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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
pNovo+ Resource Report Resource Website 1+ mentions |
pNovo+ (RRID:SCR_002860) | software resource | A de novo peptide sequencing algorithm using complementary higher-energy collisional dissociation (HCD) and electron transfer dissociation (ETD) tandem mass spectra. | mass spectrometry, proteomics, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Chinese Academy of Sciences; Beijing; China |
PMID:23272783 | Free, Freely available | biotools.pNovo_3, OMICS_02470 | https://bio.tools/pNovo_3 | SCR_002860 | 2026-08-01 12:01:57 | 7 | |||||||
|
pairheatmap Resource Report Resource Website |
pairheatmap (RRID:SCR_003109) | software resource | A software tool to compare two heatmaps and discover patterns within and across groups. In the context of biology, group can be defined based on gene ontology. | standalone software, r, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: CRAN |
PMID:24016862 | Free, Available for download, Freely available | biotools:pairheatmap, OMICS_04853 | https://www.rdocumentation.org/packages/pairheatmap/versions/1.0.1/topics/pairheatmap | SCR_003109 | pairheatmap: A tool for comparing heatmaps | 2026-08-01 12:02:02 | 0 | ||||||
|
MFEprimer Resource Report Resource Website 10+ mentions |
MFEprimer (RRID:SCR_003066) | software resource | A fast thermodynamics-based software program for checking PCR primer specificity against genomic DNA and mRNA/cDNA sequence databases. | standalone software, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:22689644 | Free, Available for download, Freely available | biotools:mfeprimer-2.0, OMICS_02355 | https://www.mfeprimer.com/ | SCR_003066 | MFEprimer-2.0 | 2026-08-01 12:02:01 | 19 | ||||||
|
eQtlBma Resource Report Resource Website 1+ mentions |
eQtlBma (RRID:SCR_003102) | software resource | Software package that implements Bayesian statistical methods to detect eQTLs jointly in multiple subgroups (e.g. tissues). Key features are to borrow information across subgroups, to explicitly model heterogeneity (qualitatively and quantitatively), and to borrow information across genes to estimate hyper-parameters from the data (empirical Bayes). | standalone software, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Chicago; Illinois; USA |
PMID:23671422 | Free, Available for download, Freely available | biotools:eqtlbma, OMICS_04875 | https://bio.tools/eqtlbma | SCR_003102 | 2026-08-01 12:02:26 | 5 | |||||||
|
Triplex Resource Report Resource Website 10+ mentions |
Triplex (RRID:SCR_003061) | software resource | Software package that provides functions for identification and visualization of potential intramolecular triplex patterns in DNA sequence. The main functionality is to detect the positions of subsequences capable of folding into an intramolecular triplex (H-DNA) in a much larger sequence. The potential H-DNA (triplexes) should be made of as many canonical nucleotide triplets as possible. The package includes visualization showing the exact base-pairing in 1D, 2D or 3D. | software package, mac os x, unix/linux, windows, r, gene regulation, sequence matching, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
PMID:23709494 | Free, Available for download, Freely available | OMICS_06259, biotools:triplex | http://www.fi.muni.cz/~lexa/triplex/, https://bio.tools/triplex | SCR_003061 | triplex - Search and visualize intramolecular triplex-forming sequences in DNA | 2026-08-01 12:02:25 | 10 | ||||||
|
bwtool Resource Report Resource Website 10+ mentions |
bwtool (RRID:SCR_003035) | software resource | A command-line utility for bigWig files designed to read bigWig files rapidly and efficiently, providing functionality for extracting data and summarizing it in several ways, globally or at specific regions. Its functionality is subdivided into subprograms that roughly fall into three categories: data extraction, analysis, and data modification, although e.g. in the case of the matrix program or the sax program, the boundary between data extraction and analysis isn't very strong. The data modification programs all have the behavior that a bigWig is inputted and a new bigWig is outputted. | standalone software, unix/linux, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:2448936 | Free, Available for download, Freely available | biotools:bwtool, OMICS_05125 | https://bio.tools/bwtool | SCR_003035 | 2026-08-01 12:02:00 | 21 | |||||||
|
SMRT View Resource Report Resource Website 1+ mentions |
SMRT View (RRID:SCR_003029) | software resource | An open source Genome Browser that visualizes data generated by PacBio Sequencing Systems. * Users can explore and interact with all types of analysis results, including resequencing, De novo, cDNA, and barcoding. * Users can also visualize base modifications, base identification and motifs analysis results. | standalone software, unix/linux, mac os x, windows, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
Free, Freely available | biotools:smrt_view, OMICS_05137 | https://bio.tools/smrt_view | SCR_003029 | SMRT-View | 2026-08-01 12:02:24 | 9 | |||||||
|
ProRata Resource Report Resource Website 1+ mentions |
ProRata (RRID:SCR_002988) | software resource | A quantitative proteomics software program for accurate protein abundance ratio estimation with confidence interval evaluation. | standalone software, mass spectrometry, proteomics, stable isotope labeling, quantitative proteomics, proteomics, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Google Code |
PMID:17037911 | GNU General Public License, v3 | biotools:prorata, OMICS_02502 | https://bio.tools/prorata | SCR_002988 | ProRata: A quantitative proteomics program for accurate protein abundance ratio estimation with confidence interval evaluation, prorata - Quantitative Proteomics Software | 2026-08-01 12:01:59 | 9 | ||||||
|
rbsurv Resource Report Resource Website 1+ mentions |
rbsurv (RRID:SCR_001175) | rbsurv | software resource | Software package that selects genes associated with survival. | microarray, gene, survival, 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:rbsurv, BioTools:rbsurv, OMICS_02088 | https://bio.tools/rbsurv, https://bio.tools/rbsurv, https://bio.tools/rbsurv | SCR_001175 | rbsurv - Robust likelihood-based survival modeling with microarray data | 2026-08-01 12:01:24 | 1 | ||||||
|
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 |
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