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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Basic4Cseq Resource Report Resource Website 1+ mentions |
Basic4Cseq (RRID:SCR_002836) | software resource | An R/Bioconductor package for basic filtering, analysis and subsequent near-cis visualization of 4C-seq data. Virtual fragment libraries can be created for any BSGenome package, and filter functions for both reads and fragments and basic quality controls are included. Fragment data in the vicinity of the experiment's viewpoint can be visualized as a coverage plot based on a running median approach and a multi-scale contact profile. | software package, unix/linux, mac os x, windows, r, quality control, visualization |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:25078398 | Free, Freely available, Available for download | OMICS_05202 | SCR_002836 | Basic4Cseq: an R/Bioconductor package for analyzing 4C-seq data | 2026-09-05 06:24:54 | 6 | |||||||
|
mzR Resource Report Resource Website 1+ mentions |
mzR (RRID:SCR_002856) | software resource | Software that provides a unified API to the common file formats and parsers available for mass spectrometry data. It comes with a wrapper for the ISB random access parser for mass spectrometry mzXML, mzData and mzML files. | standalone software, mac os x, unix/linux, windows, r, data import, infrastructure, mass spectrometry, metabolomics, proteomics |
is listed by: OMICtools has parent organization: Bioconductor |
Free, Freely available, Available for download | OMICS_02654 | SCR_002856 | mzR - parser for netCDF mzXML mzData and mzML and mzIdentML files | 2026-09-05 06:24:54 | 1 | ||||||||
|
BiGGR Resource Report Resource Website |
BiGGR (RRID:SCR_002854) | software resource | Software package that provides an interface to simulate metabolic reconstruction from the BiGG database and other metabolic reconstruction databases. The package facilitates flux balance analysis (FBA) and the sampling of feasible flux distributions. Metabolic networks and estimated fluxes can be visualized with hypergraphs. | standalone software, mac os x, unix/linux, windows, r, metabolomics, network, visualization, metabolic reconstruction, model |
uses: BiGG Database is listed by: OMICtools has parent organization: Bioconductor |
PMID:25806817 | Free, Freely available, Available for download | OMICS_02655 | SCR_002854 | BiGGR - Constraint based modeling in R using metabolic reconstruction databases | 2026-09-05 06:24:54 | 0 | |||||||
|
PAPi Resource Report Resource Website 50+ mentions |
PAPi (RRID:SCR_002857) | software resource | An R package for predicting the activity of metabolic pathways based solely on a metabolomics data set containing a list of metabolites identified and their respective abundances in different biological samples. PAPi generates hypothesis that improves the final biological interpretation. | standalone software, mac os x, unix/linux, windows, r, mass spectrometry, metabolomics |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:20929912 | Free, Freely available, Available for download | OMICS_02653 | SCR_002857 | PAPi - Predict metabolic pathway activity based on metabolomics data, Pathway Activity Profiling | 2026-09-05 06:24:54 | 56 | |||||||
|
CNVassoc Resource Report Resource Website 1+ mentions |
CNVassoc (RRID:SCR_002901) | software resource | Software package that carries out association analysis of common copy number variants in population-based studies. It includes functions for analysing association under a series of study designs (case-control, cohort, etc), using several dependent variables (class status, censored data, counts) as response, adjusting for covariates and considering various inheritance models. It also includes functions for inferring copy number (CNV genotype calling). Various classes and methods for generic functions (print, summary, plot, anova, ... ) have been created to facilitate the analysis. | standalone software, mac os x, unix/linux, windows, r |
is listed by: OMICtools has parent organization: CRAN |
PMID:21609482 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02609 | SCR_002901 | CNVassoc: Association analysis of CNV data | 2026-09-05 06:24:55 | 1 | |||||||
|
tweeDEseq Resource Report Resource Website 1+ mentions |
tweeDEseq (RRID:SCR_003038) | software resource | Software for differential expression analysis of RNA-seq using the Poisson-Tweedie family of distributions. | standalone software, unix/linux, mac os x, windows, c, r, rna-seq, differential expression, sequencing, statistical method, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
PMID:23965047 | Free, Available for download, Freely available | OMICS_02406, biotools:tweedeseq | https://bio.tools/tweedeseq | SCR_003038 | tweeDEseq: RNA-seq data analysis using the Poisson-Tweedie family of distributions | 2026-09-05 06:24:57 | 4 | ||||||
|
R-pbh5 Resource Report Resource Website |
R-pbh5 (RRID:SCR_003026) | software library, software resource, software toolkit | Software library for accessing data in HDF5 files produced by Pacific Biosciences sequencing machines. The R package supports accessing data from: cmp.h5, bas.h5, pls.h5, and trc.h5. | software package, r | is listed by: OMICtools | Free, Available for download, Freely available | OMICS_05139 | https://github.com/extemporaneousb/R-pbh5 | SCR_003026 | 2026-09-05 06:24:56 | 0 | ||||||||
|
Isopat Resource Report Resource Website |
Isopat (RRID:SCR_003025) | software resource | Software function that calculates the isotopic pattern (fine structures) for a given chemical formula. | standalone software, mac os x, unix/linux, windows, r |
is listed by: OMICtools has parent organization: CRAN |
Free, Available for download, Freely available | OMICS_02409 | https://isopat.sourceforge.net/ | SCR_003025 | isopat: Calculation of isotopic pattern for a given molecular formula | 2026-09-05 06:24:56 | 0 | |||||||
|
BRAIN Resource Report Resource Website 10+ mentions |
BRAIN (RRID:SCR_003018) | software resource | Software package for calculating aggregated isotopic distribution and exact center-masses for chemical substances (in this version composed of C, H, N, O and S). | standalone software, mac os x, unix/linux, windows, r, mass spectrometry, proteomics, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
PMID:23350948 | GNU General Public License, v2 | biotools:brain, OMICS_02410 | https://bio.tools/brain | SCR_003018 | Baffling Recursive Algorithm for Isotopic distributioN calculations, Baffling Recursive Algorithm for Isotope distributioN | 2026-09-05 06:24:56 | 47 | ||||||
|
SurvComp Resource Report Resource Website 50+ mentions |
SurvComp (RRID:SCR_003054) | survcomp | software resource | R package providing functions to assess and to compare the performance of risk prediction (survival) models. | differential expression, gene expression, visualization, mac os x, unix/linux, windows, r |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:21903630 | Free, Available for download, Freely available | OMICS_02373 | SCR_003054 | survcomp - Performance Assessment and Comparison for Survival Analysis | 2026-09-05 06:24:57 | 61 | ||||||
|
Parametric Time Warping Resource Report Resource Website |
Parametric Time Warping (RRID:SCR_003053) | ptw | software resource | Software that aligns patterns, i.e. it aims to put corresponding features at the same locations. The algorithm searches for an optimal polynomial describing the warping. It is possible to align one sample to a reference, several samples to the same reference, or several samples to several references. One can choose between calculating individual warpings, or one global warping for a set of samples and one reference. Two optimization criteria are implemented: RMS (Root Mean Square error) and WCC (Weighted Cross Correlation). | standalone software, mac os x, unix/linux, windows, r |
is listed by: OMICtools has parent organization: CRAN |
PMID:14719890 | Free, Freely available | OMICS_02392 | SCR_003053 | ptw: Parametric Time Warping | 2026-09-05 06:24:57 | 0 | ||||||
|
R-pbutils Resource Report Resource Website |
R-pbutils (RRID:SCR_002995) | software resource | An R software package providing plotting and convenience functions. | software package, r | is listed by: OMICtools | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_05140 | SCR_002995 | 2026-09-05 06:24:56 | 0 | |||||||||
|
Piano Resource Report Resource Website 100+ mentions |
Piano (RRID:SCR_003200) | data analysis software, data processing software, software application, software resource | Software R-package for running gene set analysis using various statistical methods, from different gene level statistics and a wide range of gene-set collections. The Piano package contains functions for combining the results of multiple runs of gene set analyses. | r, omics, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Chalmers University of Technology; Gothenburg; Sweden has parent organization: Bioconductor |
PMID:23444143 | Free, Available for download, Freely available | OMICS_01558, biotools:piano | https://bio.tools/piano | SCR_003200 | 2026-09-05 06:24:59 | 188 | |||||||
|
ALDEx2 Resource Report Resource Website 500+ mentions |
ALDEx2 (RRID:SCR_003364) | software resource | Software tool to examine compositional high-throughput sequence data with Welch's t-test. A differential relative count abundance analysis for the comparison of two conditions. For example, single-organism and meta-rna-seq high-throughput sequencing assays, or of selected and unselected values from in-vitro sequence selections. Uses a Dirichlet-multinomial model to infer abundance from counts, that has been optimized for three or more experimental replicates. Infers sampling variation and calculates the expected Benjamini-Hochberg false discovery rate given the biological and sampling variation using several parametric and non-parametric tests. Can to glm and Kruskal-Wallace tests on one-way ANOVA style designs. | standalone software, r, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: aldex has parent organization: Western University; Ontario; Canada |
PMID:24910773 | Free, Available for download, Freely available | biotools:aldex2, OMICS_04634 | https://bio.tools/aldex2 | SCR_003364 | 2026-09-05 06:25:02 | 609 | |||||||
|
RCircos Resource Report Resource Website 100+ mentions |
RCircos (RRID:SCR_003310) | software resource | Software package that provides a simple and flexible way to generate Circos 2D track plot images for genomic data visualization. The types of plots include: heatmap, histogram, lines, scatterplot, tiles and plot items for further decorations include connector, link (lines and ribbons), and text (gene) label. All functions require only R graphics package that comes with R base installation. | standalone software, unix/linux, mac os x, windows, r |
is listed by: OMICtools is related to: shinyCircoss has parent organization: CRAN has parent organization: Bitbucket |
PMID:23937229 | Free, Available for download, Freely available | OMICS_04661 | https://bitbucket.org/henryhzhang/rcircos/ | SCR_003310 | RCircos: Circos 2D Track Plot | 2026-09-05 06:25:01 | 285 | ||||||
|
ggbio Resource Report Resource Website 10+ mentions |
ggbio (RRID:SCR_003313) | software resource | An R package for extending the grammar of graphics for genomic data. The graphics are designed to answer common scientific questions, in particular those often asked of high throughput genomics data. All core Bioconductor data structures are supported, where appropriate. The package supports detailed views of particular genomic regions, as well as genome-wide overviews. Supported overviews include ideograms and grand linear views. High-level plots include sequence fragment length, edge-linked interval to data view, mismatch pileup, and several splicing summaries. | standalone software, unix/linux, mac os x, windows, r, infrastructure, visualization, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
PMID:22937822 | Free, Available for download, Freely available | biotools:ggbio, OMICS_04660 | http://www.tengfei.name/ggbio/, https://bio.tools/ggbio | SCR_003313 | ggbio - Visualization tools for genomic data | 2026-09-05 06:25:01 | 16 | ||||||
|
OmicCircos Resource Report Resource Website 50+ mentions |
OmicCircos (RRID:SCR_003292) | software resource | An R software application and package used to generate high-quality circular plots for visualizing genomic variations, including mutation patterns, copy number variations (CNVs), expression patterns, and methylation patterns. | standalone software, unix/linux, mac os x, windows, r, annotation, statistical method, visualization |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:24526832 | Free, Available for download, Freely available | OMICS_04659 | http://www.bioconductor.org/packages/release/bioc/html/OmicCircos.html | SCR_003292 | OmicCircos: High-quality circular visualization of omic data | 2026-09-05 06:25:01 | 83 | ||||||
|
flowQB Resource Report Resource Website |
flowQB (RRID:SCR_002144) | software resource | A fully automated R Bioconductor package to calculate automatically the detector efficiency (Q), optical background (B) and intrinsic CV of the beads. | 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_05610 | http://www.bioconductor.org/packages/release/bioc/html/flowQB.html | SCR_002144 | B and CVinstrinsic calculations, flowQB - Automated Quadratic Characterization of Flow Cytometer Instrument Sensitivity: Q, flowQB: Automated Quadratic Characterization of Flow Cytometer Instrument Sensitivity: Q | 2026-09-05 06:24:44 | 0 | |||||||
|
flowFit Resource Report Resource Website 1+ mentions |
flowFit (RRID:SCR_002286) | software resource | A Bioconductor package designed to perform quantitative analysis of cell proliferation in tracking dye-based experiments. The package uses an R implementation of the Levenberg-Marquardt algorithm (minpack.lm) to fit a set of peaks (corresponding to different generations of cells) over the proliferation-tracking dye distribution in a FACS experiment. | software package, mac os x, unix/linux, windows, r, cell based assay, flow cytometry |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:24681909 | Artistic License, v2 | OMICS_05601 | SCR_002286 | flowFit - Estimate proliferation in cell-tracking dye studies | 2026-09-05 06:24:46 | 4 | |||||||
|
spliceR Resource Report Resource Website 10+ mentions |
spliceR (RRID:SCR_002280) | software resource | An easy-to-use R package for classification of alternative splicing and prediction of coding potential from RNA-seq data. | standalone software, unix/linux, mac os x, windows, c, r, differential expression, high throughput sequencing, rna-seq, rna-seq, visualization |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:24655717 | GNU General Public License, v2 or greater | OMICS_03514 | SCR_002280 | spliceR - Classification of alternative splicing and prediction of coding potential from RNA-seq data | 2026-09-05 06:24:46 | 25 |
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