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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Biodoop Resource Report Resource Website |
Biodoop (RRID:SCR_008711) | Biodoop | software resource | A suite of parallel bioinformatics applications based upon a popular open-source Java implementation of MapReduce, Hadoop. | mapreduce/hadoop | is listed by: OMICtools | OMICS_01224 | SCR_008711 | 2026-02-07 02:07:53 | 0 | |||||||||
|
DrGaP Resource Report Resource Website 10+ mentions |
DrGaP (RRID:SCR_008670) | DrGaP | software resource | Designed to identify Driver Genes and Pathways in cancer genome sequencing studies. | is listed by: OMICtools | Cancer | OMICS_00149 | SCR_008670 | 2026-02-07 02:07:53 | 10 | |||||||||
|
InVEx Resource Report Resource Website 1+ mentions |
InVEx (RRID:SCR_008734) | InVEx | software resource | A permutation-based method (written in Python) for ascertaining genes with a somatic mutation distribution showing evidence of positive selection for non-silent mutations. |
is listed by: OMICtools has parent organization: Broad Institute |
OMICS_00151 | SCR_008734 | Introns Vs Exons | 2026-02-07 02:07:54 | 4 | |||||||||
|
flowBeads Resource Report Resource Website |
flowBeads (RRID:SCR_002440) | software resource | Software package for the analysis of flow cytometry bead data. It extends flowCore to provide functionality specific to bead data. One of the goals of this package is to automate analysis of bead data for the purpose of normalization. | software package, mac os x, unix/linux, windows, r, cell based assay, flow cytometry, infrastructure |
uses: flowCore is listed by: OMICtools has parent organization: Bioconductor |
Free, Freely available | OMICS_05592 | SCR_002440 | flowBeads: Analysis of flow bead data | 2026-02-07 02:05:55 | 0 | ||||||||
|
flowCyBar Resource Report Resource Website 1+ mentions |
flowCyBar (RRID:SCR_002319) | software resource | A software package to analyze flow cytometric data using gate information to follow population / community dynamics. | software package, mac os x, unix/linux, windows, r, cell based assay, flow cytometry, clustering, visualization |
is listed by: OMICtools has parent organization: Bioconductor |
GNU General Public License, v2 | OMICS_05597 | SCR_002319 | flowCyBar - Analyze flow cytometric data using gate information | 2026-02-07 02:05:53 | 5 | ||||||||
|
DWGSIM Resource Report Resource Website 50+ mentions |
DWGSIM (RRID:SCR_002342) | DWGSIM | software resource | Whole Genome Simulator for Next-Generation Sequencing. | next-generation sequencing, whole genome simulation |
is listed by: OMICtools is listed by: Debian |
GNU General Public License, v2 | OMICS_00249 | https://sources.debian.org/src/dwgsim/ | SCR_002342 | 2026-02-07 02:05:54 | 51 | |||||||
|
BEETL-fastq Resource Report Resource Website |
BEETL-fastq (RRID:SCR_002341) | software resource | Software tool that not only compresses FASTQ-formatted DNA reads more compactly than gzip but also permits rapid search for k-mer queries within the archived sequences. The full FASTQ record of each matching read or read pair is returned, allowing the search results to be piped directly to any of the many standard tools that accept FASTQ data as input. Searchable compressed archive for DNA reads. | Searchable compressed archive, DNA reads, compresses FASTQ-formatted DNA reads, bio.tools, |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: Burrows-Wheeler transform |
PMID:24950811 | Free, Available for download, Freely available | OMICS_04900, biotools:beetl | https://bio.tools/beetl | SCR_002341 | 2026-02-07 02:05:43 | 0 | |||||||
|
RepARK Resource Report Resource Website 1+ mentions |
RepARK (RRID:SCR_002333) | software resource | Software using a de novo repeat assembly method which avoids potential biases by using abundant k-mers of next-generation sequencing (NGS) whole genome sequencing (WGS) reads without requiring a reference genome. | standalone software | is listed by: OMICtools | PMID:24634442 | OMICS_03446 | SCR_002333 | Repetitive motif detection by Assembly of Repetitive K-mers | 2026-02-07 02:05:43 | 7 | ||||||||
|
MBASED Resource Report Resource Website 10+ mentions |
MBASED (RRID:SCR_002584) | software resource | Software package containing functions for allele-specific gene expression (ASE) analysis using meta-analysis based allele-specific expression detection. | software package, unix/linux, mac os x, windows, r, gene expression, sequencing, transcription |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:25315065 | Free, Available for download, Freely available | OMICS_05502 | http://www.bioconductor.org/packages/release/bioc/html/MBASED.html | SCR_002584 | Meta-analysis Based Allele-Specific Expression Detection, MBASED - Package containing functions for ASE analysis using Meta-analysis Based Allele-Specific Expression Detection | 2026-02-07 02:05:46 | 17 | ||||||
|
pymzML Resource Report Resource Website 10+ mentions |
pymzML (RRID:SCR_002500) | software resource | Python module to parse mzML data in Python based on cElementTree. It is an extension to Python that offers (i) an easy access to mass spectrometry (MS) data that allows the rapid development of tools, (ii) a very fast parser for mzML data and (iii) a set of functions to compare or handle spectra., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | standalone software, python, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: mzML has parent organization: University of Munster; North Rhine-Westphalia; Germany |
PMID:22302572 | Free, Available for download, Freely available | biotools:pymzml, OMICS_03355 | https://bio.tools/pymzml | SCR_002500 | 2026-02-07 02:05:45 | 18 | |||||||
|
PeptideShaker Resource Report Resource Website 100+ mentions |
PeptideShaker (RRID:SCR_002520) | software resource | Software providing a search engine independent platform for visualization of peptide and protein identification results from multiple search engines, currently supporting X!Tandem, MS-GF+, MS Amanda, OMSSA, MyriMatch, Comet, Tide, Mascot and mzIdentML. By combining the results from multiple search engines, while re-calculating PTM localization scores and redoing the protein inference, PeptideShaker attempts to give you the best possible understanding of your proteomics data. | standalone software, proteomics, mass spectrometry, java, search engine, omssa, xtandem, mascot, ms-gf, msamanda, myrimatch, comet, tide |
is listed by: OMICtools is related to: MS Amanda has parent organization: Google Code |
PMID:34709836 | Free, Available for download, Freely available | OMICS_03347 | http://peptide-shaker.googlecode.com | SCR_002520 | 2026-02-07 02:05:45 | 157 | |||||||
|
PennCNV Resource Report Resource Website 100+ mentions |
PennCNV (RRID:SCR_002518) | PennCNV | software resource | A free software tool for Copy Number Variation (CNV) detection from SNP genotyping arrays. Currently it can handle signal intensity data from Illumina and Affymetrix arrays. With appropriate preparation of file format, it can also handle other types of SNP arrays and oligonucleotide arrays. PennCNV implements a hidden Markov model (HMM) that integrates multiple sources of information to infer CNV calls for individual genotyped samples. It differs form segmentation-based algorithm in that it considered SNP allelic ratio distribution as well as other factors, in addition to signal intensity alone. In addition, PennCNV can optionally utilize family information to generate family-based CNV calls by several different algorithms. Furthermore, PennCNV can generate CNV calls given a specific set of candidate CNV regions, through a validation-calling algorithm. | imaging genomics, copy number variation, snp, genotyping array, array, oligonucleotide, hidden markov model, genotype, genome |
is listed by: OMICtools is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: VegaMC is related to: OpenBioinformatics.org has parent organization: University of Pennsylvania; Philadelphia; USA |
NIMH MH604687 | PMID:17921354 | Free | OMICS_00729, nlx_155921 | http://www.openbioinformatics.org/penncnv/ |
http://www.neurogenome.org/cnv/penncnv | SCR_002518 | PennCNV: copy number variation detection | 2026-02-07 02:05:45 | 339 | |||
|
BINOCh Resource Report Resource Website 1+ mentions |
BINOCh (RRID:SCR_002778) | BINOCh | software resource | Software that infers the identity of transcription factors used to regulate cell response to stimulus or determine a program of differentiation. It uses genome wide information on enhancer proximal nucleosome occupancy, acquired using ChIP-seq targeting enhancer related histone modifications., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 15,2026. | proximal nucleosome occupancy data, transcription factor determination, differentiation |
is listed by: OMICtools has parent organization: Dana-Farber Cancer Institute has parent organization: Harvard University; Cambridge; United States |
PMID:21551136 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00500 | SCR_002778 | Binding Inference from Nucleosome Occupancy Changes (BINOCh), BINOCh - Binding Inference from Nucleosome Occupancy Changes, Binding Inference from Nucleosome Occupancy Changes | 2026-02-07 02:05:50 | 3 | ||||||
|
sapFinder Resource Report Resource Website |
sapFinder (RRID:SCR_002685) | software resource | An R software package, for detection of the variant peptides based on tandem mass spectrometry (MS/MS)-based proteomics data. It automates (1) variation-associated database construction, (2) database searching, (3) post-processing, (4) HTML-based report generation in shotgun proteomics. | standalone software, r, mass spectrometry, proteomics, rna-seq, report writing, snp, visualization, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
PMID:25053745 | Free, Available for download, Freely available | biotools:sapfinder, OMICS_05285 | https://bio.tools/sapfinder | SCR_002685 | sapFinder - A package for variant peptides detection and visualization in shotgun proteomics. | 2026-02-07 02:05:48 | 0 | ||||||
|
leeHom Resource Report Resource Website 50+ mentions |
leeHom (RRID:SCR_002710) | software resource | Software program for the Bayesian reconstruction of ancient DNA fragments. The algorithm removes the adaptors and reconstructs the original DNA sequences using a Bayesian maximum a posteriori probability approach. | standalone software, illumina, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:25100869 | Free, Available for download, Freely available | biotools:leehom, OMICS_05254 | https://bio.tools/leehom | SCR_002710 | 2026-02-07 02:06:01 | 50 | |||||||
|
Pathview Resource Report Resource Website 500+ mentions |
Pathview (RRID:SCR_002732) | software resource | A tool set for pathway-based data integration and visualization. It maps and renders a wide variety of biological data on relevant pathway graphs. All users need is to supply their data and specify the target pathway. Pathview automatically downloads the pathway graph data, parses the data file, maps user data to the pathway, and render pathway graph with the mapped data. In addition, Pathview also seamlessly integrates with pathway and gene set (enrichment) analysis tools for large-scale and fully automated analysis. | software package, r, differential expression, gene expression, gene set enrichment, genetics, graph, network, metabolomics, microarray, pathway, proteomics, rna-seq, sequencing, systems biology, visualization, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
PMID:23740750 | Free, Freely available, Available for download | biotools:pathview, OMICS_05212 | http://pathview.r-forge.r-project.org/ https://bio.tools/pathview |
SCR_002732 | path view | 2026-02-07 02:05:48 | 502 | ||||||
|
GLProbs Resource Report Resource Website 1+ mentions |
GLProbs (RRID:SCR_002739) | software resource | Software implementing a simple and effective approach to improve the accuracy of multiple sequence alignment. | standalone software |
is listed by: OMICtools has parent organization: SourceForge |
PMID:26357079 | Free, Freely available, Available for download | OMICS_03732 | SCR_002739 | 2026-02-07 02:05:49 | 1 | ||||||||
|
rBiopaxParser Resource Report Resource Website 1+ mentions |
rBiopaxParser (RRID:SCR_002744) | software resource | A software package that provides a comprehensive set of functions for parsing, viewing and modifying BioPAX pathway data within R. At the moment BioPAX level 2 and level 3 are supported. | software package, mac os x, unix/linux, windows, data representation, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:23274212 | Free, Freely available, Available for download | biotools:rbiopaxparser, OMICS_05211 | https://github.com/frankkramer/rBiopaxParser https://bio.tools/rbiopaxparser |
SCR_002744 | rBiopaxParser - Parses BioPax files and represents them in R | 2026-02-07 02:05:48 | 4 | ||||||
|
Time-series RNA-seq Analysis Package Resource Report Resource Website 1+ mentions |
Time-series RNA-seq Analysis Package (RRID:SCR_002935) | TRAP | software resource | A comprehensive software package integrating all necessary tasks such as mapping short reads, measuring gene expression levels, finding differentially expressed genes (DEGs), clustering and pathway analysis for time-series data in a single environment. | time-series, rna-seq, analysis |
is listed by: OMICtools has parent organization: Seoul National University; Seoul; South Korea |
PMID:24518221 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02590 | SCR_002935 | 2026-02-07 02:05:52 | 3 | |||||||
|
pBuild Resource Report Resource Website 1+ mentions |
pBuild (RRID:SCR_002929) | software resource | A software tool that can compare several search engines' results and combine them together. | mass spectrometry, proteomics |
is listed by: OMICtools has parent organization: Chinese Academy of Sciences; Beijing; China |
OMICS_02468 | SCR_002929 | 2026-02-07 02:05:52 | 8 |
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