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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
sleuth Resource Report Resource Website 10+ mentions |
sleuth (RRID:SCR_016883) | data processing software, software application, data analysis software, software resource | Software tool for analysis of RNA-Seq experiments for which transcript abundances have been quantified with kallisto. Used for the differential analysis of gene expression data that utilizes bootstrapping in conjunction with response error linear modeling to decouple biological variance from inferential variance. | differential, analysis, RNA-Seq, data, gene, expression, bootstrapping, error, linear, modeling, decouple, biological, variance, inferential, bio.tools |
is listed by: Debian is listed by: bio.tools works with: kallisto |
NIDDK R01 DK094699; NHGRI R01 HG006129 |
PMID:28581496 | Free, Available for download, Freely available | biotools:sleuth, BioTools:sleuth | https://bio.tools/sleuth, https://bio.tools/sleuth, https://bio.tools/sleuth | SCR_016883 | 2026-07-30 09:30:07 | 24 | ||||||
|
ropls Resource Report Resource Website 10+ mentions |
ropls (RRID:SCR_016888) | R OPLS | data processing software, software application, data analysis software, software resource | Software R package for multivariate analysis and feature selection of omics data. Used for visualization, regression, classification, and feature selection of omics data where the number of variables exceeds the number of samples and with multicollinearity among variables. | multivariate, analysis, feature, selection, omics, data, visualization, regression, classification, variable, exceedes, number, sample, multicollinearity, bio.tools |
is listed by: Bioconductor is listed by: Debian is listed by: bio.tools is related to: R Project for Statistical Computing |
Free, Available for download, Freely available | BioTools:ropls, biotools:ropls | https://bio.tools/ropls, https://bio.tools/ropls, https://bio.tools/ropls | SCR_016888 | R Orthogonal Partial Least Squares | 2026-07-30 09:30:13 | 12 | ||||||
|
XL-mHG Resource Report Resource Website |
XL-mHG (RRID:SCR_016846) | xlmhg | data processing software, software application, data analysis software, software resource | Software Python package as a semiparametric test for enrichment in ranked lists. Used for determining gene set enrichment. | semiparametric, test, enrichment, ranked, list, gene, bio.tools |
is listed by: Debian is listed by: bio.tools |
Free, Available for download, Freely available | BioTools:XL-mHG, biotools:XL-mHG | https://bio.tools/XL-mHG, https://bio.tools/XL-mHG, https://bio.tools/XL-mHG | SCR_016846 | xlminimumhypergeometric, XL-minimum HyperGeometric test, XL-minimum HyperGeometric, xlmhg, XL-mHG | 2026-07-30 09:30:06 | 0 | ||||||
|
SCIPION Resource Report Resource Website 10+ mentions |
SCIPION (RRID:SCR_016738) | data processing software, software toolkit, software resource, software application, image processing software | Software framework for image processing to obtain 3D models of macromolecular complexes using Electron Microscopy. Open-source project for integration, reproducibility and validation in 3D electron microscopy. It integrates several software packages to execute workflows combining different software tools, while taking care of formats and conversions. Electron Microscopy (3DEM). waiting for pdf from Joe | image, processing, data, 3DEM, macromolecular, complex, electron, microscopy, format, conversion, bio.tools |
is listed by: bio.tools is listed by: Debian |
Spanish Ministry of Economy and Competitiveness ; Comunidad the Madrid ; European Union ; Instruct |
PMID:27108186 | Free, Available for download, Registration required | biotools:monores | https://github.com/I2PC/scipion, https://bio.tools/monores | SCR_016738 | 2026-07-30 09:30:12 | 20 | ||||||
|
Rampart Resource Report Resource Website 1+ mentions |
Rampart (RRID:SCR_016742) | workflow software, software resource, software application, data processing software | Software for workflow management system for de novo genome assembly of DNA sequence data.Designed to exploit high performance computing environments, such as clusters and shared memory systems. | workflow, management, system, de novo, genome, assembly, DNA, sequence, data, high, performance, computing, environment, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: The Genome Analysis Centre; Norwich; United Kingdom |
BBSRC | PMID:25637556 | Free, Available for download, Freely available | biotools:rampart | http://www.earlham.ac.uk/rampart/, https://bio.tools/rampart | SCR_016742 | 2026-07-30 09:30:06 | 2 | ||||||
|
PanoramaWeb Resource Report Resource Website |
PanoramaWeb (RRID:SCR_017136) | service resource, data repository, data access protocol, software resource, web service, data or information resource, storage service resource | Repository software for targeted mass spectrometry assays from Skyline. Targeted proteomics knowledge base. Public repository for quantitative data sets processed in Skyline. Facilitates viewing, sharing, and disseminating results contained in Skyline documents. | repository, software, targeted, mass, spectrometry, data, proteomic, quantitative, viewing, sharing, disseminating, result, , bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: University of Washington; Seattle; USA works with: Skyline |
NIGMS R01 GM103551; NIGMS R01 GM121696; NHGRI U54 HG008097; NIH R01 AR071762; University of Washington Proteomics Resource |
DOI:10.1074/mcp.RA117.000543 | Free, Freely available | biotools:panorama | https://bio.tools/panorama | SCR_017136 | 2026-07-30 09:30:10 | 0 | ||||||
|
BSA4Yeast Resource Report Resource Website 1+ mentions |
BSA4Yeast (RRID:SCR_017113) | service resource, data access protocol, data analysis service, software resource, web service, production service resource, analysis service resource | Web application for Quantitative Trait Loci mapping via bulk segregant analysis of yeast sequencing data. Application provides automated data processing, annotations, and web interface to explore identified QTLs. | quantitative, trait, loci, mapping, bulk, segregant, analysis, yeast, sequencing, data, processing, annotation, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: University of Luxembourg; Luxembourg; Luxembourg |
Fonds Nationale de la Recherche (FNR) Luxembourg | Free, Freely available, Registration required | biotools:BSA4Yeast | https://bio.tools/BSA4Yeast | SCR_017113 | Bulk Segregant Analysis for Yeast | 2026-07-30 09:30:09 | 1 | ||||||
|
ML Repo Resource Report Resource Website 1+ mentions |
ML Repo (RRID:SCR_017079) | MLRepo | storage service resource, service resource, data repository | Machine learning repository for microbiome datasets. | machine, learning, repository, microbiome, dataset, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Freely available | biotools:ML_Repo | https://bio.tools/ML_Repo | SCR_017079 | Machine Learning Repository | 2026-07-30 09:30:06 | 2 | ||||||
|
shovill Resource Report Resource Website 100+ mentions |
shovill (RRID:SCR_017077) | data processing software, sequence analysis software, data analysis software, software resource, software application | Software tool to assemble bacterial isolate genomes from Illumina paired end reads. Used for isolate data only, primarily small haploid organisms. Supports assemblers like SKESA, Velvet and Megahit. | assembly, bacteria, isolate, genome, Illumina, paired, end, read, data, haploid, organism, bio.tools |
uses: SPAdes is listed by: Debian is listed by: bio.tools is related to: Trimmomatic is related to: SAMTOOLS is related to: BWA is related to: FLASH is related to: Velvet is related to: Pilon |
Free, Available for download, Freely available | , biotools:shovill, BioTools:shovill | https://bio.tools/shovill, https://sources.debian.org/src/shovill/ | SCR_017077 | 2026-07-30 09:30:09 | 445 | ||||||||
|
VAPPER Resource Report Resource Website 1+ mentions |
VAPPER (RRID:SCR_016993) | VAPPER | data processing software, software application, data analysis software, software resource | Software tool for analysis of variant antigens in African trypanosomes. Used for quantitative analysis of antigenic diversity in systems data of genomes, transcriptomes, and proteomes, called Variant Antigen Profiling to understand how antigenic diversity relates to clinical outcome, how antigen genes may be used as epidemiological markers of virulence, and in measuring gene expression during experimental infections. | variant, antigen, profiling, data, genome, transcriptome, proteome, gene, expression, infection, Trypanosoma, bio.tools |
is listed by: Debian is listed by: bio.tools requires: Python Programming Language |
Free, Available for download, Freely available | biotools:VAPPER | https://bio.tools/VAPPER | SCR_016993 | VAP, VariantAntigenProfilingPER | 2026-07-30 09:30:05 | 1 | ||||||
|
UMI-tools Resource Report Resource Website 100+ mentions |
UMI-tools (RRID:SCR_017048) | data processing software, software application, data analysis software, software resource | Open source software package for handling Unique Molecular Identifiers in NGS data sets. | unique, molecular, identifier, NGS, data, dataset, random, oligonucleotide, barcode, sequencing, copy, molecule, PCR, amplification, bio.tools |
is listed by: Debian is listed by: bio.tools |
Medical Research Council | PMID:28100584 | Free, Available for download, Freely available | biotools:umi-tools | https://bio.tools/umi-tools | SCR_017048 | Unique Molecular Identifiers tools | 2026-07-30 09:30:15 | 126 | |||||
|
rnaSPAdes Resource Report Resource Website 50+ mentions |
rnaSPAdes (RRID:SCR_016992) | data processing software, sequence analysis software, data analysis software, software resource, software application | Software tool for assembling transcripts from RNA-Seq data. Explores surprising computational parallels between assembly of transcriptomes and single cell genomes. Suitable for all kind of organisms. Part of SPAdes package since version 3.9. | assembling, transcript, RNA-Seq, data, single, cell, genome, analysis, sequence, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: SPAdes is related to: rnaQUAST |
Russian Science Foundation 14-50-00069 | DOI:10.1101/420208 | Free, Available for download, Freely available | biotools:rnaSPAdes_autogenerated | https://bio.tools/rnaSPAdes_autogenerated | SCR_016992 | 2026-07-30 09:30:08 | 53 | ||||||
|
Goseq Resource Report Resource Website 100+ mentions |
Goseq (RRID:SCR_017052) | data processing software, software application, data analysis software, software resource | Software application for performing Gene Ontology analysis on RNAseq data and other length biased data. Used to reduce complexity and highlight biological processes in genome wide expression studies. | Gene, Ontology, analysis, RNAseq, data, sequencing, genome, expression, bio.tools |
is listed by: Bioconductor is listed by: Debian is listed by: bio.tools is related to: R Project for Statistical Computing |
PMID:20132535 | Free, Available for download, Freely available | biotools:goseq | https://bio.tools/goseq | SCR_017052 | 2026-07-30 09:30:09 | 354 | |||||||
|
Genomic Ranges Resource Report Resource Website 1+ mentions |
Genomic Ranges (RRID:SCR_017051) | data processing software, software toolkit, data analysis software, software resource, software application | Software R package for computing and annotating genomic ranges. Used for storing and manipulating genomic intervals and variables defined along genome. | computing, annotating, genomic, range, storing, manipulating, interval, variable, bio.tools |
is listed by: Bioconductor is listed by: Debian is listed by: bio.tools is related to: R Project for Statistical Computing |
NHGRI P41 HG004059; NHGRI U41 HG004059; NHLBI R01 HL086601; NHLBI R01 HL093076; NHLBI R01 HL094635 |
PMID:23950696 | Free, Available for download, Freely available | biotools:genomicranges | https://bio.tools/genomicranges | SCR_017051 | 2026-07-30 09:30:15 | 2 | ||||||
|
Salmon Resource Report Resource Website 100+ mentions |
Salmon (RRID:SCR_017036) | data processing software, software application, data analysis software, software resource | Software tool for quantifying expression of transcripts using RNA-seq data. Provides fast and bias-aware quantification of transcript expression. Transcriptome-wide quantifier to correct for fragment GC-content bias. | quantifying, expression, transcript, RNAseq, data, correct, fragment, GC, content, bias |
is listed by: Debian is listed by: OMICtools has parent organization: Stony Brook University; New York; USA has parent organization: Carnegie Mellon University; Pennsylvania; USA has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA has parent organization: Harvard University; Cambridge; Massachusetts |
Gordon and Betty Moore Foundation Data-Driven Discovery Initiative ; NHGRI R21 HG006913; NHGRI R01 HG007104; Alfred P. Sloan Research ; NCI T32 CA009337; NHGRI R01 HG005220; NSF BIO-1564917; NSF CCF-1256087; NSF CCF-1053918; NSF EF-0849899 |
PMID:28263959 | Free, Available for download, Freely available | OMICS_09075 | https://github.com/COMBINE-lab/salmon, https://sources.debian.org/src/salmon/ | SCR_017036 | 2026-07-30 09:30:15 | 357 | ||||||
|
Bridger Resource Report Resource Website 1+ mentions |
Bridger (RRID:SCR_017039) | data processing software, software application, data analysis software, software resource | Software package as de novo trascriptome assembler for RNA-Seq data. Framework for de novo transcriptome assembly using RNA-seq data. Can assemble all transcripts from short reads without using reference. Input RNA-Seq reads in fasta or fastq format, and ouput all assembled candidate transcripts in fasta format. Operating system Unix/Linux. | de novo, transcripto, assembler, RNAseq, data, short, read, sequencing, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
NSFC 61432010; NSFC 61272016; NCRR P20 RR016460; NIGMS P20 GM103429 |
PMID:25723335 | Free, Available for download, Freely available | biotools:bridger, OMICS_07535 | https://bio.tools/bridger | SCR_017039 | 2026-07-30 09:30:15 | 6 | ||||||
|
FateID Resource Report Resource Website 1+ mentions |
FateID (RRID:SCR_017244) | data processing software, software application, data analysis software, software resource | Software R package for inference of cell fate bias from single cell RNA-seq data. Iterative supervised learning algorithm for probabilistic quantification of cell fate bias in progenitor populations. | inference, cell, fate, bias, single, RNAseq, data, iterative, supervised, learning, algorithm, probabilistic, quantification, progenitor, population, bio.tools |
is listed by: bio.tools is listed by: Debian |
PMID:29630061 | Free, Available for download, Freely available | biotools:fateid | https://bio.tools/fateid | SCR_017244 | 2026-07-30 09:30:08 | 2 | |||||||
|
ascend Resource Report Resource Website 1+ mentions |
ascend (RRID:SCR_017257) | data processing software, software application, data analysis software, software resource | Software R package for analysis of single cell RNA-seq expression, normalization and differential expression data. Provides framework to perform cell and gene filtering, quality control, normalization, dimension reduction, clustering, differential expression, and visualization functions. | analysis, single, cell, RNAseq, expression, normalization, data, gene, filtering, quality, control, dimension, reduction, clustering, visualization, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: CRAN is related to: Bioconductor |
PMID:31505654 | Free, Available for download, Freely available | biotools:ascend | https://bio.tools/ascend | SCR_017257 | Normalization and Differential expression, ASCEND, Analysis of Single Cell Expression | 2026-07-30 09:30:11 | 2 | ||||||
|
IQ-TREE Resource Report Resource Website 500+ mentions |
IQ-TREE (RRID:SCR_017254) | data processing software, software application, data analysis software, software resource | Software tool as stochastic algorithm for estimating maximum likelihood phylogenies. Used for phylogenomic inference. | stochastic, algorithm, estimate, maximum, likelihood, phylogeny, phylogenomic, inference, data, dataset, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: University of Vienna; Vienna; Austria |
Austrian Science Fund ; University of Vienna |
PMID:25371430 | Free, Available for download, Freely available | biotools:ufboot2 | https://bio.tools/ufboot2/ | SCR_017254 | 2026-07-30 09:30:11 | 790 | ||||||
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EMBOSSMatcher Resource Report Resource Website 10+ mentions |
EMBOSSMatcher (RRID:SCR_017252) | data processing software, data access protocol, software resource, web service, image analysis software, alignment software, software application | Software tool for pairwise sequence alignment. Identifies local similarities in two input sequences. One of EMBL-EBI search and sequence analysis tools. | pairwise, sequence, alignment, identify, local, similarity, two, input, sequence, bio.tools |
is listed by: Debian is listed by: bio.tools |
EMBL | PMID:30976793 | Free, Freely available | biotools:ebi_search | https://bio.tools/ebi_search | SCR_017252 | EMBOSS Matcher, emboss_matcher, EMBOSS_Matcher | 2026-07-30 09:30:08 | 15 |
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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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