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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Sequedex Resource Report Resource Website 1+ mentions |
Sequedex (RRID:SCR_001233) | Sequedex | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 18,2025.Software to classify the function and phylogeny of reads as short as 30 bp. It is flexible, which can utilize multiple data modules and downstream analysis scripts. It is fast, reading in signature lists of 5-500 million peptide signatures in 1-15 minutes, and subsequently processes genomic fragments at the rate of 6 Gbp/hr. It parallelizes without significant increase in memory requirements until I/O bound on multiple input files; parallelization works well on 64 processors. | phylogenetic, function, profile, metagenomics, synthetic, dna sequence, classification, java, linux, mac os, genomic analysis, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Los Alamos National Laboratory |
PMID:22925230 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02110, biotools:sequedex | https://bio.tools/sequedex | SCR_001233 | 2026-09-12 12:55:21 | 1 | ||||||
|
PeakAnalyzer Resource Report Resource Website 1+ mentions |
PeakAnalyzer (RRID:SCR_001194) | PeakAnalyzer | software resource | A set of standalone software programs for the automated processing of any genomic loci, with an emphasis on datasets consisting of ChIP-derived signal peaks. The software is able to identify individual binding / modification sites from enrichment loci, retrieve peak region sequences for motif discovery, and integrate experimental data with different classes of annotated elements throughout the genome. PeakAnalyzer requires a peak file and a feature annotation file in BED or GTF format. Complete annotation files for the current builds of the human (HG19) and mouse (MM9) genomes are provided with the software distribution. | genome, chip, signal peak, binding site, modification site, enrichment loci, peak region, sequence, motif, chip-seq, chip-chip, c++, java, linux, mac os x, windows, bed, gtf, annotation, r, high-throughput sequencing, chromatin binding, modification loci, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: European Bioinformatics Institute |
PMID:20691053 | Free, Available for download, Freely available | biotools:peakanalyzer, OMICS_02156 | https://bio.tools/peakanalyzer | SCR_001194 | 2026-09-12 12:55:21 | 3 | ||||||
|
metahdep Resource Report Resource Website |
metahdep (RRID:SCR_001225) | metahdep | data analysis software, data processing software, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 18,2025. Software tools for meta-analysis in the presence of hierarchical (and/or sampling) dependence, including with gene expression studies. | differential expression, microarray, gene expression, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
PMID:19648140 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:metahdep, OMICS_02121 | https://bio.tools/metahdep | SCR_001225 | metahdep - Hierarchical Dependence in Meta-Analysis | 2026-09-12 12:55:21 | 0 | |||||
|
BreakSeq Resource Report Resource Website 1+ mentions |
BreakSeq (RRID:SCR_001186) | BreakSeq | software resource | Software for scanning reads from short-read sequenced genomes against a human breakpoint library to accurately identify structural variants (SVs). The library of breakpoints at nucleotide resolution were assembled from collating and standardizing ~2,000 published structural variants (SVs). For each breakpoint, its ancestral state (through comparison to primate genomes) was inferred and its mechanism of formation (e.g., nonallelic homologous recombination, NAHR). | structural variant, breakpoint, nucleotide, fasta, gff, bowtie, genomic variation, junction mapping, insertion sequence, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Yale University; Connecticut; USA |
PMID:20037582 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:breakseq, OMICS_02168 | https://bio.tools/breakseq | SCR_001186 | Breakpoint Library and BreakSeq | 2026-09-12 12:55:21 | 1 | |||||
|
SLOPE Resource Report Resource Website |
SLOPE (RRID:SCR_001185) | SLOPE | software resource | Software that consists of two command-line utilities, slope_align (which finds the best split-read alignments to the reference genome) and slope_cluster (which clusters and outputs the alignments)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | c++, alignment, cluster, command-line, reference genome, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Utah; Utah; USA |
PMID:20876606 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02169, biotools:slope | https://bio.tools/slope | SCR_001185 | 2026-09-12 12:55:21 | 0 | ||||||
|
Genometa Resource Report Resource Website |
Genometa (RRID:SCR_001181) | Genometa | software resource | A Java based bioinformatics program which allows rapid analysis of metagenomic short read datasets. Millions of short reads can be accurately analysed within minutes and visualised in the browser component. A large database of diverse bacteria and archaea has been constructed as a reference sequence. The approach is based upon the established open source visualisation tool IGB and supported by the rapid alignment program bowtie. The Picard toolset for SAM files is also made use of. | metagenomic, classify, windows, linux, java, bio.tools, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Hannover Medical School; Lower Saxony; Germany |
PMID:22927906 | Free, Available for download, Freely available | biotools:genometa, OMICS_02175 | https://bio.tools/genometa | SCR_001181 | Genometa - Rapid analysis of metagenomic short reads | 2026-09-12 12:55:20 | 0 | |||||
|
globaltest Resource Report Resource Website 10+ mentions |
globaltest (RRID:SCR_001256) | globaltest | data analysis software, data processing software, sequence analysis software, software application, software resource | A software package that tests groups of covariates (or features) for association with a response variable. The package implements the test with diagnostic plots and multiple testing utilities, along with several functions to facilitate the use of this test for gene set testing of GO and KEGG terms. | differential expression, go, microarray, one channel, pathway, bio.tools |
uses: KEGG is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: Gene Ontology has parent organization: Bioconductor |
PMID:34046931 | Free, Available for download, Freely available | biotools:globaltest, OMICS_02084 | https://bio.tools/globaltest | SCR_001256 | 2026-09-12 12:55:22 | 31 | ||||||
|
piCALL Resource Report Resource Website 1+ mentions |
piCALL (RRID:SCR_001242) | piCALL | software resource | Software to detect short insertion / deletion variants (and SNPs) from population sequence data, i.e. sequence reads generated from a population of individuals. It uses a probabilistic model to utilize sequence reads from a population of individuals to automatically account for context-specific sequencing errors associated with indels. piCALL is implemented in C for use on Linux platforms and can be applied to sequence data from different sequencing platforms. However, the method requires each individual in a dataset to be sequenced using the same platform. The reads for each individual should be aligned to the same reference genome sequence. Note that the program will not be able to call indels from individual sequence datasets or data from a small number of individuals. | c, genotyping, indel, population, high-throughput sequencing, insertion, deletion, variant, single nucleotide polymorphism, linux, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Scripps Research Institute |
PMID:21653520 | OMICS_02098, biotools:picall | https://bio.tools/picall | http://polymorphism.scripps.edu/~vbansal/software/piCALL/ | SCR_001242 | 2026-09-12 12:55:22 | 1 | ||||||
|
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 | 2026-09-12 12:55:21 | 395 | |||||
|
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 | 2026-09-12 12:55:22 | 1 | |||||
|
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 | 2026-09-12 12:55:24 | 10 | |||||||
|
pickgene Resource Report Resource Website |
pickgene (RRID:SCR_001331) | pickgene | data analysis software, data processing software, software application, software resource | Software for adaptive Gene Picking for Microarray Expression Data Analysis. | microarray, gene expression, differential expression, 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_02007, biotools:pickgene | https://bio.tools/pickgene | SCR_001331 | 2026-09-12 12:55:24 | 0 | |||||||
|
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 | 2026-09-12 12:55:24 | 13 | ||||||
|
CYCLE Resource Report Resource Website 1+ 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 | 2026-09-12 12:55:24 | 4 | ||||||
|
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 | 2026-09-12 12:55:23 | 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 | 2026-09-12 12:55:24 | 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 | 2026-09-12 12:55:24 | 76 | |||||
|
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 | biotools:pknots, nif-0000-08778 | https://bio.tools/pknots | http://selab.janelia.org/software.html | SCR_001458 | Eddy Lab: Software, Eddy Lab - Software | 2026-09-12 12:55:26 | 23 | ||||||
|
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 | 2026-09-12 12:55:23 | 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 | 2026-09-12 12:55:23 | 14 |
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