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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
CSSP Resource Report Resource Website 10+ mentions |
CSSP (RRID:SCR_012932) | CSSP | software resource | Software for power computation for ChIP-Seq data based on Bayesian estimation for local poisson counting process. |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:23665773 | Free | OMICS_00426 | SCR_012932 | ChIP-SEQ Statistical Power | 2026-02-07 02:08:49 | 16 | |||||||
|
cghMCR Resource Report Resource Website 1+ mentions |
cghMCR (RRID:SCR_012898) | cghMCR | software resource | Software package that provides functions to identify genomic regions of interest based on segmented copy number data from multiple samples. |
is listed by: OMICtools has parent organization: Bioconductor |
OMICS_00710 | SCR_012898 | 2026-02-07 02:08:48 | 5 | ||||||||||
|
RankProd Resource Report Resource Website 100+ mentions |
RankProd (RRID:SCR_013046) | RankProd | software resource | Software using a non-parametric method for identifying differentially expressed (up- or down- regulated) genes based on the estimated percentage of false predictions (pfp). |
is listed by: OMICtools has parent organization: Bioconductor |
OMICS_01313 | SCR_013046 | 2026-02-07 02:08:41 | 183 | ||||||||||
|
MEDIPS Resource Report Resource Website 100+ mentions |
MEDIPS (RRID:SCR_012996) | MEDIPS | software resource | Software developed for analyzing data derived from methylated DNA immunoprecipitation (MeDIP) experiments followed by sequencing (MeDIP-seq). |
is listed by: OMICtools has parent organization: Bioconductor |
OMICS_00613 | SCR_012996 | MeDIP-seq data analysis | 2026-02-07 02:08:53 | 168 | |||||||||
|
TurboNorm Resource Report Resource Website |
TurboNorm (RRID:SCR_012963) | TurboNorm | software resource | Software providing a fast scatterplot smoother suitable for microarray normalization based on B-splines with second-order difference penalty. Functions for microarray normalization of single-colour data i.e. Affymetrix/Illumina and two-colour data supplied as marray MarrayRaw-objects or limma RGList-objects are available. |
is listed by: OMICtools has parent organization: Bioconductor |
OMICS_00856 | SCR_012963 | 2026-02-07 02:08:51 | 0 | ||||||||||
|
Ringo Resource Report Resource Website 10+ mentions |
Ringo (RRID:SCR_012973) | Ringo | software resource | Software package that facilitates the primary analysis of ChIP-chip data. |
is listed by: OMICtools is listed by: SoftCite has parent organization: Bioconductor |
OMICS_00809 | SCR_012973 | 2026-02-07 02:08:52 | 38 | ||||||||||
|
phyloseq Resource Report Resource Website 1000+ mentions |
phyloseq (RRID:SCR_013080) | phyloseq | software resource | Software for handling and analysis of high-throughput microbiome census data. | bio.tools |
is used by: microViz is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
DOI:10.1371/journal.pone.0061217 | OMICS_01520, biotools:phyloseq | https://bio.tools/phyloseq https://sources.debian.org/src/r-bioc-phyloseq/ |
SCR_013080 | 2026-02-07 02:08:42 | 2613 | |||||||
|
BayesPeak Resource Report Resource Website 10+ mentions |
BayesPeak (RRID:SCR_013011) | BayesPeak | software resource | Software package that is an implementation of the BayesPeak algorithm for peak-calling in ChIP-seq data. |
is listed by: OMICtools has parent organization: Bioconductor |
OMICS_00432 | SCR_013011 | BayesPeak - Bayesian Analysis of ChIP-seq Data | 2026-02-07 02:08:39 | 13 | |||||||||
|
ChIPseqR Resource Report Resource Website |
ChIPseqR (RRID:SCR_013016) | ChIPseqR | software resource | Software that identifies protein binding sites from ChIP-seq and nucleosome positioning experiments. |
is listed by: OMICtools has parent organization: Bioconductor |
OMICS_00501 | SCR_013016 | 2026-02-07 02:08:39 | 0 | ||||||||||
|
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 | 2026-02-07 02:07:50 | 1602 | ||||||||||
|
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 | 2026-02-07 02:07:20 | 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 | 2026-02-07 02:07:15 | 37 | ||||||||||
|
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 | methVisual - Methods for visualization and statistics on DNA methylation data | 2026-02-07 02:07:15 | 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 | seqbias - Estimation of per-position bias in high-throughput sequencing data | 2026-02-07 02:07:27 | 27 | ||||||
|
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 | flowMerge - Cluster Merging for Flow Cytometry Data | 2026-02-07 02:05:41 | 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 | flowPhyto - Methods for Continuous Flow Cytometry | 2026-02-07 02:05:41 | 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 | BS-Seq Epimutation Analysis Toolkit, BEAT - BS-Seq Epimutation Analysis Toolkit | 2026-02-07 02:05:44 | 118 | |||||||
|
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 | CAMERA - Collection of annotation related methods for mass spectrometry data | 2026-02-07 02:05:44 | 4 | |||||
|
MethylAid Resource Report Resource Website 50+ mentions |
MethylAid (RRID:SCR_002659) | software resource | Software for visual and interactive quality control of large Illumina 450k data sets. Bad quality samples are detected using sample-dependent and sample-independent controls present on the array and user adjustable thresholds. In depth exploration of bad quality samples can be performed using several interactive diagnostic plots of the quality control probes present on the array. Furthermore, the impact of any batch effect provided by the user can be explored. | software package, illumina, mac os x, unix/linux, windows, r, dna methylation, gui, methylation array, microarray, quality control, two channel, visualization, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
PMID:25147358 | Free, Available for download, Freely available | biotools:methylaid, OMICS_05457 | http://www.bioconductor.org/packages/release/bioc/html/MethylAid.html http://shiny.bioexp.nl/MethylAid/ https://bio.tools/methylaid |
SCR_002659 | MethylAid - Visual and interactive quality control of large Illumina 450k data sets, MethylAid: Visual and interactive quality control of large Illumina 450k data sets | 2026-02-07 02:05:47 | 64 | ||||||
|
CGHnormaliter Resource Report Resource Website 1+ mentions |
CGHnormaliter (RRID:SCR_002936) | software resource | Software for normalization and centralization of array comparative genomic hybridization (aCGH) data with imbalanced aberrations. The algorithm uses an iterative procedure that effectively eliminates the influence of imbalanced copy numbers. This leads to a more reliable assessment of copy number alterations (CNAs). | standalone software, mac os x, unix/linux, windows, r, array comparative genomic hybridization, copy number alteration, microarray, preprocessing |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:20418341 | Free, Available for download, Freely available | OMICS_02572 | http://www.bioconductor.org/packages/release/bioc/html/CGHnormaliter.html | SCR_002936 | CGHnormaliter - Normalization of array CGH data with imbalanced aberrations. | 2026-02-07 02:05:52 | 2 |
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