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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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Bandage Resource Report Resource Website 10+ mentions |
Bandage (RRID:SCR_022772) | data analysis software, data processing software, software application, software resource | Software tool for visualising de novo assembly graphs. By displaying connections which are not present in contigs file, opens up new possibilities for analysing de novo assemblies. Used for interactive visualization of de novo genome assemblies. | interactive visualization, de novo genome assemblies, visualising de novo assembly graphs, analysing de novo assemblies |
is listed by: Debian is listed by: OMICtools |
PMID:26099265 | Free, Available for download, Freely available | OMICS_09013 | https://github.com/rrwick/Bandage, https://sources.debian.org/src/bandage/ | SCR_022772 | SciCrunch Registry | Bioinformatics Application for Navigating De novo Assembly Graphs Easily | 2026-09-26 02:17:22 | 27 | ||||||
|
OptiType Resource Report Resource Website 50+ mentions |
OptiType (RRID:SCR_022279) | data analysis software, data processing software, software application, software resource | Software tool for precision HLA typing from next generation sequencing data. | Precision HLA typing, next generation sequencing data, HLA typing, NGS data |
is listed by: Debian is listed by: OMICtools |
German Federal Ministry of Education and Research ; German Research Foundation |
PMID:25143287 | Free, Available for download, Freely available | OMICS_05461 | https://sources.debian.org/src/optitype/ | SCR_022279 | SciCrunch Registry | 2026-09-26 02:17:18 | 50 | ||||||
|
GLAD Resource Report Resource Website 100+ mentions |
GLAD (RRID:SCR_001284) | GLAD | software resource | Software for analysis of array CGH data: detection of breakpoints in genomic profiles and assignment of a status (gain, normal or loss) to each chromosomal regions identified. | comparative genomic hybridization, breakpoint, copy number variation, microarray |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:15381628 | Free, Available for download, Freely available | OMICS_02053 | SCR_001284 | SciCrunch Registry | GLAD - Gain and Loss Analysis of DNA, Gain and Loss Analysis of DNA | 2026-09-26 02:17:25 | 292 | ||||||
|
Bycom Resource Report Resource Website |
Bycom (RRID:SCR_000659) | software resource | A software which can perform methylcytosine calling from BS-seq (WGBS and RRBS), and permits either unmapped reads (FASTQ) or mapped reads (SAM/BAM) to be used as the input data. Certain SNPs (C>A/G) can also be selected in the output. | methylcytosine, bs-seq, fastq, sam, bam, snps, snp, wgbs, rrbs, sorftw |
is listed by: OMICtools has parent organization: SourceForge |
PMID:25255082 | Free, Available for download, Freely available | OMICS_00594 | SCR_000659 | SciCrunch Registry | 2026-09-26 02:17:25 | 0 | ||||||||
|
RMassBank Resource Report Resource Website 1+ mentions |
RMassBank (RRID:SCR_002797) | data processing software, software application, software resource, workflow software | Workflow software to process tandem MS files and build MassBank records. Functions include automated extraction of tandem MS spectra, formula assignment to tandem MS fragments, recalibration of tandem MS spectra with assigned fragments, spectrum cleanup, automated retrieval of compound information from Internet databases, and export to MassBank records. | standalone software, mac os x, unix/linux, windows, r, mass spectrometry, metabolomics |
is listed by: OMICtools has parent organization: Bioconductor |
Free, Freely available, Available for download | OMICS_02657 | SCR_002797 | SciCrunch Registry | 2026-09-26 02:17:26 | 9 | |||||||||
|
Cufflinks Resource Report Resource Website 5000+ mentions |
Cufflinks (RRID:SCR_014597) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software tool for transcriptome assembly and differential expression analysis for RNA-Seq. Includes script called cuffmerge that can be used to merge together several Cufflinks assemblies. It also handles running Cuffcompare as well as automatically filtering a number of transfrags that are likely to be artifacts. If the researcher has a reference GTF file, the researcher can provide it to the script to more effectively merge novel isoforms and maximize overall assembly quality. | transcriptome, rna-seq, rna seq, cuffmerge, cufflink, cuffcompare, transfrags, artifacts, gtf file, transcriptome assembly, expression analysis, bio.tools, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools is listed by: SoftCite works with: GeneScissors is hosted by: GitHub |
DOI:10.1038/nbt.1621 | Acknowledgement requested, Source code available on GitHub | biotools:cufflinks, OMICS_01304, SCR_013307 | https://github.com/cole-trapnell-lab/cufflinks, https://bio.tools/cufflinks, https://sources.debian.org/src/cufflinks/ | SCR_014597 | SciCrunch Registry | 2026-09-26 02:15:27 | 9083 | |||||||
|
Prokka Resource Report Resource Website 1000+ mentions |
Prokka (RRID:SCR_014732) | data analysis software, data processing software, sequence analysis software, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software tool for the rapid annotation of prokaryotic genomes. It produces GFF3, GBK and SQN files that are ready for editing in Sequin and ultimately submitted to Genbank/DDJB/ENA. A typical 4 Mbp genome can be fully annotated in less than 10 minutes on a quad-core computer, and scales well to 32 core SMP systems., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | annotation, prokaryote, genome, prokaryotic genome, sequence analysis software, annotation software, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
DOI:10.1093/bioinformatics/btu153 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_04220, biotools:prokka | https://bio.tools/prokka, https://sources.debian.org/src/prokka/, https://sources.debian.org/src/prokka/ | SCR_014732 | SciCrunch Registry | 2026-09-26 02:15:28 | 4882 | |||||||
|
SeaView Resource Report Resource Website 1000+ mentions |
SeaView (RRID:SCR_015059) | data analysis software, data processing software, data visualization software, sequence analysis software, software application, software resource | Graphical user interface for multiple sequence alignment and molecular phylogeny. SeaView also generates phylogenetic trees. | sequence alignment, molecular phylogeny, phylogenetic tree, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
PMID:19854763 DOI:10.1093/molbev/msp259 |
Free, Available for download | OMICS_08908, biotools:seaview | https://bio.tools/seaview, https://sources.debian.org/src/seaview/ | SCR_015059 | SciCrunch Registry | 2026-09-26 02:15:32 | 1817 | |||||||
|
libRoadRunner Resource Report Resource Website 10+ mentions |
libRoadRunner (RRID:SCR_014763) | simulation software, software application, software resource | Simulation engine for systems and synthetic biology to be used with other software applications. It retains the original functionality of RoadRunner but has changes in performance, back-end design, event handling, new C++ API, and stochastic simulation support. | simulation engine, simulation software, road runner, roadrunner, systems biology, synthetic biology |
is listed by: Debian is listed by: OMICtools |
NIGMS GM081070 | DOI:10.1093/bioinformatics/btv363 | Open source, Available for download | OMICS_09368 | https://sources.debian.org/src/libroadrunner-dev/ | SCR_014763 | SciCrunch Registry | 2026-09-26 02:15:29 | 11 | ||||||
|
SEER Resource Report Resource Website 500+ mentions |
SEER (RRID:SCR_015499) | data analysis software, data processing software, sequence analysis software, software application, software resource, source code | Sequence element enrichment analysis tool to perform pan-genome-wide association studies in bacteria. | bacterial genome association, sequence element enrichment analysis, kmer enrichment analysis |
is listed by: Debian is listed by: OMICtools is hosted by: GitHub |
DOI:10.1038/ncomms12797 DOI:10.1101/038463 |
Available for download | OMICS_21699 | https://sources.debian.org/src/seer/ | SCR_015499 | SciCrunch Registry | 2026-09-26 02:15:34 | 547 | |||||||
|
GIIRA Resource Report Resource Website 1+ mentions |
GIIRA (RRID:SCR_015507) | data analysis software, data processing software, sequence analysis software, software application, software resource | Gene prediction method that identifies potential coding regions based on the mapping of reads from an RNA-Seq experiment. | gene prediction, rna seq, coding region, potential coding region |
is listed by: Debian is listed by: OMICtools |
DOI:10.1093/bioinformatics/btt577 | Available for download | OMICS_07360 | http://www.rki.de/EN/Content/Institute/DepartmentsUnits/JuniorGroups/JRG4.html, https://sources.debian.org/src/giira/ | SCR_015507 | SciCrunch Registry | 2026-09-26 02:15:34 | 3 | |||||||
|
GADMA Resource Report Resource Website 1+ mentions |
GADMA (RRID:SCR_017680) | GADMA | data analysis software, data processing software, software application, software resource | Software tool to implement methods for automatic inferring joint demographic history of multiple populations from genetic data. Genetic algorithm for inferring demographic history of multiple populations from allele frequency spectrum data. | Inferring, demographic, history, population, genetic, data, allele, frequency, spectrum, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
DOI:10.1101/407734 | Free, Available for download, Freely available | biotools:GADMA | https://bio.tools/GADMA | SCR_017680 | SciCrunch Registry | Genetic Algorithm for Demographic Model Analysis | 2026-09-26 02:16:01 | 3 | |||||
|
GeneATLAS Resource Report Resource Website 100+ mentions |
GeneATLAS (RRID:SCR_017577) | analysis service resource, atlas, data analysis service, data or information resource, database, production service resource, service resource | Database of associations between traits and variants using UK Biobank cohort. Searchable atlas of genetic associations. Assists researchers to query UK Biobank. Provides unbiased view of phenotype and genotype associations across of traits. | Association, trait, variant, UK Biobank, cohort, atlas, genetic, phenotype, genotype, FASEB list |
is listed by: OMICtools has parent organization: University of Edinburgh; Scotland; United Kingdom |
Free, Available for download, Freely available | SCR_017577 | SciCrunch Registry | Gene ATLAS, Gene Atlas | 2026-09-26 02:16:00 | 158 | |||||||||
|
immuneXpresso Resource Report Resource Website |
immuneXpresso (RRID:SCR_017578) | data or information resource, service resource, software application, software resource, text-mining software | Software tool as text-mining engine that structures and standardizes knowledge of immune intercellular communication. Knowledgebase contains interactions and separate mentions of cells or cytokines in context of thousands of diseases. Intercellular interactions were text-mined from all available PubMed abstracts across disease conditions. | Structure, standardize, immune, cellular, interaction, cytokine, disease, cell, PubMed, abstract |
is listed by: NIDDK Information Network (dkNET) is listed by: OMICtools |
NIAID ; NIH ; Rappaport Family Institute for Research in the Medical Sciences |
PMID:29912209 | Free, Freely available | SCR_017578 | SciCrunch Registry | 2026-09-26 02:16:00 | 0 | ||||||||
|
BioAssay Express Resource Report Resource Website 1+ mentions |
BioAssay Express (RRID:SCR_017594) | data access protocol, service resource, software resource, web service | Web based tool for annotating bioassay protocols using semantic web terms. Enables searching, sorting, clustering and analyzing of assays without needing to read through original text. Exploits Common Assay Template based on underlying vocabularies and semantic standards from BioAssay Ontology, Drug Target Ontology, Cell Line Ontology and others. Users can identify similar assays and examine similarity of assays between and within organizations. | Annotating, bioassay, protocol, semantic, web, term, ontology | is listed by: OMICtools | NCATS R44 TR000185 | DOI:10.7717/peerj-cs.61 | Free, Freely available | https://github.com/cdd/bioassay-template | SCR_017594 | SciCrunch Registry | 2026-09-26 02:16:00 | 1 | |||||||
|
Bustools Resource Report Resource Website 10+ mentions |
Bustools (RRID:SCR_018210) | data analysis software, data processing software, software application, software resource | Software tool for manipulating BUS files for single cell RNA-Seq datasets. Used to error correct barcodes, collapse UMIs, produce gene count or transcript compatibility count matrices, and is useful for many other tasks. | Single cell RNAseq workflow, single cell RNAseq dataset, error correct barcode, collapse UMI, produce gene count, produce transcript compatibility count matrice |
is listed by: Debian is listed by: OMICtools works with: kb_python |
DOI:10.1101/673285 | Free, Available for download, Freely available | OMICS_33004 | https://sources.debian.org/src/bustools/ | SCR_018210 | SciCrunch Registry | 2026-09-26 02:16:05 | 19 | |||||||
|
ChromHMM Resource Report Resource Website 50+ mentions |
ChromHMM (RRID:SCR_018141) | data analysis software, data processing software, software application, software resource | Software tool for chromatin state discovery and characterization. Used for chromatin state discovery and genome annotation of non coding genome using epigenomic information across one or multiple cell types. Combines multiple genome wide epigenomic maps, and uses combinatorial and spatial mark patterns to infer complete annotation for each cell type. Provides automated enrichment analysis of resulting annotations. | Chromatin state discovery, chromatin characterization, genome annotation, non coding genome, epigenomic, cell, annotation, analysis, pattern |
is listed by: Debian is listed by: OMICtools |
Alfred P. Sloan Fellowship ; CAREER Award ; NHGRI RC1HG005334; NHGRI U01 HG007912; NHGRI U54 HG004570; NIEHS R01 ES024995; NIMH U01 MH105578; NSF 0905968 |
PMID:29120462 PMID:22373907 |
Free, Available for download, Freely available | OMICS_03490 | https://sources.debian.org/src/chromhmm/ | SCR_018141 | SciCrunch Registry | 2026-09-26 02:16:04 | 50 | ||||||
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Phyutility Resource Report Resource Website 10+ mentions |
Phyutility (RRID:SCR_018545) | data analysis software, data processing software, software application, software resource | Command line program that performs analyses or modifications on both trees and data matrices. Software phyloinformatics tool for trees, alignments and molecular data. Used for summarizing and manipulating phylogenetic trees, manipulating molecular data and retrieving data from NCBI. | Data matrice analysis, data matrice modification, phyloinformatics, phylogenetic tree, alignment, molecular data manipulation, data analysis |
is listed by: Debian is listed by: OMICtools is listed by: SoftCite is related to: NCBI |
NSF Cyberinfrastructure for Phylogenetic Research EF 0331654 | PMID:18227120 | Free, Freely available | OMICS_21687 | https://sources.debian.org/src/phyutility/ | SCR_018545 | SciCrunch Registry | 2026-09-26 02:16:08 | 46 | ||||||
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Minimap2 Resource Report Resource Website 1000+ mentions |
Minimap2 (RRID:SCR_018550) | alignment software, data processing software, image analysis software, software application, software resource | Software tool as pairwise alignment for nucleotide sequences. Alignment program to map DNA or long mRNA sequences against large reference database. Versatile pairwise aligner for genomic and spliced nucleotide sequences. | Pairwise alignment, nucleotide sequence, map DNA sequence, map mRNA sequence, reference database, spliced nucleotide sequence, bio.tools, FASEB list |
is used by: D-GENIES is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
NHGRI R01 HG010040 | PMID:29750242 | Free, Available for download, Freely available | OMICS_31658, biotools:minimap2 | https://bio.tools/minimap2, https://sources.debian.org/src/libminimap2-dev/ | SCR_018550 | SciCrunch Registry | 2026-09-26 02:16:08 | 1593 | ||||||
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COG Resource Report Resource Website 1000+ mentions |
COG (RRID:SCR_007139) | COG, COG Cluster, COG Function, COG Pathway | data or information resource, database | A database for phylogenetic classification for proteins encoded in complete genomes. Clusters of Orthologous Groups of proteins (COGs) were delineated by comparing protein sequences encoded in complete genomes, representing major phylogenetic lineages. Each COG consists of individual proteins or groups of paralogs from at least 3 lineages and thus corresponds to an ancient conserved domain. Please be aware that COGs hasn't been updated in many years and will not be. | ortholog, protein, cog, conserved protein sequence, unicellular cluster, genome, order, class, phyla, eukaryotic cluster, gold standard |
is listed by: OMICtools is related to: MLTreeMap is related to: ProOpDB is related to: Conserved Domain Database has parent organization: NCBI is parent organization of: Clusters of Orthologous Groups Analysis Ontology |
PMID:12969510 PMID:9381173 |
OMICS_01688, nif-0000-02672 | SCR_007139 | SciCrunch Registry | COG Database, Clusters of Orthologous Groups of proteins, COGs, COGs - Clusters of Orthologous Groups of proteins, COGs - Phylogenetic classification of proteins encoded in complete genomes, COG Cluster, COG Pathway, COG Function | 2026-09-26 02:18:31 | 1278 |
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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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