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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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ReactomePA Resource Report Resource Website 50+ mentions |
ReactomePA (RRID:SCR_019316) | software application, data visualization software, data processing software, software resource, data analysis software | Software R package provides functions for pathway analysis based on REACTOME pathway database. It implements enrichment analysis, gene set enrichment analysis and several functions for visualization. | pathway analysis, REACTOME pathway, REACTOME database, enrichment analysis, gene set enrichment analysis, bio.tools |
is listed by: Bioconductor is listed by: bio.tools is listed by: Debian |
PMID:26661513 | Free, Available for download, Freely available | biotools:reactomepa | https://bio.tools/reactomepa | SCR_019316 | Reactome Pathway Analysis | 2026-02-15 09:22:29 | 76 | ||||||
|
MSnbase Resource Report Resource Website 10+ mentions |
MSnbase (RRID:SCR_019317) | software application, data visualization software, data processing software, software resource, data analytics software, software toolkit | Software R package provides infrastructure for manipulation, processing and visualisation of mass spectrometry and proteomics data, ranging from raw to quantitative and annotated data. Used for isobaric tagged mass spectrometry data visualization, processing and quantitation. | Mass spectrometry data processing, mass spectrometry data visualization, raw mass spectrometry data | is listed by: Bioconductor | BBSRC Tools and Resources Development Fund ; European Union 7th Framework Program |
PMID:22113085 PMID:32902283 |
Free, Available for download, Freely available | SCR_019317 | 2026-02-15 09:22:23 | 10 | ||||||||
|
biomaRt Resource Report Resource Website 1000+ mentions |
biomaRt (RRID:SCR_019214) | software application, data processing software, data analysis software, software resource | Software package that integrates BioMart data resources with data analysis software in Bioconductor. Can annotate range of gene or gene product identifiers including Entrez Gene and Affymetrix probe identifiers with information such as gene symbol, chromosomal coordinates, Gene Ontology and OMIM annotation. Enables retrieval of genomic sequences and single nucleotide polymorphism information, which can be used in data analysis. | BioMart databases, Bioconductor, data analysis, BioMart data integration, gene annotation, gene product identifiers annotation, gene symbol retrival, chromosomal coordinates retrival, genomic sequence retrival, nucleotide polimorphism information, , bio.tools |
is listed by: Bioconductor is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: BioMart Project is related to: BioMart MartView is related to: Entrez Gene is related to: Affymetrix is related to: Gene Ontology is related to: OMIM is related to: Affymetrix |
PMID:16082012 | Free, Available for download, Freely available | biotools:biomart | https://bio.tools/biomart | SCR_019214 | biomaRt v 2.42.1 | 2026-02-15 09:22:28 | 2638 | ||||||
|
GSVA Resource Report Resource Website 100+ mentions |
GSVA (RRID:SCR_021058) | GSVA | software application, data processing software, software resource, software toolkit, data analysis software | Open source software R package for assaying variation of gene set enrichment over sample population.Used for microarray and RNA-seq data analysis. Gene set enrichment method that estimates variation of pathway activity over sample population in unsupervised manner. | Gene set enrichment, variation estimation, pathway activity, sample population, microarray, RNA-seq, data analysis | is listed by: Bioconductor | ISCIII COMBIOMED ; Spanish MINECO ; NCI U54 CA149237 |
PMID:23323831 | Free, Available for download, Freely available | SCR_021058 | Gene Set Variation Analysis | 2026-02-15 09:22:31 | 256 | ||||||
|
SimFFPE Resource Report Resource Website 1+ mentions |
SimFFPE (RRID:SCR_021085) | software application, simulation software, software resource | Software R package to simulate artifact chimeric reads specifically generated in next generation sequencing process of formalin fixed paraffin embedded tissue. Simulates normal reads as well as artifact chimeric reads that are enriched in FFPE samples. These artifact chimeric reads can lead to large amounts of false positive structural variant calls. | FFPE, NGS read simulator, artifact chimeric read, next generation sequencing process, normal reads simulation, artifact chimeric reads simulation, formalin fixed paraffin embedded tissue, |
is listed by: Bioconductor is related to: CRAN |
Free, Available for download, Freely available | SCR_021085 | NGS Read Simulator for FFPE Tissue, Simulator for FFPE Tissue | 2026-02-15 09:21:56 | 1 | |||||||||
|
PhenStat Resource Report Resource Website 1+ mentions |
PhenStat (RRID:SCR_021317) | software application, data processing software, software resource, software toolkit, data analysis software | Software R package for statistical analysis of phenotypic data.Tool kit for standardized analysis of high throughput phenotypic data. | Statistical analysis, phenotypic data, standardized analysis, bio.tools, Bioconductor |
is listed by: Bioconductor is listed by: bio.tools |
Wellcome Trust ; NHGRI U54 HG006370 |
PMID:26147094 | Free, Available for download, Freely available | biotools:phenstat | https://bio.tools/phenstat | SCR_021317 | 2026-02-15 09:22:27 | 8 | ||||||
|
svaNUMT Resource Report Resource Website 1+ mentions |
svaNUMT (RRID:SCR_021381) | software application, data processing software, data analysis software, software resource | Software R package for Nuclear Mitochondrial integration events NUMT detection using structural variant calls. | Nuclear mitochondrial integration events, NUMT, NUMT detection, structural variant calls. | is listed by: Bioconductor | Free, Available for download, Freely available | https://bioconductor.org/packages/svaNUMT/ | SCR_021381 | 2026-02-15 09:22:02 | 1 | |||||||||
|
DESeq2 Resource Report Resource Website 10000+ mentions |
DESeq2 (RRID:SCR_015687) | software tool, software application, data processing software, software resource, data analysis software | Software package for differential gene expression analysis based on the negative binomial distribution. Used for analyzing RNA-seq data for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates. | differential, gene, expression, analysis, binominal, distribution, RNA-seq data, Bioconductor, bio.tools |
is used by: Glimma is used by: TEtranscripts is listed by: Bioconductor is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: SARTools works with: tximport |
International Max Planck Research School for Computational Biology and Scientific Computing ; NCI T32 CA009337; European Union’s 7th Framework Programme |
Free, Available for download, Freely available | biotools:deseq2 | https://github.com/mikelove/DESeq2 https://bio.tools/deseq2 |
SCR_015687 | 2026-02-15 09:21:36 | 43994 | |||||||
|
AUCell Resource Report Resource Website 10+ mentions |
AUCell (RRID:SCR_021327) | software application, data processing software, software resource, software toolkit, data analysis software | Software R package to identify cells with active gene sets in single cell RNA-seq data. Used for analysis of gene set activity in single cell RNA-seq data.Used to calculate whether critical subset of input gene set is enriched within expressed genes for each cell. | Identify cells with active gene sets, single cell RNA-seq data, gene set activity analysis | is listed by: Bioconductor | Free, Available for download, Freely available | SCR_021327 | Area Under the Curve | 2026-02-15 09:22:01 | 40 | |||||||||
|
PICS Resource Report Resource Website 1+ mentions |
PICS (RRID:SCR_001093) | software application, sequence analysis software, data processing software, software resource, data analysis software | R package with tools that use probabilistic inference of ChIP-Seq. It follows an empirical Bayes mixture model approach. | chip seq, bayes, data, r, sequence analysis software |
is listed by: OMICtools is hosted by: Bioconductor |
PMID:20528864 | Free, Available for download, Freely available | OMICS_00455 | SCR_001093 | Probabilistic inference of ChIP-seq | 2026-02-15 09:18:02 | 3 | |||||||
|
ascend Resource Report Resource Website 1+ mentions |
ascend (RRID:SCR_017257) | software application, data processing software, 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 | 2026-02-15 09:22:00 | 2 | ||||||
|
Scfind Resource Report Resource Website 1+ mentions |
Scfind (RRID:SCR_017339) | software application, data or information resource, data processing software, software resource | Software R package as search tool for single cell RNA-seq data by gene lists. Builds index from scRNA-seq datasets which organizes information in suitable and compact manner so that datasets can be very efficiently searched for either cells or cell types in which given list of genes is expressed. | Single, cell, RNA-seq, data, gene, list, build, index, organize |
is listed by: Bioconductor has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
Free, Available for download, Freely available | https://genat.uk/post/scfind/ http://bioconductor.org/packages/scfind/ https://github.com/hemberg-lab/scfind |
SCR_017339 | 2026-02-15 09:22:03 | 1 | |||||||||
|
Extending Guilt by Association by Degree Resource Report Resource Website 1+ mentions |
Extending Guilt by Association by Degree (RRID:SCR_018427) | EGAD | software application, data processing software, software resource, software toolkit, data analysis software | Software package implements series of highly efficient tools to calculate functional properties of networks based on guilt by association methods. Ultra fast functional analysis of gene networks. | Extending guilt, association by degree, functional properties calculation, guilt network, association method, functional analysis, gene network | is listed by: Bioconductor | Free, Available for download, Freely available | SCR_018427 | EGAD Bioconductor, Extending guilt by association by degree | 2026-02-15 09:21:37 | 6 | ||||||||
|
topGO Resource Report Resource Website 1000+ mentions |
topGO (RRID:SCR_014798) | software toolkit, software resource | Software package which provides tools for testing GO terms while accounting for the topology of the GO graph. Different test statistics and different methods for eliminating local similarities and dependencies between GO terms can be implemented and applied. | r, go, go graph, local similarities, software tool, software package, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: SoftCite works with: Gene Ontology is hosted by: Bioconductor |
Available for download | biotools:topgo | https://bio.tools/topgo | SCR_014798 | 2026-02-15 09:21:03 | 2839 | ||||||||
|
ReadqPCR Resource Report Resource Website |
ReadqPCR (RRID:SCR_000030) | software application, standalone software, software resource | A software package that provides functions to read raw RT-qPCR data of different platforms. | standalone software, mac os x, unix/linux, windows, r, data import, gene expression, microtitre plate assay, qpcr, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor has parent organization: University College London; London; United Kingdom |
PMID:22748112 | Free, Available for download, Freely available | biotools:readqpcr, OMICS_03936 | https://bio.tools/readqpcr | SCR_000030 | ReadqPCR - Read qPCR data | 2026-02-15 09:17:51 | 0 | ||||||
|
GEO2R Resource Report Resource Website 50+ mentions |
GEO2R (RRID:SCR_016569) | software application, data processing software, data analysis software, software resource | Software as an interactive web tool to compare two or more groups of samples in a Gene Expression Omnibus (GEO) series regardless of data type and quality. Used to identify genes that are differentially expressed across experimental conditions. Results are presented as a table of genes ordered by significance. | compare, group, sample, gene, expression, omnibus, data, identify, differentially, expressed, across, condition, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: Bioconductor is related to: GEOquery is related to: LIMMA |
Free, Available for download, Freely available | biotools:GEO2R | https://bio.tools/GEO2R | SCR_016569 | 2026-02-15 09:21:08 | 58 | ||||||||
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VisR Resource Report Resource Website 1+ mentions |
VisR (RRID:SCR_016658) | VisR | software application, data visualization software, data processing software, software resource, software toolkit, data analysis software | Software as an R-based visual framework for analysis of sequencing datasets. Provides a framework for integrative and interactive analyses. | visual, framework, analysis, sequencing, data, dataset, integrative, interactive, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Bioconductor |
Michael Smith Foundation for Health Research ; Canadian Institutes of Health Research (CIHR) and Genome BC ; NSERC PGS-D |
PMID:26328469 | Free, Available for download, Freely available | biotools:VisR | https://bio.tools/VisR | SCR_016658 | VisRseq, VisR | 2026-02-15 09:21:09 | 5 | ||||
|
riboSeqR Resource Report Resource Website 1+ mentions |
riboSeqR (RRID:SCR_016947) | software application, data processing software, data analysis software, software resource | Software tool for analysis of sequencing data from ribosome profiling experiments. Used for plotting functions, frameshift detection and parsing of sequencing data from ribosome profiling experiments. | analysis, sequencing, data, ribosome, profiling, experiment, plotting, function, frameshift, detect, parsing |
is listed by: Bioconductor is related to: R Project for Statistical Computing |
Free, Available for download, Freely available | SCR_016947 | 2026-02-15 09:21:56 | 4 | ||||||||||
|
Rsubread Resource Report Resource Website 100+ mentions |
Rsubread (RRID:SCR_016945) | software application, data processing software, software resource, alignment software, image analysis software, data analysis software | Software R package for sequence alignment and counting for R. Used for analyses of second and third generation sequencing data, for read mapping, read counting, SNP calling, short and long read alignment, quantification and mutation discovery. Includes assessment of sequence reads, read alignment, read summarization, exon-exon junction detection, fusion detection, detection of short and long indels, absolute expression calling and SNP calling. Can be used with reads generated from any of the major sequencing platforms including Illumina GA/HiSeq/MiSeq, Roche GS-FLX, ABI SOLiD and LifeTech Ion PGM/Proton sequencers. | sequence, alignment, counting, multi, seed, strategy, mapping, read, reference, genome, analysis, data, SNP, calling, mutation, discovery, bio.tools |
is listed by: Bioconductor is listed by: Debian is listed by: bio.tools is related to: R Project for Statistical Computing is related to: Subread |
Australian National Health and Medical Research Council ; Victorian State Government Operational Infrastructure Support ; Australian Government |
PMID:23558742 | Free, Available for download, Freely available | biotools:rsubread | https://bio.tools/rsubread | SCR_016945 | 2026-02-15 09:21:51 | 188 | ||||||
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scran Resource Report Resource Website 50+ mentions |
scran (RRID:SCR_016944) | SCRAN | software application, data processing software, data analysis software, software resource | Software package for low-level analyses of single-cell RNA-seq data. Used for quality control, data exploration and normalization, cell cycle phase assignment, identification of highly variable and correlated genes, clustering into subpopulations and marker gene detection. | low, level, analysis, scRNA-seq, data, normalization, cell, cycle, phase, gene, variable, correlation, cluster, subpopulation, marker, bio.tools |
is listed by: Bioconductor is listed by: Debian is listed by: bio.tools is related to: R Project for Statistical Computing |
Cancer Research UK ; National Health and Medical Research Council of Australia ; EMBL |
PMID:27909575 | Free, Available for download, Freely available | biotools:scran | https://bio.tools/scran | SCR_016944 | Single-Cell Rna-seq data ANalysis, SCRAN | 2026-02-15 09:21:52 | 92 |
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