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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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DESeq2 Resource Report Resource Website 10000+ mentions |
DESeq2 (RRID:SCR_015687) | data analysis software, data processing software, software application, software resource, software tool | 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 |
European Union’s 7th Framework Programme ; International Max Planck Research School for Computational Biology and Scientific Computing ; NCI T32 CA009337 |
Free, Available for download, Freely available | biotools:deseq2 | https://github.com/mikelove/DESeq2, https://bio.tools/deseq2 | SCR_015687 | SciCrunch Registry | 2026-11-07 12:00:51 | 50789 | |||||||
|
GSVA Resource Report Resource Website 100+ mentions |
GSVA (RRID:SCR_021058) | GSVA | data analysis software, data processing software, software application, software resource, software toolkit | 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 ; NCI U54 CA149237; Spanish MINECO |
PMID:23323831 | Free, Available for download, Freely available | SCR_021058 | SciCrunch Registry | Gene Set Variation Analysis | 2026-11-07 12:00:20 | 333 | ||||||
|
SimFFPE Resource Report Resource Website 1+ mentions |
SimFFPE (RRID:SCR_021085) | simulation software, software application, 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 | SciCrunch Registry | NGS Read Simulator for FFPE Tissue, Simulator for FFPE Tissue | 2026-11-07 12:00:20 | 1 | |||||||||
|
PhenStat Resource Report Resource Website 10+ mentions |
PhenStat (RRID:SCR_021317) | data analysis software, data processing software, software application, software resource, software toolkit | 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 |
NHGRI U54 HG006370; Wellcome Trust |
PMID:26147094 | Free, Available for download, Freely available | biotools:phenstat | https://bio.tools/phenstat | SCR_021317 | SciCrunch Registry | 2026-11-07 11:59:54 | 11 | ||||||
|
svaNUMT Resource Report Resource Website 1+ mentions |
svaNUMT (RRID:SCR_021381) | data analysis software, data processing software, software application, 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 | SciCrunch Registry | 2026-11-07 12:00:18 | 1 | |||||||||
|
AUCell Resource Report Resource Website 50+ mentions |
AUCell (RRID:SCR_021327) | data analysis software, data processing software, software application, software resource, software toolkit | 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 | SciCrunch Registry | Area Under the Curve | 2026-11-07 12:00:44 | 56 | |||||||||
|
iontree Resource Report Resource Website |
iontree (RRID:SCR_002813) | software resource | Software package that provides utility functions to manage and analyse MS2/MS3 fragmentation data from ion trap mass spectrometry. It was designed for high throughput metabolomics data with many biological samples and a large numer of ion trees collected. Tests have been done with data from low-resolution mass spectrometry but could be readily extended to precursor ion based fragmentation data from high resoultion mass spectrometry. | standalone software, mac os x, unix/linux, windows, r, mass spectrometry, metabolomics, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
PMID:24958264 | Free, Freely available, Available for download | OMICS_02656, biotools:iontree | https://bio.tools/iontree | SCR_002813 | SciCrunch Registry | iontree: Data management and analysis of ion trees from ion-trap mass spectrometry | 2026-11-07 12:00:39 | 0 | ||||||
|
GeneNetworkBuilder Resource Report Resource Website 1+ mentions |
GeneNetworkBuilder (RRID:SCR_006455) | GeneNetworkBuilder | software application, software resource | Software application for discovering direct or indirect targets of transcription factors (TFs) using ChIP-chip or ChIP-seq, and microarray or RNA-seq gene expression data. Inputting a list of genes of potential targets of one TF from ChIP-chip or ChIP-seq, and the gene expression results, it generates a regulatory network of the TF. | transcription factor, graph, network, microarray, sequencing, chip-chip, chip-seq, gene expression, regulatory network, target |
is listed by: OMICtools has parent organization: Bioconductor |
GNU General Public License, v2 or greater | OMICS_00806, OMICS_01971 | http://www.bioconductor.org/packages/release/bioc/html/GeneNetworkBuilder.html | SCR_006455 | SciCrunch Registry | GeneNetworkBuilder - Build Regulatory Network from ChIP-chip/ChIP-seq and Expression Data | 2026-11-07 12:03:38 | 2 | ||||||
|
topGO Resource Report Resource Website 1000+ mentions |
topGO (RRID:SCR_014798) | software resource, software toolkit | 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 | SciCrunch Registry | 2026-11-07 12:03:54 | 3080 | ||||||||
|
KEGGgraph Resource Report Resource Website 10+ mentions |
KEGGgraph (RRID:SCR_023788) | software resource, software toolkit | Software R package interface between KEGG pathway and graph object as well as collection of tools to analyze, dissect and visualize these graphs. | Kyoto Encyclopedia of Genes and Genomes, KEGG, KEGG pathways, graph models, graph object, graphs visualization, | is listed by: Bioconductor | PMID:19307239 | Free, Available for download, Freely available | SCR_023788 | SciCrunch Registry | Kyoto Encyclopedia of Genes and Genomes graph | 2026-11-07 12:04:12 | 15 | ||||||||
|
ncdfFlow Resource Report Resource Website |
ncdfFlow (RRID:SCR_000009) | software resource | Software package that provides netCDF storage based methods and functions for manipulation of flow cytometry data. | software package, mac os x, unix/linux, windows, r, flow cytometry |
is listed by: OMICtools has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_05617 | SCR_000009 | SciCrunch Registry | ncdfFlow: A package that provides ncdf based storage for flow cytometry data | 2026-11-07 12:08:08 | 0 | ||||||||
|
Orthology.eg.db Resource Report Resource Website 1+ mentions |
Orthology.eg.db (RRID:SCR_024740) | software resource, software toolkit | Software R package to provide orthology mappings between species, based on NCBI Gene IDs and NCBI orthology mappings. | orthology mappings between species, NCBI Gene IDs, NCBI orthology mappings, | is listed by: Bioconductor | Free, Available for download, Freely available | SCR_024740 | SciCrunch Registry | 2026-11-07 12:05:40 | 1 | ||||||||||
|
ExperimentHub Resource Report Resource Website 1+ mentions |
ExperimentHub (RRID:SCR_024820) | software resource, software toolkit | Software R package provides central location where curated data from experiments, publications or training courses can be accessed. | data access, curated data from experiments, publications data, training courses data, | is listed by: Bioconductor | Free, Available for download, Freely available | SCR_024820 | SciCrunch Registry | 2026-11-07 12:06:05 | 2 |
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