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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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Necklace Resource Report Resource Website 1+ mentions |
Necklace (RRID:SCR_016103) | alignment software, data processing software, image analysis software, software application, software resource | Software that combines reference and assembled transcriptomes for RNA-Seq analysis. It replaces many manual steps in the pipeline of RNA-Seq analyses involving species with incomplete genome or annotations. | RNA, Transcriptome, Non-model species, bio.tools |
is listed by: bio.tools is listed by: Debian |
PMID:28836999 | Free, Available for download | biotools:necklace | https://bio.tools/necklace | SCR_016103 | SciCrunch Registry | Lace software | 2026-11-07 11:58:11 | 3 | ||||||
|
RELION Resource Report Resource Website 100+ mentions |
RELION (RRID:SCR_016274) | data analysis software, data processing software, software application, software resource, standalone software | Software for determination of cryo-EM structures. It employs an empirical Bayesian approach to refinement of (multiple) 3D reconstructions or 2D class averages in electron cryo-microscopy. | cryo, cryogenic, cryo em, determination, analysis, bayesian, statistic, map, maximum a posteriori, electron, cryomicroscopy |
is listed by: Debian is listed by: OMICtools |
UK Medical Research Council | PMID:23000701 | Free, Available for download, Tutorial available | OMICS_15597 | https://sources.debian.org/src/relion-bin+mpi+gui/ | SCR_016274 | SciCrunch Registry | RELION, REgularised LIkelihood OptimisatioN, RELION-3 | 2026-11-07 11:58:24 | 440 | |||||
|
BLINK Resource Report Resource Website 1+ mentions |
BLINK (RRID:SCR_016288) | algorithm resource, data analysis software, data processing software, software application, software resource | Software for next level of genome wide association studies with both individuals and markers in millions. The method releases the requirement that causative genes are evenly distributed on genome and consequently boosts statistical power. | GWAS, SNP, dataset, r, genome, bayesian, linkage, nested, keyway, statistic, bio.tools |
is listed by: Debian is listed by: bio.tools |
Free, Available for download, Tutorial available | biotools:BLINK | https://bio.tools/BLINK | SCR_016288 | SciCrunch Registry | BLINK (Bayesian-information and Linkage-disequilibrium Iteratively Nested Keyway) | 2026-11-07 11:58:14 | 2 | |||||||
|
MetaCyto Resource Report Resource Website 1+ mentions |
MetaCyto (RRID:SCR_016415) | data analysis software, data processing software, software application, software resource, software toolkit | Software tool for automated meta-analysis of mass and flow cytometry data. Provides functions for preprocessing, automated gating and meta-analysis of cytometry data and collection of cytometry data from the ImmPort database. | automated, analysis, meta, flow, cytometry, data, bio.tools |
is listed by: Bioconductor is listed by: NIDDK Information Network (dkNET) is listed by: bio.tools is listed by: Debian is related to: The Immunology Database and Analysis Portal (ImmPort) |
the National Institute of Allergy and Infectious Diseases HHSN272201200028C | Free, Available for download, Freely available | biotools:metacyto | https://bio.tools/metacyto | SCR_016415 | SciCrunch Registry | 2026-11-07 11:58:26 | 5 | |||||||
|
SMAGEXP Resource Report Resource Website 1+ mentions |
SMAGEXP (RRID:SCR_016360) | SMAGEXP | data analysis software, data processing software, software application, software resource, software toolkit | Software toolkit for transcriptomics data meta-analysis. It integrates metaMA and metaRNAseq packages into Galaxy, carries out meta-analysis of gene expression data, handles microarray data from Gene Expression Omnibus (GEO) database, and more. | transcriptomics, data, meta, analysis, MicroArrays, RNA-Seq, Galaxy, gene, expression, next, generation, sequencing, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Galaxy is related to: Gene Expression Omnibus is related to: metaMA is related to: metaRNASeq |
PMID:30698691 | Free, Available for download, Freely available | biotools:SMAGEXP | https://bio.tools/SMAGEXP | SCR_016360 | SciCrunch Registry | Statistical Meta Analysis for Gene EXPression | 2026-11-07 11:58:40 | 2 | |||||
|
FluxModeCalculator Resource Report Resource Website 1+ mentions |
FluxModeCalculator (RRID:SCR_016290) | data analysis software, data processing software, software application, software resource | Software for performing flux mode analysis in stoichiometric models. FluxModeCalculator enables large-scale elementary flux mode (EFM) computation and uses the OpenMP API to optimally exploit processor architectures with multiple cores., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | efm, flux, stoichiometry, algorithm, matlab, linux, model, magnitude, bio.tools |
is listed by: Debian is listed by: bio.tools |
Biobanking and Biomolecular Resources Research Infrastructure (BBMRI) ; CardioVascular Research Netherlands (CVON-ENERGISE) ; Center of Medical Systems Biology (CMSB) ; European Network for Genetic and Genomic Epidemiology (ENGAGE) ; Netherlands Consortium for Systems Biology (NCSB) |
PMID:26685305 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:fluxmodecalculator, OMICS_10894 | https://bio.tools/fluxmodecalculator | SCR_016290 | SciCrunch Registry | Flux Mode Calculator | 2026-11-07 11:58:34 | 1 | |||||
|
Lifebit Deploit Resource Report Resource Website 1+ mentions |
Lifebit Deploit (RRID:SCR_016428) | analysis service resource, data analysis service, data management software, production service resource, service resource, software application, software resource | Platform for computing management for data analysis on the cloud from the Lifebit company. Allows the computational analyses to be permanently linked to live analyses pipelines. | Lifebit, compute, management, data, analysis, cloud, integrate, data, reproduce, transparent, bio.tools |
is listed by: Debian is listed by: bio.tools |
PMID:28398311 | Commercially available | biotools:nextflow | https://bio.tools/nextflow | SCR_016428 | SciCrunch Registry | 2026-11-07 11:58:36 | 2 | |||||||
|
Microscopy Image Browser Resource Report Resource Website 100+ mentions |
Microscopy Image Browser (RRID:SCR_016560) | MIB | data analysis software, data processing software, data visualization software, image processing software, software application, software resource, standalone software | Software package for advanced image processing, analysis, segmentation and visualization of multi-dimensional (2D-4D) light and electron microscopy datasets. | segmentation, analysis, multidimentional, dataset, light, electron, microscopy, image, processing, visualization, data, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: MATLAB |
Biocenter Finland ; Biological Imaging Network Academy of Finland ; University of Helsinki |
PMID:26727152 | Free, Available for download, Freely available | biotools:mib | https://www.youtube.com/watch?v=I9FWmJX_nl0&index=1&list=PLGkFvW985wz8cj8CWmXOFkXpvoX_HwXzj, https://bio.tools/mib | SCR_016560 | SciCrunch Registry | MIB, Microscopy Image Browser | 2026-11-07 11:58:19 | 160 | ||||
|
DINIES Resource Report Resource Website 1+ mentions |
DINIES (RRID:SCR_016505) | DINIES | data analysis software, data processing software, sequence analysis software, software application, software resource, web application | Web server for predicting unknown drug-target interaction networks from various types of biological data in the framework of supervised network inference. | predict, drug, target, interaction, network, biological, data, chemical, structure, protein, amino acid, sequence, domain, bio.tools |
is listed by: GenomeNet is listed by: Debian is listed by: bio.tools is related to: KEGG has parent organization: Kyoto University; Kyoto; Japan |
Ministry of Education ; Culture ; Sports ; Science and Technology of Japan ; the Japan Science and Technology Agency ; the Japan Society for the Promotion of Science |
PMID:24838565 | Free, Freely available | biotools:dinies | https://bio.tools/dinies | SCR_016505 | SciCrunch Registry | Drug target Interaction Network Inference Engine based on Supervised analysis | 2026-11-07 11:58:18 | 6 | ||||
|
MentaLiST Resource Report Resource Website 10+ mentions |
MentaLiST (RRID:SCR_016469) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software for a MLST (multi-locus sequence typing) caller, based on a k-mer counting algorithm and written in the Julia language. Designed and implemented to handle large typing schemes. | next, generation, sequencing, multi, locus, sequence, typing, pathogen, surveillance, gene, identify, strain, type, housekeeping, whole, genome, sequencing, data, bacteria, genotyping, bio.tools |
is listed by: bio.tools is listed by: Debian |
Canadian Institute for Health Research ; Genome BC ; Genome Canada |
PMID:29319471 | Free, Available for download, Freely available | biotools:mentalist | https://bio.tools/mentalist | SCR_016469 | SciCrunch Registry | 2026-11-07 11:58:28 | 15 | ||||||
|
cisTEM Resource Report Resource Website 50+ mentions |
cisTEM (RRID:SCR_016502) | cisTEM | data processing software, image processing software, software application, software resource | Software to process cryo-EM images of macromolecular complexes and obtain high-resolution 3D reconstructions from them. | data, processing, high, resolution, electron, cryo, macroscopy, single, particle, averaging, image, macromolecule, high, resolution, 3D, bio.tools |
is listed by: bio.tools is listed by: Debian |
Howard Hughes Medical Institute | DOI:10.7554/eLife.35383 | Open source, Trial available | biotools:cistem | https://bio.tools/cistem | SCR_016502 | SciCrunch Registry | computational imaging system for Transmission Electron Microscopy | 2026-11-07 11:58:28 | 67 | ||||
|
kallisto Resource Report Resource Website 100+ mentions |
kallisto (RRID:SCR_016582) | data analysis software, data processing software, software application, software resource | Software tool for quantifying abundances of transcripts from RNA-Seq data or target sequences using high-throughput sequencing reads. | bio.tools |
is listed by: Debian is listed by: bio.tools works with: sleuth works with: kb_python |
PMID:27043002 | Free, Available for download, Freely available | biotools:kallisto | https://pachterlab.github.io/kallisto/download.html, https://bio.tools/kallisto, https://sources.debian.org/src/kallisto/ | SCR_016582 | SciCrunch Registry | kallisto v0.43.1 | 2026-11-07 11:58:19 | 148 | ||||||
|
Prodigal Resource Report Resource Website 1000+ mentions |
Prodigal (RRID:SCR_011936) | Prodigal | simulation software, software application, software resource | Software tool for protein coding gene prediction for prokaryotic genomes. |
is listed by: OMICtools is listed by: Debian is listed by: SoftCite has parent organization: Oak Ridge National Laboratory |
PMID:20211023 | Free, Available for download, Freely available | SCR_021246, OMICS_01493 | https://sources.debian.org/src/prodigal/ | http://prodigal.ornl.gov/ | SCR_011936 | SciCrunch Registry | , PROkaryotic DYnamic programming Gene-finding ALgorithm, Prokaryotic Dynamic Programming Genefinding Algorithm | 2026-11-07 11:57:30 | 3398 | |||||
|
Oases Resource Report Resource Website 100+ mentions |
Oases (RRID:SCR_011896) | Oases | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software tool as de novo transcriptome assembler designed to produce transcripts from short read sequencing technologies, such as Illumina, SOLiD, or 454 in the absence of any genomic assembly. | bio.tools, transcriptome assembler |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: European Bioinformatics Institute |
DOI:10.1093/bioinformatics/bts094 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01322, biotools:oases | https://bio.tools/oases | https://sources.debian.org/src/oases/ | SCR_011896 | SciCrunch Registry | 2026-11-07 11:57:22 | 289 | |||||
|
TopHat-Fusion Resource Report Resource Website 100+ mentions |
TopHat-Fusion (RRID:SCR_011899) | TopHat-Fusion | software resource | An algorithm for Discovery of Novel Fusion Transcripts with the ability to align reads across fusion points, which results from the breakage and re-joining of two different chromosomes, or from rearrangements within a chromosome. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University of Maryland; Maryland; USA |
PMID:21835007 | OMICS_01359, biotools:tophat-fusion | https://bio.tools/tophat-fusion | SCR_011899 | SciCrunch Registry | TopHat-Fusion: An algorithm for Discovery of Novel Fusion Transcripts | 2026-11-07 11:57:33 | 162 | ||||||
|
MetAMOS Resource Report Resource Website 10+ mentions |
MetAMOS (RRID:SCR_011914) | MetAMOS | data processing software, software application, software resource, workflow software | A modular and open source metagenomic assembly and analysis pipeline. | microbiome, pipeline, microbiome, workflow software, metagenomic assembly, metagenomic assembly, bio.tools |
is listed by: OMICtools is listed by: Human Microbiome Project is listed by: bio.tools is listed by: Debian is hosted by: GitHub |
Open source, Available for download | OMICS_01426, biotools:metamos | https://github.com/marbl/metAMOS, https://bio.tools/metamos | SCR_011914 | SciCrunch Registry | 2026-11-07 11:57:30 | 14 | |||||||
|
BLAT Resource Report Resource Website 1000+ mentions |
BLAT (RRID:SCR_011919) | BLAT | software resource | Software designed to quickly find sequences of 95% and greater similarity of length 25 bases or more. | bio.tools |
is used by: deFuse is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of California at Santa Cruz; California; USA is required by: RelocaTE |
biotools:blat, OMICS_01434 | https://bio.tools/blat | SCR_011919 | SciCrunch Registry | 2026-11-07 11:57:34 | 3808 | ||||||||
|
BBSeq Resource Report Resource Website 1+ mentions |
BBSeq (RRID:SCR_011877) | BBSeq | software resource | A Powerful and Flexible Approach to the Analysis of RNA Sequence Count Data. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA |
biotools:bbseq, OMICS_01300 | https://bio.tools/bbseq | SCR_011877 | SciCrunch Registry | 2026-11-07 11:57:32 | 3 | ||||||||
|
IDBA-UD Resource Report Resource Website 500+ mentions |
IDBA-UD (RRID:SCR_011912) | IDBA-UD | software resource | Software for an iterative De Bruijn Graph De Novo Assembler for Short Reads Sequencing data with Highly Uneven Sequencing Depth. |
is listed by: OMICtools is listed by: Debian is related to: Meta-IDBA |
PMID:22495754 DOI:10.1093/bioinformatics/bts174 |
Acknowledgement requested | OMICS_01423 | https://sources.debian.org/src/idba/ | SCR_011912 | SciCrunch Registry | 2026-11-07 11:57:22 | 524 | |||||||
|
KisSplice Resource Report Resource Website 10+ mentions |
KisSplice (RRID:SCR_011893) | KisSplice | data analysis software, data processing software, software application, software resource | Software tool that enables analysis of RNA-seq data with or without reference genome. Local transcriptome assembler for SNPs, indels and AS events. | RNA-seq data analysis, with reference genome, without reference genome, local transcriptome assembler, SNPs, indels, AS events., bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
DOI:10.1186/1471-2105-13-S6-S5 | Free, Available for download, Freely available | biotools:KisSplice, OMICS_01321 | https://bio.tools/KisSplice, https://sources.debian.org/src/kissplice/ | SCR_011893 | SciCrunch Registry | 2026-11-07 11:57:30 | 21 |
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