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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Galaxy scater Resource Report Resource Website 1+ mentions |
Galaxy scater (RRID:SCR_017394) | data analysis software, data processing software, sequence analysis software, service resource, software application, software resource, software toolkit, source code, training service resource | Software tool as Galaxy based training resource for single cell RNA-seq quality control and analyses. | scRNA-seq, single, cell, scater, Galaxy, training, quality, control, bio.tools |
is listed by: Debian is listed by: bio.tools |
BBSRC BBS/E/T/000PR9817; BBSRC BBS/E/T/000PR9818; BBSRC BBS/E/T/000PR9819; BBSRC CCG:BBS/E/T/000PR9816 |
DOI:10.1101/724047 | Free, Available for download, Freely available | biotools:Galaxy_scater | https://bio.tools/Galaxy_scater | SCR_017394 | 2026-09-12 12:58:52 | 1 | ||||||
|
Multiple Myeloma survival predictor Resource Report Resource Website 1+ mentions |
Multiple Myeloma survival predictor (RRID:SCR_017651) | data access protocol, service resource, software resource, web service | Dockerized environment for winning algorithm in 2017 Multiple Myeloma DREAM Challenge, Sub-Challenge 3. | Multiple Myeloma, prognostic model, survival analysis, GuanRank, bio.tools |
is listed by: bio.tools is listed by: Debian |
Multiple Myeloma | Restricted | biotools:Multiple_Myeloma_survival_prediction | https://bio.tools/Multiple_Myeloma_survival_prediction | SCR_017651 | 2026-09-12 12:58:55 | 2 | |||||||
|
MCScan Resource Report Resource Website 10+ mentions |
MCScan (RRID:SCR_017650) | data analysis software, data processing software, sequence analysis software, software application, software resource, software toolkit | Software package to simultaneously scan multiple genomes to identify homologous chromosomal regions and subsequently align these regions using genes as anchors.Used to identify conserved gene arrays both within same genome and across different genomes. Command line program to wrap dagchainer and combine pairwise results into multi alignments in column format. | Simultaneously, scan, multiple, genome, identify, homologous, chromosomal, region, align, gene, anchor, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: University of Georgia; Georgia; USA |
Free, Available for downoad, Freely available | biotools:MCScan | http://chibba.agtec.uga.edu/duplication/mcscan/, https://bio.tools/MCScan | SCR_017650 | Multiple Collinearity Scan | 2026-09-12 12:58:55 | 42 | |||||||
|
Blobtools Resource Report Resource Website 100+ mentions |
Blobtools (RRID:SCR_017618) | data analytics software, data processing software, data visualization software, software application, software resource | Software tool as modular command line solution for visualisation, quality control and taxonomic partitioning of genome datasets. Used for interrogation of genome assemblies. Assists in primary partitioning of data, leading to improved assemblies, and screening of final assemblies for potential contaminants. | Modular, command, line, solution, visualisation, quality, control, taxonomic, partitioning, genome, dataset, genome assembly, screening, contaminant, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: BlobTools2 |
BBSRC ; James Hutton Institute/Edinburgh University School of Biological Sciences fellowship |
DOI:10.12688/f1000research.12232.1 | Free, Available for download, Freely available | biotools:blobtools | https://github.com/DRL/blobtools, https://bio.tools/blobtools | SCR_017618 | BlobTools | 2026-09-12 12:58:55 | 225 | |||||
|
Ngmlr Resource Report Resource Website 10+ mentions |
Ngmlr (RRID:SCR_017620) | NGMLR | alignment software, data processing software, image analysis software, software application, software resource | Software tool as long read mapper designed to align PacBio or Oxford Nanopore reads to reference genome and optimized for structural variation detection. | Long, read, mapper, align, PacBio, Oxford Nanopore, read, reference, genome, structural, variantion, detection, bio.tools |
is listed by: bio.tools is listed by: Debian |
National Science Foundation ; NHGRI R01 HG006677; NHGRI UM1 HG008898 |
PMID:29713083 | Free, Available for download, Freely available | biotools:ngmlr | https://bio.tools/ngmlr | SCR_017620 | coNvex Gap-cost alignMent for Long Reads | 2026-09-12 12:58:55 | 36 | ||||
|
PatchDock Resource Report Resource Website 100+ mentions |
PatchDock (RRID:SCR_017589) | data access protocol, simulation software, software application, software resource, web service | Web server for molecular docking. Performs structure prediction of protein–protein and protein–small molecule complexes. Molecular docking algorithm based on shape complementarity principles. | Molecular, docking, structure, prediction, protein, molecule, shape, complex, bio.tools |
is listed by: Debian is listed by: bio.tools |
Hermann Minkowski-Minerva Center for Geometry at Tel Aviv University ; Israel Science Foundation ; Israeli Ministry of Science ; National Cancer Institute ; NIH |
PMID:15980490 | Free, Freely available | biotools:patchdock | https://bio.tools/patchdock | SCR_017589 | 2026-09-12 12:58:54 | 104 | ||||||
|
shinyGEO Resource Report Resource Website |
shinyGEO (RRID:SCR_017605) | analysis service resource, production service resource, service resource, software resource, web application | Web based tool to download gene expression datasets from GEO in order to perform differential expression and survival analysis for gene of interest. Produces publication ready graphics and generates R code ensuring that all analyses are reproducible. Web based application for analyzing gene expression omnibus datasets. | Gene, expression, dataset, GEO, differencial, analysis, gene, graphic, omnibus, data, bio.tools |
uses: Shiny is listed by: Debian is listed by: bio.tools has parent organization: Eastern Connecticut State University; Connecticut; United States works with: Gene Expression Omnibus (GEO) |
Google Summer of Code | PMID:27503226 | Free, Available for download, Freely available | biotools:shinygeo | https://gdancik.github.io/shinyGEO/, https://bio.tools/shinygeo | SCR_017605 | 2026-09-12 12:58:54 | 0 | ||||||
|
refgenie Resource Report Resource Website 1+ mentions |
refgenie (RRID:SCR_017574) | data management software, service resource, software application, software resource | Software tool to organize, retrieve, and share genome analysis resources. Reference genome assembly asset manager. In addition to genome indexes, can manage any files related to reference genomes, including sequences and annotation files. Includes command line interface and server application that provides RESTful API, so it is useful for both tool development and analysis. | Organize, retrive, share, genome, analysis, reference, assembly, asset, manager, sequence, annotation, file, command, line, interface, bio.tools |
is listed by: Debian is listed by: bio.tools |
DOI:10.1101/698704 | Free, Available for download, Freely available | biotools:Refgenie | https://bio.tools/Refgenie | SCR_017574 | reference genome manager | 2026-09-12 12:58:54 | 7 | ||||||
|
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 | Genetic Algorithm for Demographic Model Analysis | 2026-09-12 12:58:55 | 3 | |||||
|
CRISPy-web Resource Report Resource Website 10+ mentions |
CRISPy-web (RRID:SCR_017970) | data access protocol, software resource, web service | Web tool to design sgRNAs for CRISPR applications. Web tool based on CRISPy to design sgRNAs for any user-provided microbial genome. Implemented as standalone web application for Cas9 target prediction. | Design, sgRNA, CRISP, microbial, genome, Cas9, target, prediction, data, guide, single, editing, bio.tools |
is listed by: bio.tools is listed by: Debian |
Novo Nordisk Foundation | PMID:29062934 | Free, Freely available | biotools:crispy | https://bio.tools/crispy | SCR_017970 | single guide RNA desing | 2026-09-12 12:58:55 | 28 | |||||
|
PAFScaff Resource Report Resource Website 1+ mentions |
PAFScaff (RRID:SCR_017976) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software as Pairwise mApping Format reference based Scaffold anchoring and super scaffolding tool. Dsigned for mapping genome assembly scaffolds to closely related chromosome level reference genome assembly. | Pairwise, mapping, reference, scaffold, genomics, scaffolding, assembly, genome, chromosome, bio.tools |
is listed by: Debian is listed by: bio.tools |
Free, Freely available | biotools:PAFScaff | https://github.com/slimsuite/pafscaff/blob/master/PAFScaff.md, https://slimsuite.github.io/pafscaff/, https://bio.tools/PAFScaff | SCR_017976 | Pairwise mApping Format reference-based Scaffold | 2026-09-12 12:58:55 | 4 | |||||||
|
CandiMeth Resource Report Resource Website 1+ mentions |
CandiMeth (RRID:SCR_017974) | CandiMeth | analysis service resource, data analysis software, data processing software, production service resource, service resource, software application, software resource | Software tool for visualisation and quantification of DNA methylation at candidate features. | DNA, methylation, candidate feature, visualisation, quantification, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Galaxy |
ESRC/BBSRC ; Medical Research Council |
Free, Freely available | biotools:CandiMeth | http://bit.do/candimeth, https://usegalaxy.org/u/sarajayne-thursby/w/candimeth-8, https://bio.tools/CandiMeth | SCR_017974 | CANDIdate feature METHylation | 2026-09-12 12:58:55 | 2 | |||||
|
VEnCode Resource Report Resource Website 1+ mentions |
VEnCode (RRID:SCR_018024) | VEnCode | data analysis software, data processing software, software application, software resource | Software tool to perform intersectional genetics-related operations to find VEnCodes using databases provided by FANTOM5 consortium, namely CAGE enhancer and transcription start site (TSS) databases. | FANTOM5 consortium, data, CAGE enhancer, transcription site database, intersectional genetics, bio.tools |
is listed by: Debian is listed by: bio.tools |
DOI:10.1101/552984 | Free, Available for download, Freely available | BioTools:VEnCode, biotools:VEnCode | https://bio.tools/VEnCode, https://bio.tools/VEnCode, https://bio.tools/VEnCode | SCR_018024 | Versatile Entry Codes | 2026-09-12 12:58:56 | 1 | |||||
|
fineSTRUCTURE Resource Report Resource Website 10+ mentions |
fineSTRUCTURE (RRID:SCR_018170) | data analysis software, data processing software, software application, software resource | Software tool as algorithm for identifying population structure using dense sequencing data. Can perform model based Bayesian clustering on large datasets, including full resequencing data. | Identifying population structure, dense sequencing data, Bayesian clustering, large dataset, data, analysis, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Available for download, Freely available | biotools:finestructure | https://bio.tools/finestructure | SCR_018170 | FineSTRUCTURE version 2 | 2026-09-12 12:58:58 | 23 | |||||||
|
ChiCMaxima Resource Report Resource Website 1+ mentions |
ChiCMaxima (RRID:SCR_018178) | analysis service resource, data access protocol, production service resource, service resource, software resource, web service | Pipeline for analyzing and identificantion of chromatin loops in CHi-C promoters data. Used to capture Hi-C visualization and interaction calling. | Chromatin loop, CHi-C promoter, data, Hi-C visualization, interaction calling, data, analysis, bio.tools |
is listed by: Debian is listed by: bio.tools |
PMID:31118054 | Free, Freely available | biotools:ChiCMaxima | https://bio.tools/ChiCMaxima | SCR_018178 | 2026-09-12 12:58:58 | 2 | |||||||
|
SnpHub Resource Report Resource Website 1+ mentions |
SnpHub (RRID:SCR_018177) | software resource, web application | Web Shiny-based server framework for retrieving, analyzing and visualizing large genomic variations data. | Genomic, data, data visualization, data analysis, data retrieving, bio.tools |
is listed by: Debian is listed by: bio.tools |
National Key Research and Development Program of China 2016YFD0100801; National Key Research and Development Program of China 2018YFD0100803; National Natural Science Foundation of China 31701415 |
Free, Available for download, Freely available | biotools:SnpHub | http://guoweilong.github.io/SnpHub/, https://bio.tools/SnpHub | SCR_018177 | 2026-09-12 12:58:58 | 1 | |||||||
|
SpydrPick Resource Report Resource Website 1+ mentions |
SpydrPick (RRID:SCR_018176) | data analysis software, data processing software, software application, software resource | Software command line tool for performing direct coupling analysis of aligned categorical datasets. Used for analysis at scale of pan genomes of many bacteria. Incorporates correction for population structure, which adjusts for phylogenetic signal in data without requiring explicit phylogenetic tree. | Direct coupling analysis, aligned categorical datasets, analysis, genome, bacteria, phylogenetic signal, correction, phylogenetic tree, data, bio.tools |
is listed by: Debian is listed by: bio.tools |
COIN Center of Excellence ; Academy of Finland ; European Research Council ; Wellcome Trust |
PMID:31361894 | Free, Available for download, Freely available | biotools:SpydrPick | https://anaconda.org/bioconda/spydrpick, https://bio.tools/SpydrPick | SCR_018176 | 2026-09-12 12:58:58 | 3 | ||||||
|
CRISPRdirect Resource Report Resource Website 500+ mentions |
CRISPRdirect (RRID:SCR_018186) | analysis service resource, data access protocol, production service resource, service resource, software resource, web service | Software for designing CRISPR/Cas guide RNA with reduced off target sites. Used for rational design of CRISPR/Cas target. Web server for selecting rational CRISPR/Cas targets from input sequence. Server currently incorporates genomic sequences of human, mouse, rat, marmoset, pig, chicken, frog, zebrafish, Ciona, fruit fly, silkworm, Caenorhabditis elegans, Arabidopsis, rice, Sorghum and budding yeast. | CRISP/Cas guide RNA, reduced off target site, design of CRISP/Cas target, selecting rational target, sequence, genomic sequence, RNA, bio.tools |
is listed by: Debian is listed by: bio.tools |
Japan Science and Technology Agency ; Ministry of Education ; Culture ; Sports ; Science and Technology of Japan |
PMID:25414360 | Free, Freely available | biotools:CRISPRdirect | https://bio.tools/CRISPRdirect | SCR_018186 | 2026-09-12 12:58:58 | 588 | ||||||
|
Fcirc Resource Report Resource Website 1+ mentions |
Fcirc (RRID:SCR_018090) | Fcirc | data processing software, software application, software resource, workflow software | Software Python pipeline for linear and circular RNAs of known fusions exploration. Pipeline for exploring linear transcripts and circRNAs of known fusions based on RNA-Seq data. Known fusion genes are from multiple databases like COSMIC, ChimerDB, TicDB, FARE-CAFE and FusionCancer or user-added gene-pairs. | Fusion gene, linear and circular RNA, fusion exploration, RNAseq data, linear transcript, circRNA, gene, data, pipeline, bio.tools |
uses: HISAT2 uses: SAMTOOLS is listed by: Debian is listed by: bio.tools |
National Key Research and Development Program 2017YFC0908500 ; National Natural Science Foundation of China 31571363 ; National Natural Science Foundation of China 31771469 ; National Natural Science Foundation of China 81573023 |
Free, Available for download, Freely available | biotools:Fcirc | https://bio.tools/Fcirc | SCR_018090 | Comprehensive Pipeline for Exploration of Fusion Linear and Circular RNAs | 2026-09-12 12:58:57 | 2 | |||||
|
HingeProt Resource Report Resource Website 1+ mentions |
HingeProt (RRID:SCR_018136) | data access protocol, service resource, software resource, web service | Web server for predicting rigid protein parts and flexible hinge regions connecting them in native topology of protein chains by employing elastic network (EN) models. Automated prediction of hinges in protein structures. | Predicting protein hinges, flexible hinge region, native topology, rigid protein part, elastic network model, protein structure, bio.tools |
is listed by: Debian is listed by: bio.tools |
PMID:17847101 | Free, Available for download, Freely available | biotools:hingeprot | https://bio.tools/hingeprot | SCR_018136 | 2026-09-12 12:58:58 | 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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