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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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MetaDE Resource Report Resource Website 1+ mentions |
MetaDE (RRID:SCR_000199) | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 30, 2022. Software package that implements 12 major meta-analysis methods for differential expression analysis.Package was removed from the CRAN repository.Formerly available versions can be obtained from the archive.Archived on 2018-01-23 as check problems were not corrected in time. | standalone software, mac os x, unix/linux, windows, r |
is listed by: OMICtools has parent organization: CRAN |
PMID:22863766 | Free, Available for download, Freely available | OMICS_04033 | http://cran.r-project.org/web/packages/MetaDE/ | SCR_000199 | MetaDE: Microarray meta-analysis for differentially expressed gene detection | 2026-07-25 12:04:37 | 1 | ||||||
|
SODOCK Resource Report Resource Website 1+ mentions |
SODOCK (RRID:SCR_000193) | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. An optimization algorithm based on particle swarm optimization (PSO) for solving flexible protein-ligand docking problems. | particle swarm optimization, protein, ligand, docking, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: National Chiao Tung University; Hsinchu; Taiwan |
PMID:17186483 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:sodock, OMICS_01606 | https://bio.tools/sodock | SCR_000193 | 2026-07-25 12:04:38 | 1 | |||||||
|
UnSplicer Resource Report Resource Website 1+ mentions |
UnSplicer (RRID:SCR_000226) | software resource | An RNA-seq alignment program that provides alignment of short reads to a reference genome. The program requires two inputs that are provided by the output of GeneMark-ES: HMM model parameters and ab initio gene predictions. UnSplicer is a sister pipeline to TrueSight. | RNA, sequencing, alignment, short reads, genome, genemark-es, gene prediction |
is listed by: OMICtools has parent organization: Georgia Institute of Technology; Georgia; USA |
PMID:24259430 | Free, Available for download, Freely available | OMICS_01806 | SCR_000226 | 2026-07-25 12:04:39 | 1 | ||||||||
|
RNAmotifs Resource Report Resource Website 1+ mentions |
RNAmotifs (RRID:SCR_000263) | RNAmotifs | software resource | Software that evaluates the sequence around differentially regulated alternative exons to identify clusters of short and degenerate sequences, referred to as multivalent RNA motifs. | rna, motif |
is listed by: OMICtools has parent organization: Bitbucket |
OMICS_02287 | https://bitbucket.org/rogrro/rna_motifs | SCR_000263 | rna_motifs, rna motifs | 2026-07-25 12:04:39 | 1 | |||||||
|
Quant Resource Report Resource Website |
Quant (RRID:SCR_000267) | software resource | A software tool for the proteomics community that may help improving analysis of proteomic experimental data. | standalone software, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:17584939 | Free, Available for download, Freely available | OMICS_02504, biotools:quant | https://bio.tools/quant | SCR_000267 | 2026-07-25 12:04:41 | 0 | |||||||
|
Grinder Resource Report Resource Website 1+ mentions |
Grinder (RRID:SCR_000168) | Grinder | software resource | An open-source bioinformatic tool to create simulated omic shotgun and amplicon sequence libraries for all main sequencing platforms. The tool is available through multiple interfaces like GUI, CLI and API. It is useful for simulating clinical or environmental microbial communities and complements the use of in vitro mock communities. | simulation, amplicon, shotgun, genomic sequencing, clinical, metagenomic, transcriptomic and metatranscriptomic |
is listed by: OMICtools is listed by: Debian has parent organization: SourceForge |
PMID:22434876 DOI:10.1093/nar/gks251 |
Free, Available for download, Freely available | OMICS_01508 | https://sources.debian.org/src/grinder/ | SCR_000168 | 2026-07-25 12:04:36 | 3 | ||||||
|
CNTools Resource Report Resource Website |
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 | CNTools - Convert segment data into a region by sample matrix to allow for other high level computational analyses | 2026-07-25 12:04:41 | 0 | |||||||
|
GProX Resource Report Resource Website 1+ mentions |
GProX (RRID:SCR_000273) | software resource | A freely available complete software platform for comprehensive and integrated analysis and visualization of large proteomics datasets. | standalone software |
is listed by: OMICtools has parent organization: SourceForge |
PMID:21602510 | Free, Available for download, Freely available | OMICS_02506 | SCR_000273 | Graphical Proteomics Data Explorer | 2026-07-25 12:04:40 | 1 | |||||||
|
PeptideProphet Resource Report Resource Website 1+ mentions |
PeptideProphet (RRID:SCR_000274) | software resource | Software that automatically validates peptide assignments to MS/MS spectra made by database search programs such as SEQUEST. | standalone software, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite has parent organization: SourceForge |
PMID:12403597 | Free, Available for download, Freely available | OMICS_02520, biotools:peptideprophet | https://bio.tools/peptideprophet | SCR_000274 | 2026-07-25 12:04:41 | 4 | |||||||
|
GISTIC Resource Report Resource Website 10+ mentions |
GISTIC (RRID:SCR_000151) | GISTIC | software resource | Software to identify genes targeted by somatic copy-number alterations (SCNAs) that drive cancer growth. By separating SCNA profiles into underlying arm-level and focal alterations, they improve the estimation of background rates for each category. | somatic copy-number alteration, gene |
is listed by: OMICtools has parent organization: Massachusetts Institute of Technology; Massachusetts; USA; |
Cancer | PMID:21527027 | Free, Available for download, Freely available | OMICS_02296 | SCR_000151 | GISTIC2.0, GISTIC 2.0, GISTIC 2 | 2026-07-25 12:04:36 | 48 | |||||
|
F2DockClient Resource Report Resource Website 1+ mentions |
F2DockClient (RRID:SCR_000185) | F2DockClient | software resource | A collection of user interfaces packaged into TexMol that allows a user to interactively submit protein-protein docking jobs to a remote computing cluster, monitor the status of the jobs and retrieve and visually display/compare the results. | user interface, protein-protein docking, computing cluster, analysis, | is listed by: OMICtools | National Science Foundation ; National Institutes of Health |
PMID:23483883 | Free, Available for download, Freely available | OMICS_01599 | SCR_000185 | 2026-07-25 12:04:37 | 1 | ||||||
|
FlexX Resource Report Resource Website 1+ mentions |
FlexX (RRID:SCR_000186) | FlexX | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A software with two main applications: predicting the binding mode of three-dimensional proteins and virtual high-throughput screening (vHTS) which allows screening of compounds at rapid speeds. | protein binding, analysis, ligand, prediction, compounds, screening, protein-ligand docking, | is listed by: OMICtools | PMID:15382244 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01600 | SCR_000186 | 2026-07-25 12:04:36 | 5 | |||||||
|
TransView Resource Report Resource Website |
TransView (RRID:SCR_000358) | TransView | software resource | Software package to generate, access and display read densities of sequencing based data sets such as from RNA-Seq and ChIP-Seq. | rna-seq, chip-seq, clustering, dna methylation, data import, gene expression, methyl-seq, microarray, multiple comparison, sequencing, transcription, visualization |
is listed by: OMICtools has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_02048 | SCR_000358 | 2026-07-25 12:04:43 | 0 | ||||||||
|
pvac Resource Report Resource Website |
pvac (RRID:SCR_000359) | pvac | software resource | Software package that contains the function for filtering genes by the proportion of variation accounted for by the first principal component (PVAC). | microarray, one channel, quality control, affymetrix, principal component analysis, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
Free, Available for download, Freely available | biotools:pvac, OMICS_02031 | https://bio.tools/pvac | SCR_000359 | pvac: PCA-based gene filtering for Affymetrix arrays | 2026-07-25 12:04:44 | 0 | ||||||
|
TAPS Resource Report Resource Website 1+ mentions |
TAPS (RRID:SCR_000356) | software resource | A bioinformatic tool for the identification of allele-specific copy numbers in tumor samples using data from Affymetrix SNP arrays. | standalone software, affymetrix |
is listed by: OMICtools has parent organization: Google Code |
PMID:22023820 | OMICS_02571 | SCR_000356 | Tumor Aberration Prediction Suite | 2026-07-25 12:04:44 | 1 | ||||||||
|
PyroHMMsnp Resource Report Resource Website |
PyroHMMsnp (RRID:SCR_000357) | software resource | Software using a realignment-based SNP calling method for 454 and Ion Torrent sequencing data. | standalone software, roche |
is listed by: OMICtools has parent organization: Google Code |
PMID:23700313 | Free, Available for download, Freely available | OMICS_02617 | SCR_000357 | 2026-07-25 12:04:42 | 0 | ||||||||
|
CGAP-Align Resource Report Resource Website |
CGAP-Align (RRID:SCR_000350) | software resource | A time efficient read alignment tool built on the top of BWA. | standalone software, illumina |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23593381 | Free, Available for download, Freely available | OMICS_05480 | SCR_000350 | 2026-07-25 12:04:42 | 0 | ||||||||
|
cuteNMR Resource Report Resource Website |
cuteNMR (RRID:SCR_000347) | software resource | A multi-platform NMR processing application. | standalone software, mac os x, unix/linux, windows, c++ |
is listed by: OMICtools has parent organization: SourceForge |
Free, Available for download, Freely available | OMICS_03391 | SCR_000347 | 2026-07-25 12:04:42 | 0 | |||||||||
|
JMolDraw Resource Report Resource Website |
JMolDraw (RRID:SCR_000349) | software resource | 2-D chemical structure drawing software program. | applet, mac os x, unix/linux, windows, java |
is listed by: OMICtools has parent organization: SourceForge |
Free, Available for download, Freely available | OMICS_05000 | SCR_000349 | 2026-07-25 12:04:43 | 0 | |||||||||
|
is-rSNP Resource Report Resource Website 1+ mentions |
is-rSNP (RRID:SCR_000387) | is-rSNP | software resource | Software tool that predicts whether a single nucleotide polymorphism (SNP) is a regulatory SNP (rSNP). For a given SNP, and using a statistical framework, it can successfully predict the set of transcription factors (TFs) for which binding is affected. The algorithm provides the statistical power to scan large numbers of SNPs, making it suitable to use to screen all associated SNPs output by a typical genome-wide association studies (GWAS). | genome-wide association study, single nucleotide polymorphism, transcription factor, regulatory single nucleotide polymorphism, in silico |
is listed by: OMICtools has parent organization: University of Melbourne; Victoria; Australia |
PMID:20823317 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01930 | SCR_000387 | In silico regulatory SNP detection, is-rSNP: in silico regulatory SNP detection | 2026-07-25 12:04:45 | 1 |
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