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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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NucleoFinder Resource Report Resource Website 1+ mentions |
NucleoFinder (RRID:SCR_000368) | NucleoFinder | software resource | A software for a statistical approach for the detection of nucleosome positions in a cell population. The software identifies important features of nucleosome organization such as the spacing downstream of active promoters and the enrichment and depletion of GC/AT dinucleotides of in vitro nucleosomes. | nucleusome, position, promoter, analysis, downstream, nucleotide, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:23297036 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:nucleofinder, OMICS_00510 | https://omictools.com/nucleofinder-tool, https://bio.tools/nucleofinder | SCR_000368 | 2026-09-19 12:49:21 | 1 | ||||||
|
flowPeaks Resource Report Resource Website |
flowPeaks (RRID:SCR_000407) | software resource | Software for fast and automatic clustering to classify the cells into subpopulations based on finding the peaks from the overall density function generated by K-means. | software package, mac os x, unix/linux, windows, r, clustering, flow cytometry, gating, bio.tools |
is listed by: OMICtools is listed by: GitHub is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
PMID:22595209 | Free, Available for download, Freely available | biotools:flowpeaks, OMICS_05604 | http://www.bioconductor.org/packages/devel/bioc/html/flowPeaks.html, https://bio.tools/flowpeaks | SCR_000407 | 2026-09-19 12:49:22 | 0 | |||||||
|
TNO-DECO Resource Report Resource Website |
TNO-DECO (RRID:SCR_000440) | software resource | Matlab code for preprocessing gas chromatography mass spectrometry data. | matlab, mass spectrometry | is listed by: OMICtools | Free, Available for download, Freely available | OMICS_02660 | SCR_000440 | 2026-09-19 12:49:23 | 0 | |||||||||
|
MiRdup Resource Report Resource Website 1+ mentions |
MiRdup (RRID:SCR_000316) | software resource | A software used for the validation of pre-miRNAs predictions as well as predict the final structure of mature miRNA. | pre-miRNA, miRNA, mRNA, splicing, predictions |
is listed by: OMICtools has parent organization: McGill University; Montreal; Canada |
PMID:23748953 | Free, Available for download, Freely available | OMICS_00404 | https://www.cs.mcgill.ca/~blanchem/mirdup/ | http://This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or any later version. | SCR_000316 | 2026-09-19 12:49:20 | 1 | ||||||
|
QUALIFIER Resource Report Resource Website |
QUALIFIER (RRID:SCR_000389) | software resource | Software that provides quality control and quality assessment tools for gated flow cytometry data. | software package, mac os x, unix/linux, windows, r, cell based assay, flow cytometry, infrastructure |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:23020243 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_05618 | SCR_000389 | QUALIFIER - Quality Control of Gated Flow Cytometry Experiments | 2026-09-19 12:49:22 | 0 | |||||||
|
rtd Resource Report Resource Website |
rtd (RRID:SCR_000337) | data analysis software, data processing software, software application, software resource | Reference-free ddRADseq analysis software tools. The pipeline script generates reference-sorted, indexed BAM from uniqued reads from radtag sequencing lanes. | standalone software | is listed by: OMICtools | PMID:22675423 | Free, Available for download, Freely available | OMICS_03723 | SCR_000337 | 2026-09-19 12:49:20 | 0 | ||||||||
|
oneClickCGH Resource Report Resource Website |
oneClickCGH (RRID:SCR_000294) | oneClickCGH | data analysis software, data processing software, software application, software resource | Platform-independent array copy number analysis software that provides straightforward yet comprehensive detection and reporting of copy number changes. | array, comparative genomic hybridization, cytogenetics, copy number variant, copy number analysis, | is listed by: OMICtools | Restricted | OMICS_02050 | SCR_000294 | 2026-09-19 12:49:20 | 0 | ||||||||
|
fqzcomp Resource Report Resource Website 1+ mentions |
fqzcomp (RRID:SCR_000299) | fqzcomp | software resource | A basic fastq compressor, designed primarily for high performance. | c++ |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23533605 | Free, Available for download, Freely available | OMICS_00957 | SCR_000299 | 2026-09-19 12:49:20 | 1 | |||||||
|
miRprimer Resource Report Resource Website 1+ mentions |
miRprimer (RRID:SCR_000480) | miRprimer | software resource | Software tool for automatic design of primers for PCR amplification of microRNAs using the method miR-specific RT-qPCR (Balcells, I., Cirera, S., and Busk, P.K. (2011). Specific and sensitive quantitative RT-PCR of miRNAs with DNA primers. BMC Biotechnol. 11, 70). | ruby, primer, microrna, rt-qpcr, ms windows, pcr amplification |
is listed by: OMICtools has parent organization: SourceForge |
PMID:24472427 | Free, Available for download, Freely available | OMICS_02311 | SCR_000480 | miRprimer - Automatic design of primers for miR-specific RT-qPCR | 2026-09-19 12:49:24 | 3 | ||||||
|
BAIT Resource Report Resource Website 1+ mentions |
BAIT (RRID:SCR_000511) | BAIT | data analysis software, data processing software, data visualization software, software application, software resource | Software to create strand inheritance plots in data derived from the Strand-Seq sequencing protocol. The software is designed to be flexible with a range of species, and basic template folders can called to read in species-specific data. | create strand inheritance plots, strand-seq, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:24028793 | Free, Available for download, Freely available | biotools:bait, OMICS_01531 | https://bio.tools/bait | SCR_000511 | BAIT - Software to help analyse Strand-Seq data | 2026-09-19 12:49:25 | 1 | |||||
|
pyQPCR Resource Report Resource Website |
pyQPCR (RRID:SCR_000471) | pyQPCR | software resource | A GUI application written in python that deals with quantitative PCR (QPCR) raw data. Using quantification cycle values extracted from QPCR instruments, it uses a proven and universally applicable model to give finalized quantification resu | quantitative pcr, python, qt |
is listed by: OMICtools has parent organization: SourceForge |
Free, Available for download, Freely available | OMICS_02326 | SCR_000471 | 2026-09-19 12:49:24 | 0 | ||||||||
|
RefFinder Resource Report Resource Website 10+ mentions |
RefFinder (RRID:SCR_000472) | RefFinder | analysis service resource, data access protocol, production service resource, service resource, software resource, web service | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 1,2023. Web-based tool for evaluating and screening reference genes from extensive experimental datasets. It integrates major computational programs (geNorm, Normfinder, BestKeeper, and the comparative delta-Ct method) to compare and rank the tested candidate reference genes. Based on the rankings from each program, it assigns an appropriate weight to an individual gene and calculated the geometric mean of their weights for the overall final ranking., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene, gene expression, reference gene, web based tool |
uses: BestKeeper uses: NormFinder uses: geNORM is listed by: OMICtools has parent organization: East Carolina University; Carolina; USA |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02321 | http://www.leonxie.com/referencegene.php | SCR_000472 | 2026-09-19 12:49:24 | 45 | |||||||
|
PGS Resource Report Resource Website |
PGS (RRID:SCR_000475) | software resource | Software tool for association study of high-dimensional microRNA expression data with repeated measures. The penalized regression model incorporates a grid search method for analyzing associations of high-dimensional microRNA expression data with repeated measures. | standalone software, r, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:24947752 | Free, Available for download, Freely available | biotools:pgs, OMICS_04651 | https://bio.tools/pgs | SCR_000475 | PGS: Penalized GEE with Grid Search, Penalized GEE with Grid Search | 2026-09-19 12:49:24 | 0 | ||||||
|
DDBJ Omics Archive Resource Report Resource Website |
DDBJ Omics Archive (RRID:SCR_000597) | DOR | data or information resource, data repository, database, service resource, storage service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 6,2023. Archival database of functional genomics data generated by microarray and highly parallel new generation sequencers. Data are exchanged between ArrayExpress at EBI and DOR in common MAGE-TAB format. Supports MIAME and MINSEQE-compliant data submissions. DOR issues accession numbers, E-DORD-n to experiment and A-DORD-n to array design. DOR exchanges public data with the EBI ArrayExpress in common MAGE-TAB format. Note: At present, DOR does not accept submissions. DDBJ will announce launch of DOR when it is ready. (2013/01/31) The data can be kept private until your paper is published. You can set the hold date for a maximum of 1 year and can change it. Registered records are released according to the Data Release Policy. | functional genomics, array, sequence |
is listed by: OMICtools is related to: ArrayExpress is related to: MIAME is related to: MINSEQE is related to: MAGE-TAB has parent organization: DNA DataBank of Japan (DDBJ) |
PMID:22110025 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01026 | http://trace.ddbj.nig.ac.jp/dor | SCR_000597 | Ddbj Omics aRchive | 2026-09-19 12:49:26 | 0 | |||||
|
ContEst Resource Report Resource Website 1+ mentions |
ContEst (RRID:SCR_000595) | ContEst | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 8,2025. A software tool (and method) for estimating the amount of cross-sample contamination in next generation sequencing data. | java, contamination, next-generation sequencing, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Broad Institute |
PMID:21803805 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01038, biotools:contest | https://bio.tools/contest | SCR_000595 | 2026-09-19 12:49:26 | 6 | ||||||
|
SpeedSeq Resource Report Resource Website 1+ mentions |
SpeedSeq (RRID:SCR_000469) | software resource | Software for a lightweight, flexible, and open source pipeline that identifies genomic variation (single nucleotide variants (SNVs), indels, and structural variants (SVs)). | standalone software |
is listed by: OMICtools has parent organization: University of Virginia; Virginia; USA |
Free, Available for download, Freely available | OMICS_04673 | SCR_000469 | 2026-09-19 12:49:24 | 7 | |||||||||
|
MPscan Resource Report Resource Website |
MPscan (RRID:SCR_000587) | MPscan | data access protocol, software resource, web service | Web tool for index free mapping of multiple short reads on a genome. | linux, macos, next-generation sequencing, genome, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: ATGC: Montpellier bioinformatics platform |
Free, Available for download, Freely available | biotools:mpscan, OMICS_00670 | https://bio.tools/mpscan | SCR_000587 | MPscan: index free mapping of multiple short reads on a genome | 2026-09-19 12:49:26 | 0 | ||||||
|
MATCHCLIP Resource Report Resource Website |
MATCHCLIP (RRID:SCR_000541) | MATCHCLIP | software resource | Software program that detects the precise break points of Copy number variations (CNVs) through a fuzzy string matching algorithm using both CIGAR and POS information. In case the two break points of a CNV are in repeated regions and the break points are not unique, it reports the range where the break points can slide. | breakpoint, deletion, duplication, exon sequencing, structural variation, next generation sequencing |
is listed by: OMICtools has parent organization: University of Pennsylvania Perelman School of Medicine; Pennsylvania; USA |
PMID:23967014 | Free, Available for download, Freely available, | OMICS_02289 | SCR_000541 | matchclips2, MATCHCLIPS | 2026-09-19 12:49:25 | 0 | ||||||
|
TDARACNE Resource Report Resource Website |
TDARACNE (RRID:SCR_000498) | TDARACNE | software resource | Software package to infer gene regulatory networks from time-series measurements. The algorithm is expected to be useful in reconstruction of small biological directed networks from time course data. | microarray, time course |
is listed by: OMICtools has parent organization: Bioconductor |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02013 | SCR_000498 | TDARACNE - Network reverse engineering from time course data | 2026-09-19 12:49:24 | 0 | |||||||
|
Mfuzz Resource Report Resource Website 10+ mentions |
Mfuzz (RRID:SCR_000523) | software resource | Software package for noise-robust soft clustering of gene expression time-series data (including a graphical user interface)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | r, time series, gene expression, clustering, microarray, preprocessing, time course, visualization, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Humboldt University of Berlin; Berlin; Germany has parent organization: Bioconductor |
PMID:18084642 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:mfuzz, OMICS_02012 | https://bio.tools/mfuzz | http://itb.biologie.hu-berlin.de/~futschik/software/R/Mfuzz/ | SCR_000523 | Mfuzz - Soft clustering of time series gene expression data | 2026-09-19 12:49:25 | 16 |
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