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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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Mapsembler2 Resource Report Resource Website 1+ mentions |
Mapsembler2 (RRID:SCR_024102) | software library, software resource, software toolkit | Targeted assembly software. It takes as input any number of NGS raw read sets and starter set of input sequences.May be used to Validate assembled sequence, Check if known enzyme is present in metagenomic NGS read set, Enrich unmappable reads by extending them, Check what happens at the extremities of a contig, Check the presence / absence and quantify RNA seq splicing events, Check presence/absence of SNPs or structural variants. | Targeted assembly, NGS raw read, input sequences, | is listed by: Debian | PMID:22443449 | Free, Available for download, Freely available, | OMICS_18310 | https://sources.debian.org/src/mapsembler2/ | SCR_024102 | mapsembler2, Mapsembler | 2026-08-29 11:29:07 | 1 | ||||||
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MAXFLOW Resource Report Resource Website 1+ mentions |
MAXFLOW (RRID:SCR_024103) | software library, software resource, software toolkit | Software library that implements the maxflow-mincut algorithm.Used for computing mincut/maxflow in a graph. | computing mincut/maxflow in a graph, | is listed by: Debian | DOI:10.1109/TPAMI.2004.60 | Free, Available for download, Freely available, | https://sources.debian.org/src/maxflow/ | SCR_024103 | maxflow | 2026-08-29 11:29:07 | 1 | |||||||
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Bio-Graphics Resource Report Resource Website |
Bio-Graphics (RRID:SCR_024061) | software resource, software toolkit | Software package to generate GD images of Bio::Seq objects. | generate GD images of Bio::Seq objects, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/libbio-graphics-perl/ | SCR_024061 | Bio-Graphics - Generate GD images of Bio-Seq objects, libbio-graphics-perl | 2026-08-29 11:29:06 | 0 | ||||||||
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CLI for BioMAJ Resource Report Resource Website |
CLI for BioMAJ (RRID:SCR_023980) | software resource, software toolkit | Software package to use BioMAJ providing biomaj-cli. | is listed by: Debian | Free, Available for download, Freely available | https://sources.debian.org/src/biomaj3-cli/ | SCR_023980 | biomaj3-cli, biomaj-cli | 2026-08-29 11:29:00 | 0 | |||||||||
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BCALM 2 Resource Report Resource Website 1+ mentions |
BCALM 2 (RRID:SCR_023975) | software application, software resource, source code | Software tool for constructing compacted de Bruijn graph from sequencing data.Parallel algorithm that distributes the input based on minimizer hashing technique, allowing for good balance of memory usage throughout its execution. | constructing compacted de Bruijn graph, sequencing data, | is listed by: Debian | PMID:27307618 | Free, Available for download, Freely available | OMICS_12164 | https://sources.debian.org/src/bcalm/ | SCR_023975 | bcalm | 2026-08-29 11:29:00 | 3 | ||||||
|
GCLib Resource Report Resource Website |
GCLib (RRID:SCR_024028) | software library, software resource, software toolkit | Software genomic C++ library of reusable code for bioinformatics projects.Provides core collection of data structures, trying to avoid unnecessary code dependencies of other heavy libraries, while minimizing build time. | reusable code for bioinformatics, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/gclib/ | SCR_024028 | gclib, genome-code-lib | 2026-08-29 11:29:00 | 0 | ||||||||
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CAT and BAT Resource Report Resource Website 1+ mentions |
CAT and BAT (RRID:SCR_023988) | software resource, software toolkit | Software pipeline for taxonomic classification of contigs and metagenome-assembled genomes. Contig Annotation Tool and Bin Annotation Tool for the taxonomic classification of long DNA sequences and metagenome assembled genomes of both known and unknown microorganisms, as generated by contemporary metagenomics studies. | taxonomic classification, long DNA sequences, metagenome assembled genomes, known and unknown microorganisms, contemporary metagenomics studies, | is listed by: Debian | PMID:31640809 | Free, Available for download, Freely available | https://sources.debian.org/src/cat-bat/ | SCR_023988 | Bin Annotation Tool, Contig Annotation Tool, BAT, CAT, cat-bat, CAT/BAT | 2026-08-29 11:29:06 | 3 | |||||||
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limereg Resource Report Resource Website |
limereg (RRID:SCR_024097) | software library, software resource, software toolkit | Open source commandline based application and/or software development library, that performs 2D, rigid image registration on two greyscale images and outputs either the transformation parameters or the registered image. | 2D, rigid image registration, greyscale images, transformation parameters, registered image, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/limereg/ | SCR_024097 | 2026-08-29 11:28:57 | 0 | |||||||||
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NeoBio Resource Report Resource Website |
NeoBio (RRID:SCR_024131) | software library, software resource, software toolkit | Software library of sequence alignment algorithms implemented in Java. | bioinformatics algorithms implemented in Java, sequence alignment algorithms, | is listed by: Debian | Free, Available for download, Freely available, | OMICS_21450 | https://sources.debian.org/src/neobio/ | SCR_024131 | neobio | 2026-08-29 11:29:02 | 0 | |||||||
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Murasaki Resource Report Resource Website |
Murasaki (RRID:SCR_024132) | software library, software resource, software toolkit | Software language-theory based homology detection tool across multiple large genomes. | language-theory based homology detection, multiple large genomes, | is listed by: Debian | PMID:20885980 | Free, Available for download, Freely available, | OMICS_11714 | https://sources.debian.org/src/murasaki/ | SCR_024132 | murasaki | 2026-08-29 11:29:07 | 0 | ||||||
|
Entrez Direct Resource Report Resource Website 10+ mentions |
Entrez Direct (RRID:SCR_024136) | software library, software resource, software toolkit | Software provides access to NCBI's suite of interconnected databases (publication, sequence, structure, gene, variation, expression, etc.) from Unix terminal window. Search terms are entered as command-line arguments. Individual operations are connected with Unix pipes to construct multi-step queries. Selected records can then be retrieved in variety of formats. | access to NCBI's suite of interconnected databases, Unix terminal window, construct multi-step queries, retrive selected records, | is listed by: Debian | https://sources.debian.org/src/ncbi-entrez-direct/ | SCR_024136 | Entrez Direct: E-utilities on the Unix Command Line, EDirect, ncbi-entrez-direct | 2026-08-29 11:28:58 | 13 | |||||||||
|
NJplot Resource Report Resource Website 1+ mentions |
NJplot (RRID:SCR_024137) | software library, software resource, software toolkit | Software tool as tree drawing program to draw any phylogenetic tree expressed in Newick phylogenetic tree format (e.g., the format used by the PHYLIP package).Used for rooting the unrooted trees obtained from parsimony, distance or maximum likelihood tree-building methods. | tree drawing program, draw any phylogenetic tree, Newick phylogenetic tree format, | is listed by: Debian | Free, Available for download, Freely available, | OMICS_04815 | https://sources.debian.org/src/njplot/ | SCR_024137 | njplot | 2026-08-29 11:29:07 | 2 | |||||||
|
Libxdf Resource Report Resource Website |
Libxdf (RRID:SCR_024096) | software library, software resource, software toolkit | Software cross-platform C++ library for loading multimodal, multi-rate signals stored in XDF files. Used in biosignal viewing application SigViewer and the LSL application XDFStreamer. Can also be integrated into other C++ applications. | C++ library, loading multimodal, multi-rate signals, SigViewer, XDFStreamer, biosignal viewing, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/libxdf/, https://xdf-modules.github.io/libxdf/ | SCR_024096 | libxdf, Libxdf � a C++ library for loading XDF files | 2026-08-29 11:29:07 | 0 | ||||||||
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ROBOKOP Resource Report Resource Website 1+ mentions |
ROBOKOP (RRID:SCR_023437) | ROBOKOP | data or information resource, portal, project portal | ROBOKOP system consists of web based user interface, API server, and several worker servers. Biomedical knowledge graph that integrates and semantically harmonizes important knowledge sources. Contains nodes representing entities such as genes, chemicals, and diseases, and edges representing relationships between them. Abstraction layer and user interface for knowledge graphs to support question answering. Used for reasoning over structured biomedical knowledge databases as part of NCATS translator and reasoner programs. ROBOKOP Knowledge Graph Builder constructs KG and provides extensible framework to handle graph query over and integration of federated data sources. | NCATS translator, knowledge graphs, structured biomedical knowledge databases, genes, chemicals, diseases, node, relationships edges, | NCATS OT2R002514; NCATS OT3TR002020; NIEHS U24ES035214 |
PMID:31410449 PMID:31769676 |
Free, Freely available | https://github.com/NCATS-Gamma/robokop, http://robokopkg.renci.org/browser/, | SCR_023437 | , ROBOKOP Graph Knowledgebase; Reasoning Over Biomedical Objects linked in Knowledge Oriented Pathways, ROBOKOP Knowledge Graph Builder (KGB), ROBOKOP KG, ROBOKOP KGB, ROBOKOP Knowledge Graph | 2026-08-29 11:28:55 | 3 | ||||||
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NanoSV Resource Report Resource Website 1+ mentions |
NanoSV (RRID:SCR_024127) | software resource, software toolkit | Software package that can be used to identify structural genomic variations in long-read sequencing data, such as data produced by Oxford Nanopore Technologies� MinION, GridION or PromethION instruments, or Pacific Biosciences RSII or Sequel sequencers. | identify structural genomic variations, long-read sequencing data, Oxford Nanopore Technologies� MinION, GridION, PromethION, Pacific Biosciences RSII, Sequel sequencers. | is listed by: Debian | PMID:29109544 | Free, Available for download, Freely available, | OMICS_29732 | https://sources.debian.org/src/nanosv/ | SCR_024127 | nanosv | 2026-08-29 11:29:07 | 4 | ||||||
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CTDConverter Resource Report Resource Website |
CTDConverter (RRID:SCR_024007) | software library, software resource, software toolkit | Software Python scripts to convert CTD files into other formats such as Galaxy, CWL. | Python, scripts to convert CTD files, Galaxy format, CWL format | is listed by: Debian | Free, Available for download, Freely available | https://sources.debian.org/src/ctdconverter/ | SCR_024007 | ctdconverter | 2026-08-29 11:28:56 | 0 | ||||||||
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NanoPlot Resource Report Resource Website 100+ mentions |
NanoPlot (RRID:SCR_024128) | software library, software resource, software toolkit | Software package as plotting tool for long read sequencing data and alignments. | plotting tool, long read sequencing data and alignments, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/nanoplot/, https://nanoplot.bioinf.be/ | SCR_024128 | nanoplot | 2026-08-29 11:28:58 | 397 | ||||||||
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OBITools Resource Report Resource Website 10+ mentions |
OBITools (RRID:SCR_024141) | software library, software resource, software toolkit | Software package for analysing NGS data in DNA metabarcoding context. Used to filter and edit sequences while taking into account taxonomic annotation to set up tailor-made analysis pipelines for broad range of DNA metabarcoding applications, including biodiversity surveys or diet analyses. | analysing NGS data, DNA metabarcoding, filter and edit sequences, taxonomic annotation, analysis pipelines for DNA metabarcoding applications, | is listed by: Debian | PMID:25959493 | Free, Available for download, Freely available, | OMICS_32696 | https://sources.debian.org/src/obitools/ | SCR_024141 | obitools | 2026-08-29 11:28:58 | 39 | ||||||
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FreeImage Resource Report Resource Website 1+ mentions |
FreeImage (RRID:SCR_024022) | software library, software resource, software toolkit | Open Source software library for developers who would like to support popular graphics image formats like PNG, BMP, JPEG, TIFF and others as needed by today's multimedia applications. | support graphics image formats, PNG, BMP, JPEG, TIFF | is listed by: Debian | Free, Available for download, Freely available | https://sources.debian.org/src/freeimage/ | SCR_024022 | freeimage | 2026-08-29 11:29:00 | 2 | ||||||||
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Orthanc Resource Report Resource Website 1+ mentions |
Orthanc (RRID:SCR_024145) | software library, software resource, software toolkit | Open source lightweight DICOM server for medical imaging.Vendor neutral archive to automate and optimize imaging flows. Can be extended with plugins that provide solutions for teleradiology, digital pathology, or enterprise ready databases. | DICOM server, medical imaging, | is listed by: Debian | PMID:29725964 | Free, Available for download, Freely available, | https://sources.debian.org/src/orthanc/ | SCR_024145 | orthanc | 2026-08-29 11:29:02 | 4 |
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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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