expression Omnibus and ArrayExpress. Comprehensive database for interactive analysis and visualization of miRNA expression profiles. | cancer miRNome interactive analysis, human miRNome data, cancer data, miRNA expression profiles |
is related to: The Cancer Genome Atlas is related to: ArrayExpress |
National Natural Science Foundation of China ; Riverside Faculty Start-up Fund ; Science and Technology Project of Guizhou Province ; UC Academic Senate CoR Research Grant ; UC Cancer Research Coordinating Committee Competition Award ; United States Department of Agriculture |
DOI:10.1093/nar/gkab784 | Free, Freely available | SCR_022092 | SciCrunch Registry | 2026-10-31 12:18:20 | 48 | ||||||||
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CEU Mass Mediator Resource Report Resource Website 10+ mentions |
CEU Mass Mediator (RRID:SCR_022090) | CMM | data access protocol, software resource, web service | Software tool for searching metabolites in different databases including Kegg, HMDB, LipidMaps, Metlin, NP Atlas, KNApSAcK, MINE and in house library. Designed for searches through experimental masses obtained from mass spectrometry techniques. Metabolite annotation tool that uses expert system to score putative annotation based on analytical information acquired under different configurations. | Metabolite annotation, searching metabolites in different databases, experimental masses, mass spectrometry, | DOI:10.1016/j.jpba.2018.02.046 DOI:10.1021/acs.jproteome.8b00720 |
Free, Freely available | SCR_022090 | SciCrunch Registry | CEU Mass Mediator version 3.0, CMM 2.0, CMM 3.0, CEU Mass Mediator 2.0 | 2026-10-31 12:18:24 | 35 | ||||||||
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Rcorrector Resource Report Resource Website 10+ mentions |
Rcorrector (RRID:SCR_022011) | data analysis software, data processing software, software application, software resource | Software tool as kmer based error correction method for RNAseq data. Can also be applied to other types of sequencing data where read coverage is nonuniform, such as single cell sequencing. Used for error correction for Illumina RNAseq reads. | RNA-seq, k-mer, random sequencing errors correction, kmer based error correction, RNA-seq data, sequencing data, nonuniform read coverage, Illumina RNAseq reads error correction | NSF ABI1159078; NSF ABI1356078 |
DOI:10.1186/s13742-015-0089-y | Free, Available for download, Freely available | SCR_022011 | SciCrunch Registry | RNA-seq error CORRECTOR | 2026-10-31 12:18:17 | 39 | ||||||||
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Creative Biogene Aerobic Cultivation Service Resource Resource Report Resource Website |
Creative Biogene Aerobic Cultivation Service Resource (RRID:SCR_022099) | service resource | Aerobic cultivation services to culture various microorganisms that can be isolated from readily available sources. | Creative Biogene, Aerobic Cultivation, Aerobic cultivation services, biomedical service | has parent organization: Creative Biogene | Restricted | SCR_022099 | SciCrunch Registry | 2026-10-31 12:18:26 | 0 | ||||||||||
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ntCard Resource Report Resource Website 1+ mentions |
ntCard (RRID:SCR_022010) | software resource | Software tool for estimating k-mer coverage histogram of genomics data. Streaming algorithm for estimating frequencies of k-mers in genomics datasets. | K-mer, estimating k-mer coverage histogram, genomics data, estimating frequencies of k-mers | British Columbia Cancer Foundation ; Genome British Columbia ; Genome Canada ; NHGRI R01 HG007182 |
DOI:10.1093/bioinformatics/btw832 | Free, Available for download, Freely available | https://github.com/bcgsc/ntCard | SCR_022010 | SciCrunch Registry | 2026-10-31 12:18:26 | 1 | ||||||||
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Creative Biogene Strain Anaerobic Culture Service Resource Resource Report Resource Website |
Creative Biogene Strain Anaerobic Culture Service Resource (RRID:SCR_022097) | service resource | Service for anaerobic bacteria cultivation and culture using variety of culture media and culture conditions. Includes collection, strain cultivation, isolation, identification and strain preservation. | Strain Anaerobic Culture, anaerobic bacteria cultivation, collection, strain isolation, identification and strain preservation, Creative Biogene, biomedical service | has parent organization: Creative Biogene | Restricted | SCR_022097 | SciCrunch Registry | 2026-10-31 12:18:25 | 0 | ||||||||||
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AHo’s Amazing Atlas of Antibody Anatomy Resource Report Resource Website |
AHo’s Amazing Atlas of Antibody Anatomy (RRID:SCR_022095) | AAAAA | data access protocol, software resource, web service | AAAAA aims to become the ultimate tool for antibody structural analysis, modelling and engineering. | antibody structural analysis, modelling and engineering, antibody anatomy atlas | Free, Freely available | SCR_022095 | SciCrunch Registry | 2026-10-31 12:18:18 | 0 | ||||||||||
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Connect TBI Resource Report Resource Website |
Connect TBI (RRID:SCR_022009) | data or information resource, portal, topical portal | Portal for traumatic brain injury data. Common Data Elements (CDEs) and Unique Data Elements (UDEs) for digital neuropathological data and clinical data that will be collected in all CONNECT-TBI center projects. Goal is to establish multi-center, digital neuropathological data and clinical data reporting network with case accrual from each center project. Collected neuropathological data and clinical data available by sharing with center site investigators approved by Administrative Core and by submitting into FITBIR. Central TBI data repository by collecting digital neuropathological data and clinical data from TBI cases and normal controls at each center and posting library of their holdings. | brain injury, traumatic brain injury, digital neuropathological data, clinical data | Free, Freely available | SCR_022009 | SciCrunch Registry | Connect-TBI, THE COLLABORATIVE NEUROPATHOLOGY NETWORK CHARACTERIZING OUTCOMES OF TBI | 2026-10-31 12:18:19 | 0 | ||||||||||
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Neuronanalyser Resource Report Resource Website 1+ mentions |
Neuronanalyser (RRID:SCR_022007) | 2d time-series analysis software, data analysis software, data processing software, software application, software resource, time-series analysis software | Software analysis toolkit for tracking blobs and extracting intensity values from imaging data, designed for use with ratiometric fluorescent sensors. | tracking blobs, extracting intensity values, imaging data, ratiometric fluorescent sensors | ERC - European Research Council 269058 | Free, Available for download, Freely available | SCR_022007 | SciCrunch Registry | 2026-10-31 12:18:17 | 3 | ||||||||||
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PLUMED 2 Resource Report Resource Website 10+ mentions |
PLUMED 2 (RRID:SCR_021952) | software library, software resource, software toolkit | Open source, community developed library that provides range of different methods, which include enhanced sampling algorithms, free energy methods, tools to analyze vast amounts of data produced by molecular dynamics simulations. PLUMED 2 is complete rewrite of the code in object oriented programming language C plus plus. This new version introduces greater flexibility and greater modularity, which both extends its core capabilities and makes it far easier to add new methods and CVs. It also has simpler interface with the MD engines and provides single software library containing both tools and core facilities. | Molecular dynamics analysis, enhanced sampling algorithms, free energy methods, PLUMED | CeCAM ; European Research Council ; Marie Curie Intra European Fellowship ; MIUR grant FIRB ; SISSA |
DOI:10.1016/j.cpc.2013.09.018 | Free, Available for download, Freely available | www.plumed-code.org | SCR_021952 | SciCrunch Registry | PLUgin for MolEcular Dynamics 2 | 2026-10-31 12:18:23 | 34 | |||||||
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StAMPP Resource Report Resource Website 1+ mentions |
StAMPP (RRID:SCR_022022) | data analysis software, data processing software, software application, software resource | Software R package for statistical analysis of mixed ploidy populations.Used for calculation of population structure and differentiation based on single nucleotide polymorphism genotype data from populations of any ploidy level, and/or mixed ploidy levels. | statistical analysis, mixed ploidy populations, single nucleotide polymorphism genotype data | is related to: R Project for Statistical Computing | Australian Postgraduate Award ; Dairy Futures CRC ; Geoffrey Gardiner Foundation ; Meat and Livestock Australia ; New Zealand Agriseeds ; Christchurch ; New Zealand ; Victorian Department of Primary Industries |
DOI:10.1111/1755-0998.12129 | Free, Available for download, Freely available | https://github.com/lpembleton/StAMPP | SCR_022022 | SciCrunch Registry | 2026-10-31 12:18:24 | 6 | |||||||
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hierfstat Resource Report Resource Website 10+ mentions |
hierfstat (RRID:SCR_022021) | data analysis software, data processing software, software application, software resource | Software R package for estimation and tests of hierarchical F statistics.Used to estimate hierarchical F-statistics from haploid or diploid genetic data with any numbers of levels in hierarchy.Intended for analysis of population structure using genetic markers. | estimation and tests of hierarchical F statistics, haploid or diploid genetic data, analysis of population structure, genetic markers | DOI:10.1093/genetics/144.4.1933 DOI:10.1534/genetics.116.198424 |
Free, Available for download, Freely available | https://github.com/jgx65/hierfstat | SCR_022021 | SciCrunch Registry | 2026-10-31 12:18:17 | 11 | |||||||||
|
BayeScan Resource Report Resource Website 50+ mentions |
BayeScan (RRID:SCR_022018) | data analysis software, data processing software, software application, software resource | Software tool to identify candidate loci under natural selection from genetic data, using differences in allele frequencies between populations. | identify candidate loci under natural selection, genetic data, differences in allele frequencies between populations |
has parent organization: University of Bern; Bern; Switzerland has parent organization: SIB Swiss Institute of Bioinformatics |
Swiss National Science Foundation ; University of Bern Research Foundation |
DOI:10.1534/genetics.108.092221 DOI:10.1111/j.1365-294X.2010.04820.x DOI:10.1111/j.1365-294X.2011.05015.x |
Free, Available for Download, Freely available | SCR_022018 | SciCrunch Registry | 2026-10-31 12:18:26 | 89 | ||||||||
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HiCExplorer Resource Report Resource Website 100+ mentions |
HiCExplorer (RRID:SCR_022111) | data analysis software, data processing software, software application, software resource | Software tool to analyse Hi-C and capture Hi-C data. Command line suite of tools to process, normalize and visualize Hi-C data. | Hi-C, process, normalize, visualize, Hi-C data, capture Hi-C data | Free, Available for download, Freely available | SCR_022111 | SciCrunch Registry | 2026-10-31 12:18:21 | 133 | |||||||||||
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Genie 2000 Basic Resource Report Resource Website 1+ mentions |
Genie 2000 Basic (RRID:SCR_021933) | data acquisition software, data analysis software, data processing software, software application, software resource | Software tool as comprehensive environment for data acquisition, display and analysis of gamma and alpha spectrometry data. | Data acquisition, display, analysis, gamma and alpha spectrometry data | Restricted | SCR_021933 | SciCrunch Registry | Genie 2000 Basic Spectroscopy Software, Marion Technologies Genie 2000 Basic Spectroscopy Software, Marion Technologies Genie 2000 Basic | 2026-10-31 12:18:23 | 3 | ||||||||||
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Creative Peptides Cosmetic Peptides Service Resource Resource Report Resource Website 1+ mentions |
Creative Peptides Cosmetic Peptides Service Resource (RRID:SCR_022108) | service resource | Service to synthesize cosmetic peptides. Provides any level of cosmetic peptides, including GMP grades, using advanced peptide synthesis equipment. Used for development and production of cosmetic peptides. | Creative Peptides, biomedical service, cosmetic peptide synthesis, cosmetic peptide company, cosmetic ingredients peptides | has parent organization: Creative Peptides | Restricted | SCR_022108 | SciCrunch Registry | 2026-10-31 12:18:26 | 1 | ||||||||||
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Creative Peptides Backbone Cyclized Peptides Service Resource Resource Report Resource Website |
Creative Peptides Backbone Cyclized Peptides Service Resource (RRID:SCR_022106) | service resource | Service for chemical synthesis and biosynthesis. Scientists will tailor the most appropriate methods. Every step of peptide synthesis is subject to quality control. Typical delivery specifications include HPLC chromatogram, Mass spec analysis, Synthesis report, Certificate of Analyses. | Creative Peptides, biomedical service, backbone cyclic peptide, backbone cyclized peptides price | has parent organization: Creative Peptides | Restricted | SCR_022106 | SciCrunch Registry | Backbone-Cyclized Peptides | 2026-10-31 12:18:25 | 0 | |||||||||
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IBM SPSS Statistics Resource Report Resource Website 1000+ mentions |
IBM SPSS Statistics (RRID:SCR_016479) | data analysis software, data processing software, data visualization software, software application, software resource | Software package for statistics. Used to analyze and visualize data. Extensions can be used, Python and R programming language code, to integrate with open source software. Available for Windows and Mac operating systems.Versions that were produced by SPSS Inc. before the IBM acquisition (Versions 18 and earlier) would be given origin or publisher of SPSS Inc. in Chicago. Versions that were released after the acquisition would be given origin or publisher of IBM Corp. in Armonk, NY. | Statistics, data analysis, data visualization, statistical analysis, IBM, IBM SPSS, advanced analytics |
is related to: SPSS is related to: IBM SPSS Amos |
Restricted | SCR_019096, SCR_021965 | https://www.ibm.com/support/pages/downloading-ibm-spss-statistics-24, https://www.ibm.com/support/pages/how-cite-ibm-spss-statistics-or-earlier-versions-spss#:~:text=IBM%20SPSS%20Statistics%20for%20Windows%2C%20Version%2025.0, Armonk%2C%20NY%3A%20IBM%20Corp.&text=For%20platforms%20other%20than%20Windows, Statistics%20for%20Macintosh%2C%20Version%2027.0. | SCR_016479 | SciCrunch Registry | SPSS Statistics v26, SPSS Statistics v27, SPSS Statistics v24, SPSS Statistics v25 | 2026-10-31 12:18:16 | 1172 |
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