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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
mapDamage Resource Report Resource Website 100+ mentions |
mapDamage (RRID:SCR_001240) | mapDamage | software resource | Software for tracking and quantifying DNA damage patterns among ancient DNA sequencing reads generated by Next-Generation Sequencing platforms. | python, r, illumina, windows, perl, dna damage, dna sequencing, next-generation sequencing, dna, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Copenhagen; Copenhagen; Denmark |
PMID:23613487 PMID:21659319 DOI:10.1093/bioinformatics/btt193 |
Free, Available for download, Freely available | OMICS_02099, biotools:mapdamage | https://bio.tools/mapdamage, https://sources.debian.org/src/mapdamage/ | SCR_001240 | mapDamage 2.0, mapDamage: tracking and quantifying damage patterns in ancient DNA sequences, mapDamage2.0 | 2026-08-01 12:01:35 | 363 | |||||
|
DSK Resource Report Resource Website 1+ mentions |
DSK (RRID:SCR_001246) | DSK | software resource | A k-mer counting software that can count k-mers of large Illumina datasets on laptops and desktop computers. | illumina, k-mer, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:23325618 | Free, Freely available | biotools:dsk, OMICS_02094 | https://bio.tools/dsk | SCR_001246 | disk streaming of k-mers, DSK: disk streaming of k-mers | 2026-08-01 12:01:44 | 1 | |||||
|
wateRmelon Resource Report Resource Website 100+ mentions |
wateRmelon (RRID:SCR_001296) | wateRmelon | software resource | Software package for Illumina 450 methylation array normalization and metrics including 15 flavors of betas and three performance metrics, with methods for objects produced by methylumi, minfi and IMA packages. | dna methylation, microarray, preprocessing, quality control, two channel, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
PMID:23631413 | Free, Available for download, Freely available | OMICS_02039, biotools:watermelon | https://bio.tools/watermelon | SCR_001296 | 2026-08-01 12:01:46 | 296 | ||||||
|
NGSrich Resource Report Resource Website 10+ mentions |
NGSrich (RRID:SCR_001333) | software resource | Software for target enrichment performance for next-generation sequencing. | standalone software, java, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:22290614 | Free, Available for download, Freely available | OMICS_03603, biotools:ngsrich | https://bio.tools/ngsrich | SCR_001333 | 2026-08-01 12:01:39 | 10 | |||||||
|
oneChannelGUI Resource Report Resource Website 10+ mentions |
oneChannelGUI (RRID:SCR_001325) | oneChannelGUI | software resource | Software library that provides a graphical interface for microarray gene and exon level analysis as well as miRNA/mRNA-seq data analysis. The package was developed to simplify the use of Bioconductor tools for beginners having limited or no experience in writing R code. | differential expression, gui, microarray, multiple comparison, preprocessing, quality control, rna-seq, exon, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
PMID:17875544 | Free, Available for download, Freely available | biotools:onechannelgu, OMICS_02004 | http://www.bioconductor.org/packages/release/bioc/html/oneChannelGUI.html | SCR_001325 | 2026-08-01 12:01:27 | 13 | ||||||
|
CYCLE Resource Report Resource Website 10+ mentions |
CYCLE (RRID:SCR_001328) | CYCLE | software resource | Software package for the identification of periodically expressed genes using Fourier analysis and the statistical assessment of significance using different background models. | r, microarray, time course, periodic expression pattern, time-series, 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:18310054 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02010, biotools:cycle | http://www.bioconductor.org/packages/release/bioc/html/cycle.html, https://bio.tools/cycle | SCR_001328 | 2026-08-01 12:01:28 | 31 | ||||||
|
affylmGUI Resource Report Resource Website 10+ mentions |
affylmGUI (RRID:SCR_001320) | affylmGUI | software resource | R software package providing a Graphical User Interface for analysis of Affymetrix microarray data, using the limma package (Linear Models for MicroArray data). While not as powerful as limma to the expert user, it offers a simple point-and-click interface to many of the commonly-used limma and affy functions. You need to have R 1.9.0 or later, Tcl/Tk 8.3 or later (ActiveTcl for Windows, Tcl/Tk Source for Linux/Unix, or X11 Tcl/Tk for MacOSX) and the limma, affylmGUI, and tkrplot R packages. It has been succesfully tested on Windows 2000, Windows XP, RedHat/Fedora Linux, and on Mac OSX with X11. | affymetrix, differential expression, r, data import, differential expression, gui, microarray, multiple comparison, one channel, preprocessing, quality control, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Walter and Eliza Hall Institute of Medical Research; Victoria; Australia has parent organization: Bioconductor |
PMID:16455752 | Free, Available for download, Freely available | biotools:affylmgui, OMICS_02016 | http://www.bioconductor.org/packages/release/bioc/html/affylmGUI.html, https://bio.tools/affylmgui | SCR_001320 | Affymetrix linear modeling Graphical User Interface | 2026-08-01 12:01:47 | 31 | |||||
|
plgem Resource Report Resource Website 10+ mentions |
plgem (RRID:SCR_001355) | plgem | software resource | Software to detect differential expression in microarray and proteomics datasets. Its use has been shown to improve the detection of differentially expressed genes or proteins in these datasets. | differential expression, microarray, proteomics, 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 | OMICS_01984, biotools:plgem | https://bio.tools/plgem | SCR_001355 | Power Law Global Error Model | 2026-08-01 12:01:49 | 16 | ||||||
|
fRMA Resource Report Resource Website 50+ mentions |
fRMA (RRID:SCR_001345) | fRMA | software resource | Preprocessing and analysis software for single microarrays and microarray batches. | microarray, preprocessing, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
PMID:23044545 | Free, Available for download, Freely available | biotools:frma, OMICS_01994 | https://bio.tools/frma | SCR_001345 | fRMA - Frozen RMA and Barcode | 2026-08-01 12:01:28 | 74 | |||||
|
dyebias Resource Report Resource Website |
dyebias (RRID:SCR_001308) | dyebias | software resource | Software package using the GASSCO method for correcting for slide-dependent gene-specific dye bias. | microarray, preprocessing, quality control, two channel, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
PMID:17623705 | GNU General Public License, v3 | biotools:dyebias, OMICS_02025 | https://bio.tools/dyebias | SCR_001308 | dyebias - The GASSCO method for correcting for slide-dependent gene-specific dye bias | 2026-08-01 12:01:27 | 0 | |||||
|
limmaGUI Resource Report Resource Website 10+ mentions |
limmaGUI (RRID:SCR_001306) | limmaGUI | software resource | Software package for a Graphical User Interface for the limma Microarray package. | differential expression, gui, microarray, multiple comparison, preprocessing, quality control, two channel, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
PMID:15297296 | Free, Available for download, Freely available | OMICS_02027, biotools:limmagui | https://bio.tools/limmagui | SCR_001306 | limmaGUI - GUI for limma package | 2026-08-01 12:01:47 | 14 | |||||
|
ffpe Resource Report Resource Website 100+ mentions |
ffpe (RRID:SCR_001307) | ffpe | software resource | Software to identify low-quality data using metrics developed for expression data derived from Formalin-Fixed, Paraffin-Embedded (FFPE) data. Also a function for making Concordance at the Top plots (CAT-plots). | formalin-fixed, paraffin-embedded, gene expression, microarray, quality control, 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 | OMICS_02026, biotools:ffpe | https://bio.tools/ffpe | SCR_001307 | ffpe - Quality assessment and control for FFPE microarray expression data | 2026-08-01 12:01:38 | 496 | ||||||
|
Eddy Lab Software Resource Report Resource Website 10+ mentions |
Eddy Lab Software (RRID:SCR_001458) | software resource | Software library containing tools for statistical manipulations of data. Tools include profile hidden Markov models for biological sequence analysis, RNA structure analysis, and a prototype noncoding RNA genefinder. | software repository, statistics, data, statistical analysis, statistical manipulation, markov model, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Janelia Research has parent organization: Howard Hughes Medical Institute |
Free, Available for download, Freely available | nif-0000-08778, biotools:pknots | https://bio.tools/pknots | http://selab.janelia.org/software.html | SCR_001458 | Eddy Lab: Software, Eddy Lab - Software | 2026-08-01 12:01:30 | 21 | ||||||
|
PyLOH Resource Report Resource Website 1+ mentions |
PyLOH (RRID:SCR_001511) | software resource | Software for deconvolving tumor purity and ploidy by integrating copy number alterations and loss of heterozygosity. The model resolves the identifiability problem by integrating two types of sequencing information - somatic copy number alterations and loss of heterozygosity - within an unified probabilistic framework. | standalone software, python, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:24695406 | Free, Available for download, Freely available | OMICS_03559, biotools:pyloh | https://bio.tools/pyloh | SCR_001511 | 2026-08-01 12:01:42 | 4 | |||||||
|
TANGO Resource Report Resource Website 100+ mentions |
TANGO (RRID:SCR_001770) | TANGO | software resource | A computer algorithm to predict aggregation nucleating regions in proteins as well the effect of mutations and environmental conditions on the aggregation propensity of these regions. | polypeptide chain, polypeptide, peptide, protein, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Center for Genomic Regulation; Barcelona; Spain |
PMID:15361882 | Free, Freely available | biotools:tango, OMICS_03859 | https://bio.tools/tango | SCR_001770 | 2026-08-01 12:01:35 | 114 | ||||||
|
Cuffdiff Resource Report Resource Website 1000+ mentions |
Cuffdiff (RRID:SCR_001647) | Cuffdiff | software resource | Software that estimates expression at transcript-level resolution and controls for variability evident across replicate libraries. | differential expression, rna-seq, transcript, splicing, promoter, coding sequence, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: Cufflinks has parent organization: University of Maryland; Maryland; USA |
PMID:23222703 | Free, Available for download, Freely available | biotools:cuffdiff, OMICS_01969 | https://bio.tools/cuffdiff | SCR_001647 | Cuffdiff 2 | 2026-08-01 12:01:46 | 3832 | |||||
|
PennSeq Resource Report Resource Website 1+ mentions |
PennSeq (RRID:SCR_001763) | PennSeq | software resource | Software for isoform-specific gene expression quantification in RNA-Seq by modeling non-uniform read distribution. Instead of making parametric assumptions, they give adequate weight to the underlying data by the use of a non-parametric approach. The rationale is that regardless what factors lead to non-uniformity, whether it is due to hexamer priming bias, local sequence bias, positional bias, RNA degradation, mapping bias or other unknown reasons, the probability that a fragment is sampled from a particular region will be reflected in the aligned data. This empirical approach thus maximally reflects the true underlying non-uniform read distribution. | isoform, gene expression, rna-seq, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:24362841 | Free, Available for download, Freely available | biotools:pennseq, OMICS_01946 | https://bio.tools/pennseq | SCR_001763 | 2026-08-01 12:02:02 | 4 | ||||||
|
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 | 2026-08-01 12:01:18 | 0 | ||||||
|
Flicker Resource Report Resource Website |
Flicker (RRID:SCR_000288) | software resource | An open-source stand-alone computer program for visually comparing 2D gel images. | mac os x, unix/linux, windows, java, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:10027264 | Free, Available for download, Freely available | OMICS_02538, biotools:nci_flicker | https://bio.tools/nci_flicker | SCR_000288 | 2026-08-01 12:01:13 | 0 | |||||||
|
MeQA Resource Report Resource Website |
MeQA (RRID:SCR_000317) | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 31, 2022. Software for pre-processing, quality assessment, read distribution and methylation estimation for MeDIP-sequence datasets. It has the ability to quickly analyze sequence data for DNA methylation. This software integrates customized scripting and existing utilities tools that work on both paired end and single end data. | quality assessment, read distribution, methylation estimation, medip, medip-sequence, dna methylation, utilities tool, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Tongji University; Shanghai; China |
PMID:22199384 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:meqa, OMICS_00616 | https://bio.tools/meqa | SCR_000317 | 2026-08-01 12:01:17 | 0 |
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