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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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CNTools Resource Report Resource Website 1+ mentions |
CNTools (RRID:SCR_000281) | CNTools | software resource | Software package that provides tools to convert the output of segmentation analysis using DNAcopy to a matrix structure with overlapping segments as rows and samples as columns so that other computational analyses can be applied to segmented data. | copy number variation, microarray |
is listed by: OMICtools has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_02061 | SCR_000281 | SciCrunch Registry | CNTools - Convert segment data into a region by sample matrix to allow for other high level computational analyses | 2026-11-07 11:53:57 | 1 | |||||||
|
htSeqTools Resource Report Resource Website 10+ mentions |
htSeqTools (RRID:SCR_006614) | htSeqTools | software resource | Software tools for quality control, visualization and processing for High-Throughput Sequencing data. These include MDS plots (analogues to PCA), detecting inefficient immuno-precipitation or over-amplification artifacts, tools to identify and test for genomic regions with large accumulation of reads, and visualization of coverage profiles. | high-throughput sequencing, chip-seq, rnaseq |
is listed by: OMICtools has parent organization: Bioconductor |
OMICS_01233 | SCR_006614 | SciCrunch Registry | 2026-11-07 11:55:58 | 11 | |||||||||
|
DeconRNASeq Resource Report Resource Website 10+ mentions |
DeconRNASeq (RRID:SCR_006713) | DeconRNASeq | software resource | An R package for deconvolution of heterogeneous tissues based on mRNA-Seq data. It modeled expression levels from heterogeneous cell populations in mRNA-Seq as the weighted average of expression from different constituting cell types and predicted cell type proportions of single expression profiles. |
is listed by: OMICtools has parent organization: Bioconductor |
OMICS_01230 | SCR_006713 | SciCrunch Registry | 2026-11-07 11:56:16 | 44 | ||||||||||
|
methVisual Resource Report Resource Website 1+ mentions |
methVisual (RRID:SCR_006705) | methVisual | software resource | Software package that allows the visualization of DNA methylation data after bisulfite sequencing. |
is listed by: OMICtools has parent organization: Bioconductor |
GNU General Public License, v2 or greater | OMICS_00604 | SCR_006705 | SciCrunch Registry | methVisual - Methods for visualization and statistics on DNA methylation data | 2026-11-07 11:55:59 | 1 | ||||||||
|
seqbias Resource Report Resource Website 10+ mentions |
seqbias (RRID:SCR_006832) | seqbias | software resource | Software package that implements a model of per-position sequencing bias in high-throughput sequencing data using a simple Bayesian network, the structure and parameters of which are trained on a set of aligned reads and a reference genome sequence. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
GNU Lesser General Public License | OMICS_01237, biotools:seqbias, BioTools:seqbias | https://bio.tools/seqbias, https://bio.tools/seqbias, https://bio.tools/seqbias | SCR_006832 | SciCrunch Registry | seqbias - Estimation of per-position bias in high-throughput sequencing data | 2026-11-07 11:56:03 | 31 | ||||||
|
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 | 2026-11-07 11:56:36 | 1729 | ||||||||||
|
VisR Resource Report Resource Website 1+ mentions |
VisR (RRID:SCR_016658) | VisR | data analysis software, data processing software, data visualization software, software application, software resource, software toolkit | 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 |
Canadian Institutes of Health Research (CIHR) and Genome BC ; Michael Smith Foundation for Health Research ; NSERC PGS-D |
PMID:26328469 | Free, Available for download, Freely available | biotools:VisR | https://bio.tools/VisR | SCR_016658 | SciCrunch Registry | VisRseq, VisR | 2026-11-07 11:58:20 | 5 | ||||
|
riboSeqR Resource Report Resource Website 1+ mentions |
riboSeqR (RRID:SCR_016947) | data analysis software, data processing software, software application, 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 | SciCrunch Registry | 2026-11-07 11:58:42 | 4 | ||||||||||
|
Rsubread Resource Report Resource Website 100+ mentions |
Rsubread (RRID:SCR_016945) | alignment software, data analysis software, data processing software, image analysis software, software application, software resource | 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 Government ; Australian National Health and Medical Research Council ; Victorian State Government Operational Infrastructure Support |
PMID:23558742 | Free, Available for download, Freely available | biotools:rsubread | https://bio.tools/rsubread | SCR_016945 | SciCrunch Registry | 2026-11-07 11:58:36 | 203 | ||||||
|
scran Resource Report Resource Website 100+ mentions |
scran (RRID:SCR_016944) | SCRAN | data analysis software, data processing software, software application, 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 ; EMBL ; National Health and Medical Research Council of Australia |
PMID:27909575 | Free, Available for download, Freely available | biotools:scran | https://bio.tools/scran | SCR_016944 | SciCrunch Registry | Single-Cell Rna-seq data ANalysis, SCRAN | 2026-11-07 11:58:25 | 100 | ||||
|
Biostrings Resource Report Resource Website 100+ mentions |
Biostrings (RRID:SCR_016949) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software package for efficient manipulation of biological strings. Memory efficient string containers, string matching algorithms, and other utilities, for fast manipulation of large biological sequences or sets of sequences. | manipulation, biological, string, memory, efficient, container, sequence, set, DNA, RNA, protein |
is used by: riboWaltz is listed by: Bioconductor is related to: R Project for Statistical Computing has parent organization: Stanford University; Stanford; California |
Free, Available for download, Freely available | https://web.stanford.edu/class/bios221/labs/biostrings/lab_1_biostrings.html | SCR_016949 | SciCrunch Registry | 2026-11-07 11:58:25 | 182 | |||||||||
|
ConsensusClusterPlus Resource Report Resource Website 100+ mentions |
ConsensusClusterPlus (RRID:SCR_016954) | data analysis software, data processing software, software application, software resource | Software written in R for determining cluster count and membership by stability evidence in unsupervised analysis. Provides quantitative and visual stability evidence for estimating the number of unsupervised classes in a dataset with item tracking, item consensus and cluster consensus plots. | cluster, count, stability, evidence, unsupervised, analysis, , bio.tools |
is listed by: Bioconductor is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
NCI F32CA142039; NCI U24 CA126554; Thomas G. Labrecque Foundation |
PMID:20427518 | Free, Available for download, Freely available | biotools:consensusclusterplus | https://bio.tools/consensusclusterplus | SCR_016954 | SciCrunch Registry | 2026-11-07 11:58:36 | 196 | ||||||
|
GenomicFeatures Resource Report Resource Website 50+ mentions |
GenomicFeatures (RRID:SCR_016960) | data analysis software, data processing software, software application, software resource, software toolkit | Software R package for making and manipulating transcript centric annotations. Used to download the genomic locations of the transcripts, exons and cds of a given organism, from either the UCSC Genome Browser or a BioMart database. | making, manipulating, transcript, centric, annotation, genomic, location, exon, cds, bio.tools |
is used by: riboWaltz 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:genomicfeatures | https://bio.tools/genomicfeatures | SCR_016960 | SciCrunch Registry | 2026-11-07 11:58:45 | 71 | ||||||
|
FlowSOM Resource Report Resource Website 100+ mentions |
FlowSOM (RRID:SCR_016899) | data analysis software, data processing software, data visualization software, software application, software resource | Software tool to analyze Flow or mass cytometry data using a Self-Organizing Map. Used to obtain an overview of how all markers are behaving on all cells, and to detect subsets that might be missed otherwise. | flow, cytometry, data, analysis, self, organizing, map, marker, cell, detect, bio.tools |
is listed by: Bioconductor is listed by: bio.tools is listed by: Debian is related to: R Project for Statistical Computing is a plug in for: FlowJo |
PMID:25573116 | Free, Available for download, Freely available | biotools:flowsom | https://bioconductor.org/packages/release/bioc/html/FlowSOM.html, https://www.flowjo.com/exchange/#/plugin/profile?id=7, https://bio.tools/flowsom | SCR_016899 | SciCrunch Registry | FlowSOM, Flow Self Organizing Map | 2026-11-07 11:58:35 | 125 | ||||||
|
ropls Resource Report Resource Website 10+ mentions |
ropls (RRID:SCR_016888) | R OPLS | data analysis software, data processing software, software application, 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 | SciCrunch Registry | R Orthogonal Partial Least Squares | 2026-11-07 11:58:45 | 15 | ||||||
|
Goseq Resource Report Resource Website 100+ mentions |
Goseq (RRID:SCR_017052) | data analysis software, data processing software, software application, 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 | SciCrunch Registry | 2026-11-07 11:58:46 | 382 | |||||||
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Genomic Ranges Resource Report Resource Website 1+ mentions |
Genomic Ranges (RRID:SCR_017051) | data analysis software, data processing software, software application, software resource, software toolkit | 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 | SciCrunch Registry | 2026-11-07 11:58:44 | 2 | ||||||
|
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 | 2026-11-07 11:58:43 | 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 | 2026-11-07 11:58:50 | 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 | 2026-11-07 11:57:24 | 30 |
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