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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
ZINBA Resource Report Resource Website 10+ mentions |
ZINBA (RRID:SCR_010868) | ZINBA | software resource | Software to identify genomic regions enriched in a variety of ChIP-seq and related next-generation sequencing experiments (DNA-seq), calling both broad and narrow modes of enrichment across a range of signal-to-noise ratios. ZINBA models and accounts for factors that co-vary with background or experimental signal, such as G/C content, and identifies enrichment in genomes with complex local copy number variations. ZINBA provides a single unified framework for analyzing DNA-seq experiments in challenging genomic contexts. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA |
PMID:21787385 | GNU General Public License, v3 | biotools:zinba, OMICS_00465 | https://bio.tools/zinba | SCR_010868 | zinba - Zero Inflated Negative Binomial Algorithm, Zero Inflated Negative Binomial Algorithm | 2026-08-01 12:04:18 | 13 | |||||
|
Aroma.affymetrix Resource Report Resource Website 10+ mentions |
Aroma.affymetrix (RRID:SCR_010919) | Aroma.affymetrix | software resource | An R package for analyzing large Affymetrix data sets. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
OMICS_00703, biotools:aroma.affymetrix | https://bio.tools/aroma.affymetrix | SCR_010919 | 2026-08-01 12:04:18 | 32 | ||||||||
|
NURD Resource Report Resource Website 50+ mentions |
NURD (RRID:SCR_010988) | NURD | software resource | An algorithm to inference isoform expression., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
THIS RESOURCE IS NO LONGER IN SERVICE | biotools:nurd, OMICS_01283 | https://bio.tools/nurd | SCR_010988 | 2026-08-01 12:04:19 | 72 | |||||||
|
libmgf Resource Report Resource Website |
libmgf (RRID:SCR_002664) | software resource | A flex/bison-based C++ Mascot Generic Format (MGF) parser library. | standalone software, c++, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:20334363 | Free, Available for download, Freely available | OMICS_03343, biotools:libmgf, BioTools:libmgf | https://bio.tools/libmgf, https://bio.tools/libmgf, https://bio.tools/libmgf | SCR_002664 | MGFp, libmgf (formerly MGFp) | 2026-08-01 12:02:12 | 0 | ||||||
|
ExomeDepth Resource Report Resource Website 100+ mentions |
ExomeDepth (RRID:SCR_002663) | software resource | Software that calls copy number variants (CNVs) from targeted sequence data, typically exome sequencing experiments designed to identify the genetic basis of Mendelian disorders. | software package, unix/linux, mac os x, windows, r, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: CRAN |
PMID:22942019 | Free, Available for download, Freely available | OMICS_05443, biotools:exomedepth | https://bio.tools/exomedepth | SCR_002663 | 2026-08-01 12:01:52 | 262 | |||||||
|
libCSAM Resource Report Resource Website 1+ mentions |
libCSAM (RRID:SCR_002766) | software resource | Contains several C++ codes for compress, decompress, and access each of the fields of any SAM format file. | standalone software, c++, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:24728856 | Free, Freely available, Available for download | OMICS_03750, biotools:libcsam | https://bio.tools/libcsam | SCR_002766 | 2026-08-01 12:02:16 | 1 | |||||||
|
RopeBWT2 Resource Report Resource Website 10+ mentions |
RopeBWT2 (RRID:SCR_002673) | software resource | A software tool for constructing the FM-index for a collection of DNA sequences. It works by incrementally inserting one or multiple sequences into an existing pseudo-BWT position by position, starting from the end of the sequences. This algorithm can be largely considered a mixture of BCR and dynamic FM-index. Nonetheless, ropeBWT2 is unique in that it may implicitly sort the input into reverse lexicographical order (RLO) or reverse-complement lexicographical order (RCLO) while building the index. | standalone software, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: Burrows-Wheeler transform |
PMID:25107872 | Free, Available for download, Freely available | biotools:ropebwt2, OMICS_05300 | https://bio.tools/ropebwt2 | SCR_002673 | 2026-08-01 12:02:13 | 11 | |||||||
|
NetPathMiner Resource Report Resource Website 1+ mentions |
NetPathMiner (RRID:SCR_002757) | software resource | Software that implements a flexible module-based process flow for network path mining and visualization, which can be fully inte-grated with user-customized functions. It supports construction of various types of genome scale networks from three different pathway file formats (KGML, SBML and BioPAX), enabling its utility to most common pathway databases. In addition, it provides different visualization techniques to facilitate the analysis of even thousands of output paths. | software package, mac os x, unix/linux, windows, r, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:25075120 | Free, Freely available, Available for download | biotools:netpathminer, OMICS_05210 | https://bio.tools/netpathminer | SCR_002757 | NetPathMiner: R package for network path mining through gene expression | 2026-08-01 12:01:54 | 3 | ||||||
|
GATE Resource Report Resource Website 100+ mentions |
GATE (RRID:SCR_002756) | data analysis resource | Model-based, open source software analysis tool for chromatin states prediction based on time-course epigenetic marks data. It uses a combinatory Finite Mixture model nested with HMM to model the time course marks data in which each single hidden markov model describes the hidden states for a region set across different time points. | chromatin state prediction software, time course epigenetic data, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:23033340 | Free, Freely available, Available for download | OMICS_03065, biotools:gate | https://github.com/yu68/GATE, https://bio.tools/gate | SCR_002756 | Genomic Annotation from Time-couse Epigenomic data, Genomic Annotation from Time-couse Epigenomic data (GATE) | 2026-08-01 12:02:16 | 317 | ||||||
|
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 | ||||||
|
CUDA-EC Resource Report Resource Website 1+ mentions |
CUDA-EC (RRID:SCR_001090) | CUDA-EC | software resource | A fast parallel error correction tool for short reads. | c, gpu/cuda, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:20426693 | Free, Available for download, Freely available | OMICS_01100, biotools:cuda-ec | https://bio.tools/cuda-ec | SCR_001090 | Compute Unified Device Architecture | 2026-08-01 12:01:31 | 1 | |||||
|
GimmeMotifs Resource Report Resource Website 1+ mentions |
GimmeMotifs (RRID:SCR_001146) | GimmeMotifs | software resource | Software that provides a de novo motif prediction pipeline, especially suited for ChIP-seq datasets. It incorporates several existing motif prediction algorithms in an ensemble method to predict motifs and clusters these motifs using the WIC similarity scoring metric., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | linux, chip-seq, motif, cluster, python, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Radboud University; Nijmegen; The Netherlands |
PMID:21081511 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:gimmemotifs, OMICS_02150 | https://bio.tools/gimmemotifs | SCR_001146 | GimmeMotifs: a systematic de novo motif prediction pipeline | 2026-08-01 12:01:23 | 4 | |||||
|
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 |
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