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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Sherman Resource Report Resource Website 100+ mentions |
Sherman (RRID:SCR_001294) | Sherman | software resource | Software tool to simulate FastQ files for high-throughput sequencing experiments. It allows the user to introduce various "contaminants" into the sequences, such as basecall errors, SNPs, adapter fragments etc., in order to evaluate the influence of common problems observed in many Next-Gen Sequencing experiments. | perl, bisulfite sequencing, high-throughput sequencing, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Babraham Institute |
Free, Available for download, Freely available | biotools:sherman, OMICS_02041 | http://www.bioinformatics.babraham.ac.uk/projects/sherman/ | SCR_001294 | Sherman - bisulfite-treated Read FastQ Simulator | 2026-08-01 12:01:37 | 122 | ||||||
|
GenomicTools Resource Report Resource Website |
GenomicTools (RRID:SCR_001205) | GenomicTools | software resource | A flexible computational platform, comprising both a command-line set of tools and a C++ API, for the analysis and manipulation of high-throughput sequencing data such as DNA-seq, RNA-seq, ChIP-seq and MethylC-seq. It implements a variety of mathematical operations between sets of genomic regions thereby enabling the prototyping of computational pipelines that can address tasks from preprocessing and quality control to meta-analyses. The user can create average read profiles across transcriptional start sites or enhancer sites, quickly prototype customized peak discovery methods for ChIP-seq experiments, perform genome-wide statistical tests such as enrichment analyses, design controls via appropriate randomization schemes, among other applications. In addition to enabling rapid prototyping, the platform is designed to analyze large-datasets in a single-pass fashion in order to minimize memory and intermediate file requirements. The platform supports the widely used BED format to facilitate visualization as well as integration with existing platforms and pipelines such as Galaxy or BioConductor. | high-throughput sequencing, rna-seq, chip-seq, genomics, sequencing, hi-c, epigenetics, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Google Code |
PMID:22113082 | Free, Available for download, Freely available | biotools:genomictools, OMICS_02144 | https://bio.tools/genomictools | SCR_001205 | GenomicTools: a computational platform for developing high-throughput analytics in genomics. | 2026-08-01 12:01:34 | 0 | |||||
|
PARalyzer Resource Report Resource Website 1+ mentions |
PARalyzer (RRID:SCR_001208) | PARalyzer | software resource | Software tool to generate a high resolution map of interaction sites between RNA-binding proteins and their targets. The algorithm utilizes the deep sequencing reads generated by the newly developed PAR-CLIP (Photoactivatable-Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation) protocol. The use of photoactivatable nucleotides in the PAR-CLIP protocol results in a more efficient crosslinking between the RNA-binding protein and its target relative to other CLIP methods; in addition a nucleotide substitution occurs at the site of crosslinking during Illumina library preparation. PARalyzer utilizes this nucleotide substition in a kernel density estimate classifier to generate the high resolution set of Protein-RNA interaction sites. | interaction, rna-binding protein, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Duke University; North Carolina; USA |
PMID:21851591 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:paralyzer, OMICS_02137 | https://bio.tools/paralyzer | SCR_001208 | PAR-CLIP data analyzer, PARalyzer (PAR-CLIP data analyzer) | 2026-08-01 12:01:42 | 6 | |||||
|
ProbRNA Resource Report Resource Website 1+ mentions |
ProbRNA (RRID:SCR_001288) | ProbRNA | software resource | Software for computational identification of protein binding sites on RNAs using high-throughput RNA structure-probing data. | high-throughput sequencing, probe, rna structure, rna, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Chinese University of Hong Kong; Hong Kong; China |
PMID:24376038 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:probrna, OMICS_02195 | https://bio.tools/probrna | SCR_001288 | 2026-08-01 12:01:37 | 1 | ||||||
|
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 | 2026-08-01 12:01:25 | 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 | 2026-08-01 12:01:34 | 3 | ||||||
|
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 | 2026-08-01 12:01:24 | 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 | 2026-08-01 12:01:34 | 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 | 2026-08-01 12:01:34 | 0 | |||||
|
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 | 2026-08-01 12:01:44 | 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 | 2026-08-01 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 |
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