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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
ASprofile Resource Report Resource Website 10+ mentions |
ASprofile (RRID:SCR_001833) | ASprofile | software resource | A suite of programs for extracting, quantifying and comparing alternative splicing (AS) events from RNA-seq data. | alternative splicing event, rna-seq, alternative splicing |
is listed by: OMICtools has parent organization: Johns Hopkins University; Maryland; USA |
NHGRI R01-HG006677 | PMID:24555089 | Free, Available for download, Freely available | OMICS_01942 | SCR_001833 | 2026-08-01 12:01:37 | 37 | ||||||
|
NASTIseq Resource Report Resource Website 1+ mentions |
NASTIseq (RRID:SCR_001797) | NASTIseq | software resource | Software for integrated detection of natural antisense transcripts using strand-specific RNA sequencing data. | r, antisense transcript, rna, antisense, transcript, linux, windows, strand-specific rna sequencing, cis-natural antisense transcript |
is listed by: OMICtools has parent organization: Duke University; North Carolina; USA |
PMID:23816784 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01945 | SCR_001797 | 2026-08-01 12:02:03 | 1 | |||||||
|
OrderedList Resource Report Resource Website 10+ mentions |
OrderedList (RRID:SCR_001834) | software resource | An R / bioconductor package for detecting similarity in ordered gene lists. Thereby, either simple lists can be compared or gene expression data can be used to deduce the lists. Significance of similarities is evaluated by shuffling lists or by resampling in microarray data, respectively. | standalone software, mac os x, unix/linux, windows, r, differential expression, microarray, multiple comparison |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:16844712 | Free, Available for download, Freely available | OMICS_03525 | http://compdiag.molgen.mpg.de/software/OrderedList.shtml | SCR_001834 | OrderedList - Similarities of Ordered Gene Lists | 2026-08-01 12:02:04 | 11 | ||||||
|
R Project for Statistical Computing Resource Report Resource Website 10000+ mentions |
R Project for Statistical Computing (RRID:SCR_001905) | R | software resource | Software environment and programming language for statistical computing and graphics. R is integrated suite of software facilities for data manipulation, calculation and graphical display. Can be extended via packages. Some packages are supplied with the R distribution and more are available through CRAN family.It compiles and runs on wide variety of UNIX platforms, Windows and MacOS. | R software, statistical, computing, graphics, programming, language, bio.tools |
is used by: UTR is used by: MSstats is used by: CummeRbund is used by: deFuse is used by: JASP is used by: Boruta is used by: NMRProcFlow is used by: PlotsOfData is used by: rtransparent is used by: shinyCircoss is listed by: OMICtools is listed by: bio.tools is listed by: Debian is affiliated with: CRAN is affiliated with: factoextra is affiliated with: dendsort is affiliated with: viridis is affiliated with: RColorBrewer is affiliated with: statmod is related to: Sweave is related to: rOpenSci is related to: R Manuals is related to: Bioconductor is related to: ggplot2 is related to: madsim is related to: Solas is related to: braincog is related to: clustree is related to: PhenoSpD is related to: geomorph is related to: NeuroAnatomy Toolbox is related to: dplyr is related to: glmmADMB is related to: clusterProfiler is related to: ropls is related to: mixOmics is related to: FlowSOM is related to: Rtsne is related to: scran is related to: Rsubread is related to: riboSeqR is related to: Biostrings is related to: riboWaltz is related to: GenomicFeatures is related to: devtools is related to: affy is related to: affydata is related to: Heatmapper is related to: toxprofileR is related to: LTRpred is related to: RaceID is related to: PRSice is related to: Genomic Ranges is related to: Goseq is related to: GAGE is related to: metagear is related to: pagoda2 is related to: dndSCV is related to: tidyr is related to: ClustVis is related to: IDR is related to: NeuroAnatomy Toolbox is related to: rjags is related to: gProfiler2 is related to: knitr is related to: EpiEstim is related to: Minimum-Hypergeometric Test is related to: Network-Based R-Statistics is related to: seqpac is related to: survminer is related to: Vector Generalized Linear and Additive Models is related to: LEA is related to: StAMPP is related to: Betareg is related to: Harrell Miscellaneous is related to: simplePHENOTYPES is related to: Bayesian Generalized Linear Regression is related to: ranger is related to: h2o4gpu is related to: ridge regression Best Linear Unbiased Prediction is related to: Classification And Regression Training is related to: Rphenograph is related to: Peptides is related to: taxize is related to: seqinr is related to: reshape2 is related to: monaLisa is related to: mia is related to: Rtsne is related to: R package:stats-package is related to: R package: maxstat is related to: stats |
PMID:18252159 | SCR_021974, nif-0000-10474, OMICS_01147, biotools:r | https://cran.r-project.org/src/base/R-3/, https://bio.tools/r | SCR_001905 | R software, The R Project for Statistical Computing, R project, R Project, R, R version 3.5.1, R Package, R-3, R version 3.6.1, R Project for Statistical Computing | 2026-08-01 12:02:06 | 47818 | ||||||
|
Pecan Resource Report Resource Website 50+ mentions |
Pecan (RRID:SCR_001909) | software resource | A Java consistency based multiple sequence alignment software program. | java, sequence, alignment, consistency, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of California at Santa Cruz; California; USA |
PMID:18849524 | Free, Available for download, Freely available | OMICS_03739, biotools:pecan | http://hgwdev.cse.ucsc.edu/~benedict/code/Pecan.html, https://bio.tools/pecan | SCR_001909 | 2026-08-01 12:02:06 | 50 | |||||||
|
flowClust Resource Report Resource Website 10+ mentions |
flowClust (RRID:SCR_001807) | software resource | A Bioconductor software package for automated gating of flow cytometry data that implements a robust model-based clustering approach based on multivariate t mixture models with the Box-Cox transformation. | software package, mac os x, unix/linux, windows, r, clustering, flow cytometry, visualization |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:19442304 | Artistic License, v2 | OMICS_05595 | SCR_001807 | flowClust - Clustering for Flow Cytometry | 2026-08-01 12:02:03 | 15 | |||||||
|
HSA Resource Report Resource Website 1+ mentions |
HSA (RRID:SCR_001809) | HSA | software resource | A splice alignment software tool of RNA-Seq reads mapping. | rna-seq, next generation sequencing | is listed by: OMICtools | PMID:24564867 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01944 | SCR_001809 | 2026-08-01 12:01:36 | 1 | |||||||
|
COMPASS Resource Report Resource Website 1+ mentions |
COMPASS (RRID:SCR_001801) | software resource | Software for combinatorial polyfunctionality analysis of single cells. It is a statistical framework that enables unbiased analysis of antigen-specific T-cell subsets. It uses a Bayesian hierarchical framework to model all observed cell-subsets and select the most likely to be antigen-specific while regularizing the small cell counts that often arise in multi-parameter space. The model provides a posterior probability of specificity for each cell subset and each sample, which can be used to profile a subject's immune response to external stimuli such as infection or vaccination. | software package, mac os x, unix/linux, windows, r, flow cytometry |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:26006008 | Free, Available for download, Freely available | OMICS_05640 | SCR_001801 | Combinatorial Polyfunctionality Analysis of Single Cells, COMPASS - Combinatorial Polyfunctionality Analysis of Single Cells, COMPASS: Combinatorial Polyfunctionality Analysis of Single Cells | 2026-08-01 12:01:36 | 2 | |||||||
|
TCW Resource Report Resource Website 1+ mentions |
TCW (RRID:SCR_001875) | TCW | software resource | Software package for assembling, annotating, querying, and comparing transcript and expression level data that consists of two parts: * singleTCW (sTCW): Single transcript sets or assemblies; annotation; differential expression (EdgeR, DEGSeq, DESeq, GoSeq) * multiTCW (mTCW): Comparison of multiple transcript sets; ortholog grouping (e.g., OrthoMCL) It has been tested on Linux and uses Java, mySQL and optionally R. | transcript, assembly annotation, differential expression, transcript set, ortholog, expression, linux, java, mysql, r, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University of Arizona; Arizona; USA |
NSF IOS-1044821 | PMID:23874959 | Free, Available for download, Freely available | OMICS_01940, biotools:tCW | https://bio.tools/TCW | SCR_001875 | Transcriptome Computational Workbench, TCW: Transcriptome Computational Workbench | 2026-08-01 12:01:53 | 2 | ||||
|
flowUtils Resource Report Resource Website 1+ mentions |
flowUtils (RRID:SCR_001879) | software resource | Software that provides utilities for flow cytometry data. | software package, mac os x, unix/linux, windows, r, cell based assay, flow cytometry, decision tree, infrastructure |
is listed by: OMICtools has parent organization: Bioconductor |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_05614 | SCR_001879 | flowUtils - Utilities for flow cytometry | 2026-08-01 12:01:38 | 6 | ||||||||
|
TEMP Resource Report Resource Website 100+ mentions |
TEMP (RRID:SCR_001788) | software resource | Software package for detecting transposable elements (TEs) insertions and excisions from pooled high-throughput sequencing data. | standalone software, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Massachusetts Medical School; Massachusetts; USA |
PMID:24753423 | Free, Available for download, Freely available | OMICS_03821, biotools:temp | https://bio.tools/temp | SCR_001788 | 2026-08-01 12:02:03 | 211 | |||||||
|
EXTREME Resource Report Resource Website 10+ mentions |
EXTREME (RRID:SCR_001821) | software resource | A motif discovery algorithm designed to find DNA-binding motifs in ChIP-Seq and DNase-Seq data. | java, perl, python | is listed by: OMICtools | PMID:24532725 | Free, Available for download, Freely available | OMICS_03428 | SCR_001821 | 2026-08-01 12:02:04 | 28 | ||||||||
|
GLiMMPS Resource Report Resource Website 1+ mentions |
GLiMMPS (RRID:SCR_001787) | GLiMMPS | software resource | Software to characterize the genetic variation of alternative splicing using a robust statistical method for detecting splicing quantitative trait loci (sQTLs) from RNA-seq data. It takes into account the individual variation in sequencing coverage and the noise prevalent in RNA-seq data. | alternative splicing, rna-seq, genetic variation, splicing quantitative trait loci |
is listed by: OMICtools has parent organization: University of California at Los Angeles; California; USA |
PMID:23876401 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01947 | SCR_001787 | 2026-08-01 12:01:36 | 2 | |||||||
|
SAMstrt Resource Report Resource Website 10+ mentions |
SAMstrt (RRID:SCR_001780) | SAMstrt | software resource | Software package that provides the significance analysis of sequencing data with spike-in normalization. The statistical backgrounds and the benefits depend on SAMseq of the samr package. | differential expression, r |
is listed by: OMICtools has parent organization: Karolinska Institute; Stockholm; Sweden |
Karolinska Institutet ; Strategic Research Area Grant for Diabetes |
PMID:23995393 | Free, Available for download, Freely available | OMICS_01951 | SCR_001780 | 2026-08-01 12:02:02 | 17 | ||||||
|
flowTrans Resource Report Resource Website 1+ mentions |
flowTrans (RRID:SCR_002093) | software resource | Software for profile maximum likelihood estimation of parameters for flow cytometry data transformations. | software package, mac os x, unix/linux, windows, r, flow cytometry |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:21050468 | Free, Available for download, Freely available | OMICS_05612 | SCR_002093 | flowTrans - Parameter Optimization for Flow Cytometry Data Transformation | 2026-08-01 12:01:59 | 4 | |||||||
|
AffyPipe Resource Report Resource Website 1+ mentions |
AffyPipe (RRID:SCR_002032) | software resource | An open-source software pipeline for Affymetrix Axiom genotyping workflow. | affymetrix, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
Italian Ministry of Education University and Research 505/Ric; project GenHome ; European Union FP7 project Gene2Farm 289592 |
PMID:25028724 | Free, Available for download, Freely available | biotools:affypipe, OMICS_05203 | https://bio.tools/affypipe | SCR_002032 | AffyPipe: an open-source pipeline for Affymetrix Axiom genotyping workflow | 2026-08-01 12:01:57 | 5 | |||||
|
CanSNPer Resource Report Resource Website 10+ mentions |
CanSNPer (RRID:SCR_001980) | software resource | Software that is a hierarchical genotype classifier of clonal pathogens. | python, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:24574113 | Free, Available for download, Freely available | biotools:cansnper, OMICS_03706 | https://bio.tools/cansnper | SCR_001980 | 2026-08-01 12:01:40 | 18 | |||||||
|
DMET-Analyzer Resource Report Resource Website 1+ mentions |
DMET-Analyzer (RRID:SCR_002030) | DMET-Analyzer | software resource | Software tool for the automatic association analysis among the variation of the patient genomes and the clinical conditions of patients, i.e. the different response to drugs. The system allows: (i) to automatize the workflow of analysis of DMET (drug metabolism enzymes and transporters)-SNP (Single Nucleotide Polymorphism) data avoiding the use of multiple tools; (ii) the automatic annotation of DMET-SNP data and the search in existing databases of SNPs (e.g. dbSNP), (iii) the association of SNP with pathway through the search in PharmaKGB, a major knowledge base for pharmacogenomic studies. It has a simple graphical user interface that allows users (doctors/biologists) to upload and analyze DMET files produced by Affymetrix DMET-Console in an interactive way. | drug, metabolism, enzyme, transporter, affymetrix, variation, genome, clinical, affymetrix dmet, single nucleotide polymorphism, annotation, analysis, pharmacogenomic, pathway |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23035929 | Free, Available for download, Freely available | OMICS_01920 | SCR_002030 | DMETANALYZER, DMETANALYZER - A tool for supporting pharmacogenomics data analysis | 2026-08-01 12:02:07 | 1 | ||||||
|
Ray Resource Report Resource Website 1+ mentions |
Ray (RRID:SCR_001916) | Ray | software resource | Software that assembles reads obtained with new sequencing technologies (Illumina, 454, SOLiD) using MPI 2.2. | mpi, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:20958248 DOI:10.1089/cmb.2009.0238 |
Free, Available for download, Freely available | OMICS_00027, biotools:ray | https://bio.tools/ray, https://sources.debian.org/src/ray/ | SCR_001916 | Ray - a de novo assembler using MPI 2.2, Ray - Parallel genome assemblies for parallel DNA sequencing | 2026-08-01 12:01:55 | 1 | |||||
|
SeqMonk Resource Report Resource Website 500+ mentions |
SeqMonk (RRID:SCR_001913) | SeqMonk | software resource | Software tool to visualize and analyse high throughput mapped sequence data. | java, high throughput sequencing, mapped, visualization, analysis |
is listed by: OMICtools has parent organization: Babraham Institute |
Free, Available for download, Freely available | OMICS_01936 | http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/ | SCR_001913 | 2026-08-01 12:01:54 | 594 |
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