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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
minfi Resource Report Resource Website 100+ mentions |
minfi (RRID:SCR_012830) | minfi | data visualization software, data analysis software, software resource, software application, data processing software | Software tools for analyzing and visualizing Illumina''s 450k array data. | Illumina, array data, Analyze Illumina Infinium DNA methylation arrays, DNA methylation array, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: SWAN has parent organization: Bioconductor |
PMID:28035024 | Free, Available for download, Freely available | biotools:minfi, OMICS_00799, BioTools:minfi | https://bio.tools/minfi, https://bio.tools/minfi, https://bio.tools/minfi | SCR_012830 | 2026-07-27 09:34:17 | 390 | ||||||
|
affy Resource Report Resource Website 1000+ mentions |
affy (RRID:SCR_012835) | Affy | software application, software resource, data processing software, data analysis software | Software R package of functions and classes for the analysis of oligonucleotide arrays manufactured by Affymetrix. Used to process probe level data and for exploratory oligonucleotide array analysis. | analysis, oligonucleotide, array, Affymetrix, process, probe, data, function, bio.tools |
is listed by: OMICtools is listed by: Bioconductor is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: affydata is related to: R Project for Statistical Computing is related to: OMICtools |
Danish Biotechnology Instrument Center | PMID:14960456 | Free, Available for download, Freely available | BioTools:affy, OMICS_00740, biotools:affy | https://bio.tools/affy, https://sources.debian.org/src/r-bioc-affy/ | SCR_012835 | Affymetrix, analysis of Affymetrix GeneChip data at the probe level, analysis of Affymetrix GeneChip data | 2026-07-27 09:34:17 | 2996 | ||||
|
edgeR Resource Report Resource Website 10000+ mentions |
edgeR (RRID:SCR_012802) | edgeR | software application, software resource, data processing software, data analysis software | Bioconductor software package for Empirical analysis of Digital Gene Expression data in R. Used for differential expression analysis of RNA-seq and digital gene expression data with biological replication. | empirical, analysis, digital, gene, expression, data, R, RNA-seq data, bio.tools |
is used by: Glimma is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: SARTools is related to: Bioconductor works with: tximport |
NHMRC 406657; Independent Research Institutes Infrastructure Support Scheme 361646; Victorian State Government OIS grant ; Melbourne International Research Scholarship ; Harris and IBS Honours scholarships |
PMID:19910308 DOI:10.1093/bioinformatics/btp616 |
Free, Available for download, Freely available | OMICS_01308, biotools:edger | https://bio.tools/edger, https://sources.debian.org/src/r-bioc-edger/ | SCR_012802 | edgeR, empirical analysis of digital gene expression data in R, Empirical analysis of Digital Gene Expression data in R | 2026-07-27 09:34:16 | 21899 | ||||
|
tximport Resource Report Resource Website 50+ mentions |
tximport (RRID:SCR_016752) | software application, software resource, data processing software, data analysis software | Software R package for importing pseudoaligned reads into R for use with downstream differential expression analysis. Used for import and summarize transcript level estimates for transcript and gene level analysis. | pseudoaligned, reads, R, differential, expression, analysis, gene, transcript, bio.tools |
is listed by: Bioconductor is listed by: Debian is listed by: bio.tools works with: edgeR works with: DESeq2 |
SNSF 143883; European Commission ; NCI T32 CA009337 |
DOI:10.12688/f1000research.7563.1 | Free, Available for download, Freely available | biotools:tximport | https://bioconductor.org/packages/tximport/, https://bioconductor.org/packages/devel/bioc/vignettes/tximport/inst/doc/tximport.html, https://github.com/F1000Research/tximport, https://bio.tools/tximport | https://zenodo.org/record/35123#.W_w3behKiM8 | SCR_016752 | tximport v1.4.0 | 2026-07-27 09:35:21 | 91 | ||||
|
MetaNeighbor Resource Report Resource Website 10+ mentions |
MetaNeighbor (RRID:SCR_016727) | software application, software resource, data processing software, data analysis software | Software package to assess cell type identity using both functional and random gene sets. Used for single cell replicability analysis to quantify cell type replicability across datasets using neighbor voting. | quantify, cell, type, replicability, dataset, access, cell, type, identity, functional, random, gene |
is used by: BICCN is listed by: Bioconductor is listed by: OMICtools |
Free, Available for download, Freely available | https://github.com/maggiecrow/MetaNeighbor, https://github.com/gillislab/MetaNeighbor | SCR_016727 | 2026-07-27 09:35:24 | 49 | |||||||||
|
RMassBank Resource Report Resource Website 1+ mentions |
RMassBank (RRID:SCR_002797) | software application, workflow software, software resource, data processing software | Workflow software to process tandem MS files and build MassBank records. Functions include automated extraction of tandem MS spectra, formula assignment to tandem MS fragments, recalibration of tandem MS spectra with assigned fragments, spectrum cleanup, automated retrieval of compound information from Internet databases, and export to MassBank records. | standalone software, mac os x, unix/linux, windows, r, mass spectrometry, metabolomics |
is listed by: OMICtools has parent organization: Bioconductor |
Free, Freely available, Available for download | OMICS_02657 | SCR_002797 | 2026-07-27 09:31:37 | 6 | |||||||||
|
scTHI Resource Report Resource Website 1+ mentions |
scTHI (RRID:SCR_018918) | scTHI | software application, software resource, data processing software, data analysis software | Software R package to identify active pairs of ligand receptors from single cells in order to study,among others, tumor host interactions. Contains set of signatures to classify cells from tumor microenvironment. | Ligand receptor, active pair, active pair ligand receptor, single cell, tumor interaction, tumor microenvironment, cells clasification | is listed by: Bioconductor | Free, Available for download, Freely available | SCR_018918 | 2026-07-27 09:35:51 | 1 | |||||||||
|
SynergyFinder Resource Report Resource Website 500+ mentions |
SynergyFinder (RRID:SCR_019318) | data visualization software, software resource, software application, data processing software, software toolkit | Software R package as efficient implementations for all popular synergy scoring models for drug combinations, including HSA, Loewe, Bliss and ZIP and visualization of synergy scores as either two dimensional or three dimensional interaction surface over dose matrix. Used to calculate and visualize synergy scores for drug combinations. | Synergy scores, drug combinations, popular synergy scoring models, dimensional interaction surface, dose matrix, bio.tools |
is listed by: Bioconductor is listed by: bio.tools is listed by: Debian is related to: SynergyFinder web application |
DOI:10.1007/978-1-4939-7493-1_17 | Free, Available for download, Freely available | biotools:synergyfinder | https://bio.tools/synergyfinder | SCR_019318 | synergyfinder | 2026-07-27 09:36:00 | 510 | ||||||
|
variancePartition Resource Report Resource Website 50+ mentions |
variancePartition (RRID:SCR_019204) | data analysis software, software resource, software application, data processing software, data analytics software | Software R package to quantify and interpret divers of variation in multilevel gene expression experiments.Provides statistical and visualization framework for studying drivers of variation in RNA-seq datasets in many types of high throughput genomic assays including RNA-seq gene-, exon- and isoform-level quantification, splicing efficiency, protein quantification, metabolite quantification, metagenomic assays, methylation arrays and epigenomic sequencing assays. | Repeated measures, variation in gene expression, RNA-seq datasets, high throughput genomic assays, splicing efficiency, protein quantification, metabolite quantification, metagenomic assays, methylation arrays, epigenomic sequencing assays, bio.tools |
is listed by: Bioconductor is listed by: bio.tools is listed by: Debian is related to: CRAN |
NHLBI U01 HL107388; Icahn School of Medicine at Mount Sinai |
PMID:27884101 | Free, Available for download, Freely available | biotools:variancepartition | https://bio.tools/variancepartition | SCR_019204 | 2026-07-27 09:35:57 | 52 | ||||||
|
CiteFuse Resource Report Resource Website 1+ mentions |
CiteFuse (RRID:SCR_019321) | software application, software resource, data processing software, data analysis software | Software R package consisting of suite of tools for doublet detection, modality integration, clustering, differential RNA and protein expression analysis, antibody-derived tag evaluation, ligand-receptor interaction analysis and interactive web-based visualization of CITE-seq data. | Data pre processing, modality integration, clustering, differential RNA, ADT, expression analysis, ADT evaluation, ligand receptor interaction analysis, CITE-seq data, cellular indexing of transcriptomes and epitopes by sequencing, bio.tools |
is listed by: Bioconductor is listed by: bio.tools is listed by: Debian has parent organization: University of Sydney; Sydney; Australia |
PMID:32353146 | Free, Available for download, Freely available | biotools:citefuse | https://bioconductor.org/packages/CiteFuse/, https://github.com/SydneyBioX/CiteFuse/, http://shiny.maths.usyd.edu.au/CiteFuse/, https://bio.tools/CiteFuse | SCR_019321 | Cellular Indexing of Transcriptomes and Epitopes Fuse, Cellular indexing of transcriptomes and epitopes Fuse | 2026-07-27 09:36:00 | 2 | ||||||
|
fgsea Resource Report Resource Website 100+ mentions |
fgsea (RRID:SCR_020938) | software application, software resource, data processing software, data analysis software | Software R package for fast preranked gene set enrichment analysis. Allows to make more permutations and get more fine grained p-values, which allows to use accurate stantard approaches to multiple hypothesis correction. | Gene set enrichment analysis, preranked gene set, multiple hypothesis correction, bio.tools |
is listed by: Bioconductor is listed by: bio.tools is listed by: Debian |
DOI:10.1101/060012 | Free, Available for download, Freely available | biotools:fgsea | https://github.com/ctlab/fgsea/, https://bio.tools/fgsea | SCR_020938 | fast gene set enrichment analysis, Fast Gene Set Enrichment Analysis, FGSEA | 2026-07-27 09:36:13 | 185 | ||||||
|
CATALYST Resource Report Resource Website 100+ mentions |
CATALYST (RRID:SCR_017127) | data analysis software, software resource, software application, data processing software, software toolkit | Software R package to provide pipeline for preprocessing of cytometry data, including normalization using bead standards, single cell deconvolution, and bead based compensation. | preprocessing, cytometry, data, normalization, bead, standard, single, cell, deconvulsion, compensation, bio.tools |
uses: CATALYSTLite is listed by: Bioconductor is listed by: bio.tools is listed by: Debian |
Swiss National Science Foundation ; SNSF Assistant Professorship grant ; PhosphonetPPM and MetastasiX SystemsX grant ; NIDDK UC4 DK108132; European Research Council ; Roche Postdoctoral Fellowship |
PMID:29605184 | Free, Available for download, Freely available | biotools:catalyst | https://github.com/HelenaLC/CATALYST, https://bio.tools/catalyst | SCR_017127 | Cytometry dATa anALYSis Tools | 2026-07-27 09:35:29 | 223 | |||||
|
ggtree Resource Report Resource Website 50+ mentions |
ggtree (RRID:SCR_018560) | software application, data visualization software, data processing software, software resource | Software R package for visualization and annotation of phylogenetic trees with their covariates and other tree like structures with their annotation data. Can import evolutionary data from different tree file formats and analysis programs as well as other associated data from experiments so that various sources and types of data can be displayed on tree for comparison and further analyses. | Phylogenetic tree visualization, phylogenetic tree annotation, data, bio.tools |
is listed by: CRAN is listed by: Bioconductor is listed by: Debian is listed by: bio.tools |
Seed Funding Programme for Basic Research | DOI:10.1111/2041-210X.12628 | Free, Available for download, Freely available | biotools:ggtree | https://bio.tools/ggtree | SCR_018560 | 2026-07-27 09:35:52 | 54 | ||||||
|
minet Resource Report Resource Website |
minet (RRID:SCR_018661) | data analysis software, software resource, software application, data processing software, network analysis software, software toolkit | Open source software R package for inferring large transcriptional networks using mutual information. Implements algorithms for inferring networks such as gene networks from microarray data. | Inferring transcriptional network, mutual information, gene network, microarray data, gene, statistical dependencies model, gene to gene interaciton, statistical quantification, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Bioconductor has parent organization: Free University of Brussels; Brussels; Belgium |
Communaute Francaise de Belgique | PMID:18959772 | Free, Available for download, Freely available | biotools:minet | http://minet.meyerp.com/, https://bio.tools/minet | SCR_018661 | Mutual Information NETworks | 2026-07-27 09:35:46 | 0 | |||||
|
MetaCyto Resource Report Resource Website 1+ mentions |
MetaCyto (RRID:SCR_016415) | data analysis software, software resource, software application, data processing software, software toolkit | Software tool for automated meta-analysis of mass and flow cytometry data. Provides functions for preprocessing, automated gating and meta-analysis of cytometry data and collection of cytometry data from the ImmPort database. | automated, analysis, meta, flow, cytometry, data, bio.tools |
is listed by: Bioconductor is listed by: NIDDK Information Network (dkNET) is listed by: bio.tools is listed by: Debian is related to: The Immunology Database and Analysis Portal (ImmPort) |
the National Institute of Allergy and Infectious Diseases HHSN272201200028C | Free, Available for download, Freely available | biotools:metacyto | https://bio.tools/metacyto | SCR_016415 | 2026-07-27 09:35:17 | 5 | |||||||
|
clusterProfiler Resource Report Resource Website 10000+ mentions |
clusterProfiler (RRID:SCR_016884) | data visualization software, data analysis software, software resource, software application, data processing software | Software R package for statistical analysis and visualization of functional profiles for genes and gene clusters. | data, statistical, analysis, visualization, gene, cluster, bio.tools |
is listed by: Bioconductor is listed by: Debian is listed by: bio.tools is related to: R Project for Statistical Computing |
National 973 Projects of China ; 2007 Chang-Jiang Scholars Program ; National Natural Science Foundation of China ; Guangdong Natural Science Research Grant ; Fundamental Research Funds for the Central Universities |
PMID:22455463 | Free, Available for download, Freely available | biotools:clusterprofiler | https://github.com/GuangchuangYu/clusterProfiler, https://guangchuangyu.github.io/software/clusterProfiler/, https://bio.tools/clusterprofiler | SCR_016884 | Cluster Profiler | 2026-07-27 09:35:27 | 10762 | |||||
|
RnaSeqGeneEdgeRQL Resource Report Resource Website |
RnaSeqGeneEdgeRQL (RRID:SCR_016699) | data analysis software, software resource, software application, data processing software, software toolkit | Software to study analysis of an RNA-Seq experiment using the Rsubread and edgeR packages. The workflow starts from read alignment and continues on to data exploration, to differential expression and, finally, to pathway analysis. The analysis includes plots, GO and KEGG analyses, and the analysis of a expression signature as generated by a prior experiment. | study, analysis, RNA, sequencing, read, alignment, data | is affiliated with: Bioconductor | Free, Available for download, Freely available | SCR_016699 | 2026-07-27 09:35:26 | 0 | ||||||||||
|
GAGE Resource Report Resource Website 50+ mentions |
GAGE (RRID:SCR_017067) | software application, software resource, data processing software, data analysis software | Software R package for gene set enrichment or pathway analysis. Applicable independent of microarray or RNAseq data attributes including sample sizes, experimental designs, assay platforms, and other types of heterogeneity. Pipeline routines of multiple GAGE analyses in batch, comparison between parallel analyses, and combined analysis of heterogeneous data from different sources and studies. | gene, set, enrichment, pathway, batch, comparison, parallel, analysis, heterogeneous, data |
is listed by: Bioconductor is related to: R Project for Statistical Computing |
Free, Available for download, Freely available | SCR_017067 | Generally Applicable Gene-set Enrichment for pathway analysis, gage, Generally Applicable Gene-set Enrichment, GSEA | 2026-07-27 09:35:30 | 50 | |||||||||
|
affydata Resource Report Resource Website |
affydata (RRID:SCR_016976) | AffyData | data analysis software, software resource, software application, data processing software, data or information resource | Software R package for analysis of Affymetrix Data. Contains samples data files of a large size. | analysis, Affymetrix, data, large, dataset, oligonucleotide, array |
is listed by: Bioconductor is related to: affy is related to: R Project for Statistical Computing |
Free, Available for download, Freely available | SCR_016976 | affydata, Affymetrix Data, Affymetrix Data for Demonstration Purpose | 2026-07-27 09:35:28 | 0 | ||||||||
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MSstats Resource Report Resource Website 100+ mentions |
MSstats (RRID:SCR_014353) | software application, software resource, data processing software, data analysis software | A package for statistical relative quantification of proteins and peptides in global, targeted, and data-independent proteomics. It handles shotgun, label-free, and label-based Selected Reaction Monitoring, as well as SWATH/DIA (Data Independent Acquisition) experiments. MSStats provide functionality for data processing and visualization, model-based statistical analysis, and model-based sample size calculations. | data independent acquisition, statistical relative quantification, protein, peptide, data analysis software, data processing, data visualization, proteomics |
uses: R Project for Statistical Computing is used by: Skyline is listed by: Bioconductor |
National Science Foundation CAREER award 1054826 | DOI:10.1186/1471-2105-13-S16-S6 | Acknowledgement requested, Available for download | http://www.bioconductor.org/packages/release/bioc/html/MSstats.html | SCR_014353 | MSStats | 2026-07-27 09:34:37 | 214 |
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