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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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flowMeans Resource Report Resource Website 1+ mentions |
flowMeans (RRID:SCR_002275) | software resource | Software that identifies cell populations in Flow Cytometry data using non-parametric clustering and segmented-regression-based change point detection. | software package, mac os x, unix/linux, windows, r, cell biology, clustering, flow cytometry |
is listed by: OMICtools has parent organization: Bioconductor is a plug in for: FlowJo |
PMID:21182178 | Artistic License, v2 | OMICS_05603 | SCR_002275 | SciCrunch Registry | flowMeans: Non-parametric Flow Cytometry Data Gating, flowMeans - Non-parametric Flow Cytometry Data Gating | 2026-10-24 12:44:41 | 7 | |||||||
|
flowMerge Resource Report Resource Website 1+ mentions |
flowMerge (RRID:SCR_002224) | software resource | Software for merging of mixture components for model-based automated gating of flow cytometry data using the flowClust framework. | software package, mac os x, unix/linux, windows, r, clustering, flow cytometry |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:20049161 | Free, Available for download, Freely available | OMICS_05605 | SCR_002224 | SciCrunch Registry | flowMerge - Cluster Merging for Flow Cytometry Data | 2026-10-24 12:44:44 | 2 | |||||||
|
flowPhyto Resource Report Resource Website |
flowPhyto (RRID:SCR_002183) | software resource | An R package that performs aggregate statistics on virtually unlimited collections of raw flow cytometry files and provides a memory efficient, parallelized solution for analyzing high-throughput flow cytometric data. | software package, mac os x, unix/linux, windows, r, classification, clustering, data import, flow cytometry, quality control, visualization |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:21208987 | Free, Available for download, Freely available | OMICS_05606 | http://www.bioconductor.org/packages/release/bioc/html/flowPhyto.html | SCR_002183 | SciCrunch Registry | flowPhyto - Methods for Continuous Flow Cytometry | 2026-10-24 12:44:40 | 0 | ||||||
|
BEAT Resource Report Resource Website 100+ mentions |
BEAT (RRID:SCR_002387) | software resource | Software that implements all bioinformatics steps required for the quantitative, high-resolution analysis of DNA methylation patterns from bisulfite sequencing data. | standalone software, unix/linux, mac os x, windows, r, dna methylation, epigenetics, genetics, methyl-seq |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:24618468 | GNU Lesser General Public License, v3 or greater | OMICS_03425 | SCR_002387 | SciCrunch Registry | BS-Seq Epimutation Analysis Toolkit, BEAT - BS-Seq Epimutation Analysis Toolkit | 2026-10-24 12:44:43 | 130 | |||||||
|
CAMERA - Collection of annotation related methods for mass spectrometry data Resource Report Resource Website 1+ mentions |
CAMERA - Collection of annotation related methods for mass spectrometry data (RRID:SCR_002466) | CAMERA | software resource | A Bioconductor package integrating algorithms to extract compound spectra, annotate isotope and adduct peaks, and propose the accurate compound mass even in highly complex data. | standalone software, mac os x, unix/linux, windows, r, spectra, extraction, annotation, liquid chromatography, mass spectrometry, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
PMID:22111785 | Free, Available for download, Freely available | biotools:camera, OMICS_03366 | https://bio.tools/camera | SCR_002466 | SciCrunch Registry | CAMERA - Collection of annotation related methods for mass spectrometry data | 2026-10-24 12:44:43 | 4 | |||||
|
DEGseq Resource Report Resource Website 1000+ mentions |
DEGseq (RRID:SCR_008480) | DEGseq | software resource | R package to identify differentially expressed genes from RNA-Seq data. |
is listed by: OMICtools has parent organization: Bioconductor |
OMICS_01305 | SCR_008480 | SciCrunch Registry | 2026-10-24 12:46:06 | 1729 | ||||||||||
|
PICS Resource Report Resource Website 1+ mentions |
PICS (RRID:SCR_001093) | data analysis software, data processing software, sequence analysis software, software application, software resource | 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 | SciCrunch Registry | Probabilistic inference of ChIP-seq | 2026-10-24 12:49:03 | 3 | |||||||
|
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 | 2026-10-24 12:49:12 | 50789 | |||||||
|
ascend Resource Report Resource Website 1+ mentions |
ascend (RRID:SCR_017257) | data analysis software, data processing software, software application, 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 | SciCrunch Registry | Normalization and Differential expression, ASCEND, Analysis of Single Cell Expression | 2026-10-24 12:47:46 | 2 | ||||||
|
Scfind Resource Report Resource Website 1+ mentions |
Scfind (RRID:SCR_017339) | data or information resource, data processing software, software application, 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 | SciCrunch Registry | 2026-10-24 12:47:47 | 1 | |||||||||
|
Extending Guilt by Association by Degree Resource Report Resource Website 1+ mentions |
Extending Guilt by Association by Degree (RRID:SCR_018427) | EGAD | data analysis software, data processing software, software application, software resource, software toolkit | 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 | SciCrunch Registry | EGAD Bioconductor, Extending guilt by association by degree | 2026-10-24 12:47:57 | 6 | ||||||||
|
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 | 2026-10-24 12:48:49 | 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 | 2026-10-24 12:48:49 | 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 | 2026-10-24 12:48:53 | 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 | 2026-10-24 12:48:56 | 1 | |||||||||
|
arrayMagic Resource Report Resource Website 1+ mentions |
arrayMagic (RRID:SCR_010933) | arrayMagic | software resource | Software providing a collection of utilities for quality control and processing of two-colour cDNA microarray data |
is listed by: OMICtools has parent organization: Bioconductor |
BSD License | OMICS_00743 | SCR_010933 | SciCrunch Registry | arrayMagic - two-colour cDNA array quality control and preprocessing | 2026-10-24 12:46:26 | 1 | ||||||||
|
easyRNASeq Resource Report Resource Website 10+ mentions |
easyRNASeq (RRID:SCR_012020) | easyRNASeq | software resource | Software that calculates the coverage of high-throughput short-reads against a genome of reference and summarizes it per feature of interest (e.g. exon, gene, transcript). The data can be normalized as ''RPKM'' or by the ''DESeq'' or ''edgeR'' package. | rna-seq, gene expression, genetics, preprocessing, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor has parent organization: European Molecular Biology Laboratory |
PMID:22847932 | Artistic License, v2 | OMICS_01938, biotools:easyrnaseq | https://bio.tools/easyrnaseq | SCR_012020 | SciCrunch Registry | easyRNASeq - Count summarization and normalization for RNA-Seq data | 2026-10-24 12:46:44 | 30 | |||||
|
CRLMM Resource Report Resource Website 10+ mentions |
CRLMM (RRID:SCR_012580) | CRLMM | software resource | Genotype Calling and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays. |
is listed by: OMICtools has parent organization: Bioconductor |
OMICS_00717 | SCR_012580 | SciCrunch Registry | 2026-10-24 12:46:51 | 10 | ||||||||||
|
LVSmiRNA Resource Report Resource Website |
LVSmiRNA (RRID:SCR_012752) | LVSmiRNA | software resource | Software for normalization of Agilent miRNA arrays. |
is listed by: OMICtools has parent organization: Bioconductor |
OMICS_00784 | SCR_012752 | SciCrunch Registry | 2026-10-24 12:46:53 | 0 | ||||||||||
|
MMDiff Resource Report Resource Website 1+ mentions |
MMDiff (RRID:SCR_012692) | MMDiff | software resource | Software package that detects statistically significant difference between read enrichment profiles in different ChIP-Seq samples. |
is listed by: OMICtools has parent organization: Bioconductor |
Free | OMICS_00474 | SCR_012692 | SciCrunch Registry | MMDiff - Statistical Testing for ChIP-Seq data sets | 2026-10-24 12:46:52 | 8 |
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