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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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BioConda Resource Report Resource Website 50+ mentions |
BioConda (RRID:SCR_018316) | software application, software resource | Software distribution management for life sciences. Channel for Conda package manager specializing in bioinformatics software. Consists of repository of recipes hosted on GitHub, build system turning these recipes into conda packages, repository of packages containing bioinformatics packages ready to use with conda install. | Software distribution management, bioinformatic software, package repository, GitHub, conda, bio.tools |
lists: CCS is listed by: bio.tools is listed by: Debian is related to: Conda is related to: RNAProt |
German Research Foundation ; Intramural Program of the National Institute of Diabetes and Digestive and Kidney Diseases ; Netherlands Organisation for Scientific Research ; NYU Abu Dhabi Research Institute |
PMID:29967506 | Free, Available for download, Freely available | biotools:bioconda | https://bio.tools/bioconda | SCR_018316 | SciCrunch Registry | Bioconda | 2026-09-26 02:19:29 | 73 | |||||
|
Chromosome Scale Assembler Resource Report Resource Website 1+ mentions |
Chromosome Scale Assembler (RRID:SCR_017960) | CSA | software application, software resource | Software pipeline for high-throughput chromosome level vertebrate genome assembly. Pipeline, which after contig assembly performs post assembly improvements by ordering assembly and closing gaps, as well as splitting of low supported regions. | Assembly, chromosome, vertebrate, genome, contig, closing, gap, splitting, low, supported, region, bio.tools |
is listed by: bio.tools is listed by: Debian |
German Research foundation | Free, Available for download, Freely available | biotools:csa2.6 | https://bio.tools/CSA2.6 | SCR_017960 | SciCrunch Registry | Chromosome Scale Assembler | 2026-09-26 02:19:30 | 5 | |||||
|
riborex Resource Report Resource Website 1+ mentions |
riborex (RRID:SCR_019104) | software resource, software toolkit | Software R package for identification of differential translation from Ribo-seq data. Computational tool for mapping genome wide differences in translation efficiency. | Ribo-seq data, differential translation, differential translation identification, mapping genome differences, translation efficiency, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: University of Southern California; Los Angeles; USA |
NHGRI R01 HG006015 | PMID:28158331 | Free, Available for download, Freely available | biotools:riborex | https://bio.tools/riborex | SCR_019104 | SciCrunch Registry | riborex v2.3.4 | 2026-09-26 02:19:32 | 7 | |||||
|
Tool recommender system in Galaxy Resource Report Resource Website 1+ mentions |
Tool recommender system in Galaxy (RRID:SCR_018491) | software resource, software toolkit | Software developed by analyzing workflows composed by researchers on European Galaxy server, using deep learning approach. Used to recommend tools in Galaxy. Gated recurrent units neural network. | Recommender system, Galaxy, Workflows, Deep learning, Neural networks, Gated recurrent units, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: Galaxy |
Free, Freely available | biotools:tool_recommender_system_in_galaxy | https://bio.tools/tool_recommender_system_in_galaxy | SCR_018491 | SciCrunch Registry | Galaxy tool recommendation, Tool recommender system in Galaxy using deep learning | 2026-09-26 02:19:29 | 2 | |||||||
|
ADMIXTOOLS Resource Report Resource Website 100+ mentions |
ADMIXTOOLS (RRID:SCR_018495) | software resource, software toolkit | Software package that supports formal tests of whether admixture occurred, and makes it possible to infer admixture proportions and dates. | Formal test support, admixture, infer admixture proportion, infer admixture date, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Harvard University; Cambridge; United States |
NIGMS GM100233; U.S. National Science Foundation HOMINID |
PMID:22960212 | Free, Available for download, Freely available | biotools:admixtools | http://genetics.med.harvard.edu/reich/Reich_Lab/Software.html., https://bio.tools/admixtools | SCR_018495 | SciCrunch Registry | 2026-09-26 02:19:29 | 222 | ||||||
|
CITE-seq-Count Resource Report Resource Website 50+ mentions |
CITE-seq-Count (RRID:SCR_019239) | software resource, software toolkit | Software python package that allows to count antibody TAGS from CITE-seq and/or cell hashing experiment. Software tool that allows to get UMI counts from single cell protein assay. Used to count (UMI counts) antibody-derived-tags (ADTs) or Cell Hashing tags (HTOs) in raw sequencing reads and build count matrix. | antibody TAGS count, CITE-seq, cell hashing experiment, antibody derived tags, cell hashing tags, raw sequencing reads, build count matrix, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Available for download, Freely available | biotools:https:cite-seq-count | https://cite-seq.com/computational-tools/, https://bio.tools/cite-seq-count | SCR_019239 | SciCrunch Registry | CITE-seq-Count v1.4.0, Cellular Indexing of Transcriptomes and Epitopes by Sequencing Count | 2026-09-26 02:19:32 | 60 | |||||||
|
EpiDISH R package Resource Report Resource Website 10+ mentions |
EpiDISH R package (RRID:SCR_018004) | EpiDISH | software resource, software toolkit | Software R package provides tools to infer proportions of priori known cell-types present in sample representing mixture of such cell-types. Comparison of reference based algorithms for correcting cell-type heterogeneity in Epigenome-Wide Association Studies. | Epigenetic, sample heterogeneity, reference, algorithm, correcting, cell type, bio.tools |
is listed by: bio.tools is listed by: Debian |
Chinese Academy of Sciences ; EU-FP7 ; Max-Planck Society ; NSFC 31571359; Royal Society Newton Advanced Fellowship ; Shanghai Institute for Biological Sciences |
PMID:28193155 | Free, Available for download, Freely available | biotools:epidish | https://github.com/sjczheng/EpiDISH, https://bio.tools/epidish | SCR_018004 | SciCrunch Registry | Epigenetic Dissection of Intra-Sample Heterogeneity | 2026-09-26 02:19:29 | 14 | ||||
|
Bio-Chado-Schema Resource Report Resource Website |
Bio-Chado-Schema (RRID:SCR_024059) | software application, software resource | Standard object-relational mapping layer for use with GMOD Chado database schema. This layer is implemented with DBIx::Class, generated with the help of DBIx::Class::Schema::Loader module. | Standard object-relational mapping layer, GMOD Chado database schema, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/libbio-chado-schema-perl/ | SCR_024059 | SciCrunch Registry | libbio-chado-schema-perl, Bio-Chado-Schema - A standard DBIx-Class layer for the Chado database schema | 2026-09-26 02:19:40 | 0 | ||||||||
|
pyomo Resource Report Resource Website 1+ mentions |
pyomo (RRID:SCR_024188) | software application, software resource | Open source Python-based optimization modeling language with diverse set of optimization capabilities. | Python, optimization modeling language, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/pyomo/ | SCR_024188 | SciCrunch Registry | 2026-09-26 02:19:40 | 5 | |||||||||
|
AI-FANN Resource Report Resource Website |
AI-FANN (RRID:SCR_024060) | software application, software resource | Software Perl wrapper for the Fast Artificial Neural Network library | Perl wrapper, Fast Artificial Neural Network library, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/libai-fann-perl/ | SCR_024060 | SciCrunch Registry | AI-FANN - Perl wrapper for the Fast Artificial Neural Network library, libai-fann-perl | 2026-09-26 02:19:40 | 0 | ||||||||
|
Bio-Coordinate Resource Report Resource Website |
Bio-Coordinate (RRID:SCR_024063) | software application, software resource | Software application used for working with various biological coordinate systems. See Bio::Coordinate::Collection and Bio::Collection::Pair for examples. | biological coordinate systems, | is listed by: Debian | https://sources.debian.org/src/libbio-coordinate-perl/ | SCR_024063 | SciCrunch Registry | Bio-Coordinate - Modules for working with biological coordinates, libbio-coordinate-perl | 2026-09-26 02:19:42 | 0 | |||||||||
|
Ginkgo CADx Resource Report Resource Website |
Ginkgo CADx (RRID:SCR_024031) | software application, software resource | Software advanced DICOM viewer and dicomizer that can also be used to convert png, jpeg, bmp, pdf, tiff to DICOM files. | Digital Imaging and Communication In Medicine, DICOM viewer, dicomizer, convert files, png, jpeg, bmp, pdf, tiff, convert to DICOM files, | is listed by: Debian | Free, Freely available | https://sources.debian.org/src/ginkgocadx/, https://github.com/gerddie/ginkgocadx | SCR_024031 | SciCrunch Registry | ginkgocadx | 2026-09-26 02:19:40 | 0 | ||||||||
|
HTSJDK Resource Report Resource Website 1+ mentions |
HTSJDK (RRID:SCR_024036) | software application, software resource | Software implementation of unified Java library for accessing common file formats, such as SAM and VCF, used for high-throughput sequencing data. There are also an number of useful utilities for manipulating HTS data. | accessing common file formats, SAM, VCF, manipulating HTS data, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/htsjdk/, https://github.com/samtools/htsjdk | SCR_024036 | SciCrunch Registry | htsjdk | 2026-09-26 02:19:40 | 4 | ||||||||
|
InsPecT Resource Report Resource Website 1+ mentions |
InsPecT (RRID:SCR_024038) | software application, software resource | Software tool to addresses several algorithmic problems in order to identify modified proteins.Software MS/MS database search tool specifically designed to address two crucial needs of the proteomics comminuty: post-translational modification identification and search speed. | addresses algorithmic problems, identify modified proteins, post-translational modification identification, | is listed by: Debian | PMID:16013882 | Free, Available for download, Freely available, | OMICS_02397 | https://sources.debian.org/src/inspect/ | SCR_024038 | SciCrunch Registry | Inspect, inspect | 2026-09-26 02:19:41 | 1 | ||||||
|
Bibus Resource Report Resource Website |
Bibus (RRID:SCR_023974) | software application, software resource | Bibliographic and reference management software. Allows to search, edit, and sort bibliographic records. | Bibliographic and reference management, bibliographic records, search bibliographic records, edit bibliographic records, sort bibliographic records, | is listed by: Debian | Free, Available for download, Freely available | https://sources.debian.org/src/bibus/ | SCR_023974 | SciCrunch Registry | bibus | 2026-09-26 02:19:39 | 0 | ||||||||
|
Kaptive Resource Report Resource Website 10+ mentions |
Kaptive (RRID:SCR_024046) | software application, software resource | Software tool to report information about surface polysaccharide loci for Klebsiella pneumoniae species complex and Acinetobacter baumannii genome assemblies. | report information, surface polysaccharide loci, genome assemblies, | is listed by: Debian | PMID:28348840 | Free, Available for download, Freely available, | OMICS_27932 | https://sources.debian.org/src/kaptive/ | SCR_024046 | SciCrunch Registry | kaptive | 2026-09-26 02:19:40 | 18 | ||||||
|
JabRef Resource Report Resource Website 1+ mentions |
JabRef (RRID:SCR_024047) | software application, software resource | Open source, software cross platform citation and reference management tool.Helps to collect and organize sources, find the paper, discover the latest research. | citation and reference, management tool, collect and organize sources, find the paper, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/jabref-plugin-oo/, https://github.com/JabRef/jabref | SCR_024047 | SciCrunch Registry | jabref, JabRef Bibliography Management | 2026-09-26 02:19:40 | 4 | ||||||||
|
KBibTeX Resource Report Resource Website |
KBibTeX (RRID:SCR_024048) | software application, software resource | Software tool as bibliography editor for KDE. Used in conjunction with Kile. BibTeX editor for KDE. KBibTeX's primary file format is BibTeX as known from LaTeX, but other formats such as RIS, PDF, or RTF can be imported and exported. | bibliography editor for KDE, bibliography editor, BibTeX editor for KDE, | is listed by: Debian | Restricted | https://sources.debian.org/src/kbibtex/ | SCR_024048 | SciCrunch Registry | kbibtex | 2026-09-26 02:19:40 | 0 | ||||||||
|
Lucy Resource Report Resource Website |
Lucy (RRID:SCR_024099) | software application, software resource | Software tool to clean sequence data from automated DNA sequencers prior to sequence assembly and other downstream uses. | clean sequence data from automated DNA sequencers, Sanger sequencing, | is listed by: Debian | Free, Available for download, Freely available, | OMICS_14823 | https://sources.debian.org/src/lucy/ | SCR_024099 | SciCrunch Registry | lucy, Lucy DNA sequence quality and vector trimming tool | 2026-09-26 02:19:40 | 0 | |||||||
|
rambo-k Resource Report Resource Website |
rambo-k (RRID:SCR_024198) | software application, software resource | Software tool for rapid and sensitive removal of background sequences from Next Generation Sequencing data. | removal of background sequences, Next Generation Sequencing data, | is listed by: Debian | PMID:26379285 | Free, Available for download, Freely available, | OMICS_10013 | https://sources.debian.org/src/rambo-k/ | SCR_024198 | SciCrunch Registry | 2026-09-26 02:19:42 | 0 |
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