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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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DISEASES Resource Report Resource Website 500+ mentions |
DISEASES (RRID:SCR_015664) | data or information resource, database | Database that integrates evidence on disease-gene associations from automatic text mining, manually curated literature, cancer mutation data, and genome-wide association studies. It also assigns confidence scores that facilitate comparison of the different types and sources of evidence. | disease, gene, disease-gene association, text-mining, , bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools |
Novo Nordisk Foundation Center for Protein Research NNF14CC0001; European Union Seventh Framework Programme n259348 |
PMID:25484339 | biotools:diseases | https://bio.tools/diseases | SCR_015664 | SciCrunch Registry | 2026-11-07 11:58:03 | 655 | |||||||
|
TISSUES Resource Report Resource Website 10+ mentions |
TISSUES (RRID:SCR_015665) | data or information resource, database, software resource, web application | Database that integrates evidence on tissue expression from manually curated literature, proteomics and transcriptomics screens, and automatic text mining. It maps all evidence to common protein identifiers and Brenda Tissue Ontology terms, and further unifies it by assigning confidence scores that facilitate comparison of the different types and sources of evidence. | tissue expression, proteomic, transcriptomic, text-mining, brenda tissue ontology, protein identifier, bio.tools |
uses: BRENDA Tissue and Enzyme Source Ontology is listed by: Debian is listed by: bio.tools |
Novo Nordisk Foundation NNF14CC0001; NCI U54 CA189205-01; CSIRO’s OCE Science Leader program |
PMID:26157623 | Freely available, Free, Available for download | biotools:tissues | https://bio.tools/tissues | SCR_015665 | SciCrunch Registry | TISSUES: Tissue Expression Database, Tissue Expression Database | 2026-11-07 11:58:13 | 45 | |||||
|
Hybrid-denovo Resource Report Resource Website 1+ mentions |
Hybrid-denovo (RRID:SCR_015866) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software for a de novo OTU-picking pipeline integrating single- and paired-end 16S sequence tags. It is designed to take Illumina paired-end sequencing reads as input and output the OTU BIOM table, together with their representative sequences and a phylogenetic tree of OTUs. | hybrid-denovo, 16S rRNA, microbiota pipeline, single-end, paired-end, illumina read, de novo, otu-picking pipeline, phylogenetic tree, python, bio.tools |
is listed by: bio.tools is listed by: Debian |
biotools:hybrid-denovo | https://bio.tools/hybrid-denovo | SCR_015866 | SciCrunch Registry | 2026-11-07 11:58:16 | 3 | |||||||||
|
Short Read Sequence Typing for Bacterial Pathogens Resource Report Resource Website 10+ mentions |
Short Read Sequence Typing for Bacterial Pathogens (RRID:SCR_015870) | SRST2 | data analysis software, data processing software, sequence analysis software, software application, software resource, source code | Software that is designed to take Illumina sequence data, a MLST database and/or a database of gene sequences (e.g. resistance genes, virulence genes, etc) and report the presence of STs and/or reference genes. | genotype analysis, illumina sequence data, mlst database, gene sequence, st, reference gene, short read |
uses: Bowtie uses: SAMTOOLS is listed by: Debian is listed by: OMICtools requires: SciPy requires: Python Programming Language |
infectious disease | NHMRC of Australia 1043830; NHMRC of Australia 1061409; NHMRC of Australia 1061435; Victorian Life Sciences Computation Initiative (VLSCI) VR0082 |
PMID:25422674 | Free, Available for download | OMICS_12777 | http://katholt.github.io/srst2/, https://sources.debian.org/src/srst2/ | http://srst.sourceforge.net/ | SCR_015870 | SciCrunch Registry | SRST2: Short Read Sequence Typing for Bacterial Pathogens, Short Read Sequence Typing v2 | 2026-11-07 11:58:06 | 24 | ||
|
NiftyPET Resource Report Resource Website 1+ mentions |
NiftyPET (RRID:SCR_015873) | data processing software, data visualization software, image analysis software, software application, software resource, software toolkit, source code | Python software package that offers quantitative PET image reconstruction and analysis with high accuracy and precision. It is written in CUDA C and embedded in Python C extensions. | python, cuda c, python c, pet, image reconstruction, image analysis, bio.tools |
uses: CMake is listed by: Debian is listed by: bio.tools |
DOI:10.1007/s12021-017-9352-y | Free, Available for download, Runs on Windows, Runs on Linux | biotools:niftypet | https://bio.tools/niftypet | SCR_015873 | SciCrunch Registry | 2026-11-07 11:58:35 | 7 | |||||||
|
larvalign Resource Report Resource Website 1+ mentions |
larvalign (RRID:SCR_015815) | data analysis software, data or information resource, data processing software, data set, sequence analysis software, software application, software resource, software toolkit | Software package including computational methods for aligning gene expression patterns from the larval brain of Drosophila melanogaster. Its method includes evaluation of the registration framework involved in template generation and mapping. | drosophila melanogaster, computational method, gene expression, alignment, larval brain, larvae, template generation, mapping, bio.tools |
is listed by: Debian is listed by: bio.tools |
Free, Available for download | biotools:larvalign | https://bio.tools/larvalign | SCR_015815 | SciCrunch Registry | 2026-11-07 11:58:29 | 1 | ||||||||
|
Canu Resource Report Resource Website 1000+ mentions |
Canu (RRID:SCR_015880) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software for scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Canu is a fork of the Celera Assembler and is designed for high-noise single-molecule sequencing (such as the PacBio RS II/Sequel or Oxford Nanopore MinION). | long-read, assembly, k-mer, weighting, repeat separation, adaptive, pacbio, single-molecule, sequencing, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools is related to: Celera assembler |
National Human Genome Research Institute ; National Science Foundation NSF IOS-1237993; US Department of Homeland Security (DHS) HSHQDC-07-C-00020 |
PMID:28298431 DOI:10.1101/071282 |
Free, Available for download | OMICS_14592, biotools:canu | http://canu.readthedocs.io/en/latest/, https://bio.tools/canu, https://sources.debian.org/src/canu/ | SCR_015880 | SciCrunch Registry | 2026-11-07 11:58:07 | 2451 | ||||||
|
Genesis Resource Report Resource Website 1000+ mentions |
Genesis (RRID:SCR_015775) | data analysis software, data processing software, data visualization software, software application, software resource | Software for cluster analysis of microarray data. Genesis is a platform independent Java package of tools to simultaneously visualize and analyze a whole set of gene expression experiments. | cluster analysis, microarray data, java, gene expression, visualization, analysis, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: SoftCite |
PMID:11836235 | Free for academic use, Free for non-profits, Available for download, Runs on Windows, Runs on Mac OS, Runs on Linux | biotools:genesis_microarray | https://bio.tools/genesis_microarray | SCR_015775 | SciCrunch Registry | Genesis: Cluster analysis of microarray data | 2026-11-07 11:58:15 | 1029 | ||||||
|
Baitfisher Resource Report Resource Website 1+ mentions |
Baitfisher (RRID:SCR_015985) | alignment software, data processing software, image analysis software, software application, software resource, software toolkit | Software toolkit for multispecies target DNA enrichment probe design. It consists of two programs: BaitFisher and BaitFilter, which are designed to construct hybrid enrichment baits for multiple sequence alignments or annotated features in multiple sequence alignments. | software, package, multispecies, comparative, genomics, hybrid, enrichment, DNA, probe, design, sequence, alignments |
is listed by: Debian is listed by: OMICtools |
German Research Foundation (DFG) OH81/9-1; NI 1387/1-1; Spanish Ministry of Science and Education (MEC) RYC-2014-15615 |
PMID:27009209 DOI:10.1093/molbev/msw056 |
Free, Available for download | OMICS_11740 | https://sources.debian.org/src/ballview/ | SCR_015985 | SciCrunch Registry | 2026-11-07 11:58:18 | 5 | ||||||
|
Avogadro Resource Report Resource Website 1000+ mentions |
Avogadro (RRID:SCR_015983) | data analysis software, data processing software, data visualization software, software application, software resource, software toolkit | Software for semantic chemical editing, visualization, and analysis. It is designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. | semantic, optimization, crystallography, chemical, editor, visualization, analysis, molecular, modeling, drug, design, biomolecule, simulation, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools |
Engineering Research Development Center W912HZ-11-P-0019; NSF DMR-1005413 |
PMID:22889332 DOI:10.1186/1758-2946-4-17 |
Open source, Free, Free to download | OMICS_04967, biotools:avogadro | http://avogadro.openmolecules.net/, https://github.com/avogadro, https://bio.tools/avogadro, https://sources.debian.org/src/axe-demultiplexer/ | SCR_015983 | SciCrunch Registry | 2026-11-07 11:58:37 | 2237 | ||||||
|
Bio-tradis Resource Report Resource Website 50+ mentions |
Bio-tradis (RRID:SCR_015993) | TraDIS:Transposon Directed Insertion Sequencing | data analysis software, data processing software, sequence analysis software, software application, software resource, software toolkit | Analysis software for the output from TraDIS (Transposon Directed Insertion Sequencing) analyses of dense transposon mutant libraries. The Bio-Tradis analysis pipeline is implemented as an extensible Perl library which can either be used as is, or as a basis for the development of more advanced analysis tools. | software, tool, analysis, data, sequencing, insertion, transponson, direct, mutant, library, perl, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
Alexander von Humboldt Stiftung/Foundation ; Medical Research Council G1100100/1; Wellcome Trust WT098051 |
PMID:26794317 DOI:10.1093/bioinformatics/btw022 |
Free, Available for download, Freely available | OMICS_11083, biotools:bio-tradis | https://bio.tools/bio-tradis, https://sources.debian.org/src/bio-tradis/ | SCR_015993 | SciCrunch Registry | 2026-11-07 11:58:31 | 56 | |||||
|
Barrnap Resource Report Resource Website 500+ mentions |
Barrnap (RRID:SCR_015995) | 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 to predict the location of ribosomal RNA genes in genomes. It supports bacteria, archaea, mitochondria, and eukaryotes. It takes FASTA DNA sequence as input, writes GFF3 as output, and supports multithreading., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | multithreading, fasta, sequencing, software, predict, location, ribosomal, gene, genome, RNA, prediction, bacteria, archaea, mitochondria, eukaryote, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools |
THIS RESOURCE IS NO LONGER IN SERVICE | biotools:barrnap, OMICS_13988 | https://github.com/tseemann/barrnap, https://bio.tools/barrnap, https://sources.debian.org/src/barrnap/ | SCR_015995 | SciCrunch Registry | Barrnap: Basic rapid ribosomal RNA predictor | 2026-11-07 11:58:08 | 722 | |||||||
|
Aegean Resource Report Resource Website 1+ mentions |
Aegean (RRID:SCR_015965) | data analysis software, data processing software, sequence analysis software, software application, software resource, software toolkit | Software toolkit for the analysis and evaluation of genome annotations. The toolkit includes a variety of analysis programs, e.g. for comparing distinct sets of gene structure annotations (ParsEval), computation of gene loci (LocusPocus) and more. | genome, evaluation, annotation, structure, loci |
is listed by: Debian is listed by: OMICtools |
National Science Foundation 1126267 | PMID:22852583 | Free, Available for download, Freely available, | OMICS_19721 | https://github.com/BrendelGroup/AEGeAn, https://sources.debian.org/src/aegean/ | SCR_015965 | SciCrunch Registry | AEGeAn: analysis and evaluation of genome annotations, Aegean Toolkit | 2026-11-07 11:58:18 | 9 | |||||
|
andi Resource Report Resource Website 10+ mentions |
andi (RRID:SCR_015971) | algorithm resource, alignment software, data processing software, image analysis software, software application, software resource | Software tool for rapidly computing and estimating evolutionary distance between closely related genomes. Because andi does not compute full alignments it scales even up to thousands of bacterial genomes. | algorithm, computing, estimate, analysis, genome, alignment, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
Deutsche Forschungsgemeinschaft Pf672/3-1 | PMID:25504847 | Free, Freely available, Available for download | OMICS_09287, biotools:andi | https://bio.tools/andi, https://sources.debian.org/src/andi/ | SCR_015971 | SciCrunch Registry | 2026-11-07 11:58:18 | 41 | ||||||
|
DISULFIND Resource Report Resource Website 50+ mentions |
DISULFIND (RRID:SCR_016072) | Disulfinder | 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 for predicting the disulfide bonding state of cysteines and their disulfide connectivity, starting from a protein sequence alone and may be useful in other genomic annotation tasks. | predict, disulfide, bonding, state, cysteine, protein, sequence, genomic, annotation, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools has parent organization: University of Florence; Florence; Italy |
Embark Fellowship from the Irish Research Council for Science ; Engineering and Technology ; EU NoE BIOPATTERN contract no. FP6-508803; EU STREP APrIL II contract no. FP6-508861 |
PMID:16844986 DOI:10.1093/nar/gkl266 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_04214, biotools:disulfind | https://bio.tools/disulfind, https://sources.debian.org/src/disulfinder/ | SCR_016072 | SciCrunch Registry | Cysteines Disulfide Bonding State and Connectivity Predictor | 2026-11-07 11:58:10 | 71 | ||||
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DeepNano Resource Report Resource Website 1+ mentions |
DeepNano (RRID:SCR_016070) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software for an alternative basecaller for DNA base calling in the portable Oxford Nanopore MinION sequencing device, based on deep recurrent neural networks. Used to improve base calling accuracy and reduce sequencing error rate. | DNA, basecaller, Oxford Nanopore MinON read, sequencing, device, deep, recurrent, neural, network, accuracy, reduce, error |
is listed by: Debian is listed by: OMICtools has parent organization: Comenius University; Bratislava; Slovakia |
NVIDIA Corporation ; Slovak Research and Development Agency APVV-14-0253; VEGA 1/0684/16 (BB); VEGA 1/0719/14 (TV) |
PMID:28582401 | Free, Available for download | OMICS_14561 | http://compbio.fmph.uniba.sk/deepnano/, https://sources.debian.org/src/deepnano/ | SCR_016070 | SciCrunch Registry | DeepNano: Deep recurrent neural networks for base calling in MinION nanopore reads, DeepNano: alternative basecaller for MinION reads | 2026-11-07 11:58:32 | 5 | |||||
|
TreeDyn Resource Report Resource Website 100+ mentions |
TreeDyn (RRID:SCR_015946) | data processing software, data visualization software, software application, software resource | Visualization software that links unique leaf labels to lists of variables/values pairs of annotations (meta-information), independently of the tree topologies, remaining fully compatible with the basic newick format. These relationships are used by dynamic graphics operators, information visualization methods like Projection, Localization, Labelization, Reflection allowing an interaction from annotations to trees, from trees to annotations and from trees to trees through annotations., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | tree, variable, annotation, metainfo, newick, topology, graphic, operator, projection, localization, reflection, leaf, label, bio.tools |
is listed by: bio.tools is listed by: Debian |
THIS RESOURCE IS NO LONGER IN SERVICE | biotools:treedyn | https://bio.tools/treedyn | SCR_015946 | SciCrunch Registry | 2026-11-07 11:58:36 | 357 | ||||||||
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Falcon Resource Report Resource Website 100+ mentions |
Falcon (RRID:SCR_016089) | alignment software, data processing software, image analysis software, software application, software resource | Software package for aligning long sequencing reads as a diploid-aware genome assembler. Used for assembling non-inbred or rearranged heterozygous genomes. | fast, aligner, sequencing, diploid, genome, assembly, non-inbred, rearranged, heterozygous, single-molecule |
is listed by: Debian is listed by: OMICtools is related to: Howard Hughes Medical Institute |
Gordon and Betty Moore Foundation GBMF 3034; National Science Foundation DBI-1350041; National Science Foundation IOS-1237880; National Science Foundation MCB 0929402; National Science Foundation MCB 1122246; NHGRI R01 HG006677 |
PMID:27749838 | Free, Available for download, Freely available | OMICS_13514 | https://sources.debian.org/src/falcon/ | SCR_016089 | SciCrunch Registry | 2026-11-07 11:58:10 | 293 | ||||||
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SC3 Resource Report Resource Website 10+ mentions |
SC3 (RRID:SCR_015953) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software tool for the unsupervised clustering of cells from single cell RNA-Seq experiments. SC3 is capable of identifying subclones from the transcriptomes of neoplastic cells collected from patients. | scRNA-seq, interactive, cluster, clustering, cell, single, rna, rnaseq, bio.tools |
is listed by: Debian is listed by: bio.tools |
ARC (Action de Recherche Concerte) ; Belgian Network DYSCO ; Belgian State Science Policy Office ; Bloodwise 13003; Cambridge Experimental Cancer Medicine Centre ; Cambridge NIHR Biomedical Research Center ; EPSRC EP/N014529/1; FRS-FNRS ; Kay Kendall Leukaemia Fund ; Leukemia and Lymphoma Society of America 07037; MRC ; Sanger Institute ; University of Edinburgh ; Wallonia-Brussels Federation ; Wellcome Trust 104710/Z/14/Z |
PMID:28346451 | Free, Available for download | biotools:sc3 | https://bio.tools/sc3 | SCR_015953 | SciCrunch Registry | SC3 package, Single-Cell Consensus Clustering | 2026-11-07 11:58:30 | 23 | |||||
|
Exonerate Resource Report Resource Website 100+ mentions |
Exonerate (RRID:SCR_016088) | alignment software, data processing software, image analysis software, software application, software resource, software toolkit | Software package for sequence alignment of pairwise sequence comparison. Exonerate can be used to align sequences using many alignment models, exhaustive dynamic programming, or a variety of heuristics., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | sequence, alignment, pairwise, comparison, dynamic, programming, heuristic, bio.tools |
is used by: ExonerateTransferAnnotation is listed by: Debian is listed by: bio.tools has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
PMID:15713233 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:exonerate | https://bio.tools/exonerate | SCR_016088 | SciCrunch Registry | 2026-11-07 11:58:38 | 376 |
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