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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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ArrayPlex Resource Report Resource Website |
ArrayPlex (RRID:SCR_000312) | ArrayPlex | software resource | Open source software that integrates various forms of microarray data from diverse annotation and primary data sources. This software provides a programmatic framework (API set) that will be used for collaborative development and deploys an easy to maintain client-server architecture. | microarray, programmatic framework, collaborative, client-server, |
is listed by: OMICtools has parent organization: SourceForge |
PMID:19014503 | Free, Available for download, Freely available | OMICS_00745 | SCR_000312 | SciCrunch Registry | 2026-10-17 01:24:36 | 0 | |||||||
|
Micro-Analyzer Resource Report Resource Website |
Micro-Analyzer (RRID:SCR_000394) | Micro-Analyzer | software resource | Java tool that performs the preprocessing of Expression and SNPs microarray Affymetrix. The software allows the automatic download and the use of the clustering and visualization software as the Mev 4.0. The tool is equipped by a graphical interface (Swing) that allows to the user to: Create the workspace (files .cel, preferred algorithms , output, libraries to use); Run/save analysis and workspace settings (xml); Efficient download of the libraries (http, ftp, MD5); Customize basic and graphical settings (objects serialization and deserialization). Type of SNPs: Mapping 500k or preceding chips, SNP 5.0, SNP 6.0. Available for 32 or 64 bit systems, and for Windows and Linux Systems. | windows, linux, java, java swing, gene expression, snp, microarray, affymetrix, preprocessing, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:23731720 | Free, Available for download, Freely available | OMICS_01919, biotools:microanalyzer | https://bio.tools/microanalyzer | SCR_000394 | SciCrunch Registry | microAnalyzer | 2026-10-17 01:24:41 | 0 | |||||
|
FunctSNP Resource Report Resource Website |
FunctSNP (RRID:SCR_000393) | FunctSNP | software resource | An R package for linking SNPs (Single Nucleotide Polymorphisms) to functional knowledge. | single nucleotide polymorphism |
is listed by: OMICtools has parent organization: SourceForge |
PMID:20534127 | Free, Available for download, Freely available | OMICS_01925 | SCR_000393 | SciCrunch Registry | FunctSNP - Linking SNPs to functional knowledge | 2026-10-17 01:24:38 | 0 | ||||||
|
LIPAGE Resource Report Resource Website 1+ mentions |
LIPAGE (RRID:SCR_000290) | data management software, software application, software resource | Laboratory information management system for proteomics. The software works with 2DPAGE-based proteomics workflow. | proteomics, laboratory, open source, 2dpage, management system |
is listed by: OMICtools has parent organization: SourceForge |
PMID:17018156 | Free, Available for download, Freely available | OMICS_02553 | SCR_000290 | SciCrunch Registry | LIMS for proteomics | 2026-10-17 01:24:39 | 1 | |||||||
|
fourSig Resource Report Resource Website |
fourSig (RRID:SCR_000516) | software resource | A suite of software programs for analyzing and visualizing 4C-seq data. | standalone software, perl, r |
is listed by: OMICtools has parent organization: SourceForge |
PMID:24561615 | Free, Available for download, Freely available | OMICS_02628 | SCR_000516 | SciCrunch Registry | 2026-10-17 01:24:41 | 0 | ||||||||
|
TOPPAS Resource Report Resource Website 1+ mentions |
TOPPAS (RRID:SCR_000533) | software resource | A graphical user interface (GUI) for rapid composition of HPLC-MS analysis workflows. Workflow construction is reduced to drag-and-drop of analysis tools and adding connections in between. | gui, graphical user interface, analysis, hplc-ms, workflow |
is listed by: OMICtools has parent organization: SourceForge |
PMID:22583024 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02640 | http://open-ms.sourceforge.net/workflow-integration/toppasworkflows/ | SCR_000533 | SciCrunch Registry | The OpenMS Proteomics Pipeline Assistant, TOPP Pipeline Assistant | 2026-10-17 01:24:42 | 1 | ||||||
|
Ishtar Resource Report Resource Website |
Ishtar (RRID:SCR_000538) | software resource | A program for designing primer pairs that amplify multiple target sequences using DNA thermodynamics and one class support vector machines. Written in Python. | dna, thermodynamics, sequence, primer, pairs, loci, bioinformatics | has parent organization: SourceForge | Free, Available for download, Freely available, | nlx_71525 | SCR_000538 | SciCrunch Registry | 2026-10-17 01:24:42 | 0 | |||||||||
|
Reprever Resource Report Resource Website |
Reprever (RRID:SCR_000463) | Reprever | software resource | Software that identifies (a) the insertion breakpoints where the extra duplicons inserted into the donor genome and (b) the actual sequence of the duplicon for any genomic regions that are increased in copy number. | genomics, genomic region, insertion breakpoint, insertion, breakpoint, duplicon, genome |
is listed by: OMICtools has parent organization: SourceForge has parent organization: University of California at San Diego; California; USA |
PMID:23658221 | Free, Available for download, Freely available | OMICS_01561 | SCR_000463 | SciCrunch Registry | Reprever: resolving low-copy duplicated sequences using template drive | 2026-10-17 01:24:41 | 0 | ||||||
|
ViReMa Resource Report Resource Website 1+ mentions |
ViReMa (RRID:SCR_000566) | ViReMa | data analysis software, data processing software, software application, software resource, software toolkit | Software Python package for detection, alignment and reporting of recombination events in Next-Generation Sequencing data. Detects and reports recombination or fusion events in virus genomes using deep sequencing datasets. | virus genomes deep sequencing datasets, detection, alignment and reporting of recombination events, Next-Generation Sequencing data, |
is listed by: OMICtools has parent organization: SourceForge has parent organization: Scripps Research Institute |
PMID:24137010 | Free, Available for download, Freely available, | OMICS_00225 | SCR_000566 | SciCrunch Registry | Viral Recombination Mapper | 2026-10-17 01:24:42 | 2 | ||||||
|
VariantMaster Resource Report Resource Website |
VariantMaster (RRID:SCR_000569) | VariantMaster | software resource | Software program that extracts causative variants in familial and sporadic genetic diseases. The algorithm takes into account predicted variants (SNPs and indels) in affected individuals or tumor samples and utilizes the row (BAM) data to robustly estimate the conditional probability of segregation in a family, as well as the probability of it being de novo or somatic. In familial cases, various modes of inheritance are considered: X-linked, autosomal dominant, and recessive (homozygosity or compound heterozygosity). Moreover, it integrates phenotypes and genotypes, and employs Annovar to produce additional information as allelic frequencies in general population and damaging scores. | unix/linux, clinical, genetics, high throughput sequencing, monogenic disease, variant, snp, indel |
is listed by: OMICtools has parent organization: SourceForge |
Genetic disease, Tumor | PMID:24389049 | Free, Available for download, Freely available, | OMICS_02261 | SCR_000569 | SciCrunch Registry | VariantMaster - Extract causative variants for monogenic and sporadic genetic diseases | 2026-10-17 01:24:43 | 0 | |||||
|
DeNovoGear Resource Report Resource Website 1+ mentions |
DeNovoGear (RRID:SCR_000670) | software resource | A software for detecting de novo mutations using sequencing data. It utilizes likelihood-based error modeling to reduce the false positive rate of mutative discovery in exome analysis. It also uses fragment information to identify the parental origin of germ-line mutations. | de novo, mutation, sequence, dna, rna, error modeling, exome analysis |
is listed by: OMICtools has parent organization: SourceForge has parent organization: Washington University School of Medicine in St. Louis; Missouri; USA |
PMID:23975140 | Free, Available for download, Freely available | OMICS_00083 | https://github.com/denovogear/denovogear | SCR_000670 | SciCrunch Registry | 2026-10-17 01:24:43 | 3 | |||||||
|
SRMA Resource Report Resource Website |
SRMA (RRID:SCR_000669) | SRMA | software resource | A post-alignment micro re-aligner for next-generation high throughput sequencing data. | matlab, sequence re-alignment, command-line, java, next generation sequencing, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:20932289 | Free, Available for download, Freely available | biotools:srma, OMICS_01079 | https://bio.tools/srma | SCR_000669 | SciCrunch Registry | Short Read Micro re-Aligner | 2026-10-17 01:24:43 | 0 | |||||
|
FineSplice Resource Report Resource Website 1+ mentions |
FineSplice (RRID:SCR_000691) | software resource | A software pipeline based on TopHat2 combined with a splice junction detection algorithm. | standalone software, python |
is listed by: OMICtools has parent organization: SourceForge |
PMID:24574529 | Free, Available for download, Freely available | OMICS_03274 | SCR_000691 | SciCrunch Registry | 2026-10-17 01:24:43 | 1 | ||||||||
|
CrossMap Resource Report Resource Website 10+ mentions |
CrossMap (RRID:SCR_001173) | CrossMap | software resource | A software program for convenient conversion of genome coordinates (or annotation files) between different assemblies. It supports most commonly used file formats including SAM/BAM, Wiggle/BigWig, BED, GFF/GTF, VCF. It is designed to liftover genome coordinates between assemblies. It?s not a program for aligning sequences to reference genome. CrossMap is not recommend for converting genome coordinates between species. | genome, assembly |
is listed by: OMICtools has parent organization: SourceForge |
PMID:24351709 | GNU General Public License | OMICS_02184 | SCR_001173 | SciCrunch Registry | 2026-10-17 01:24:49 | 19 | |||||||
|
ParticleCall Resource Report Resource Website |
ParticleCall (RRID:SCR_001103) | ParticleCall | software resource | A base-calling algorithm for Illumina DNA sequencing. | illumina |
is listed by: OMICtools has parent organization: SourceForge |
PMID:22776067 | OMICS_01154 | SCR_001103 | SciCrunch Registry | 2026-10-17 01:24:52 | 0 | ||||||||
|
SparseAssembler Resource Report Resource Website 1+ mentions |
SparseAssembler (RRID:SCR_001100) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software for memory-efficient genome assembly. It utilizes sparse k-mer. | genome, genomics, genome assembly, k-mer, sequence analysis software, memory |
is listed by: OMICtools has parent organization: SourceForge |
PMID:22537038 | Free, Available for download, Freely available | OMICS_00032 | SCR_001100 | SciCrunch Registry | 2026-10-17 01:24:48 | 1 | ||||||||
|
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 | SciCrunch Registry | Compute Unified Device Architecture | 2026-10-17 01:24:59 | 1 | |||||
|
qips Resource Report Resource Website |
qips (RRID:SCR_001092) | qips | software resource | A software package for analyzing ChIP-seq (Chromatin ImmunoPrecipitation on sequencing) data that finds enriched regions of arbitrary lengths and is therefore especially suited for analyzing ChIP-seq of histone marks or polymerase. | command-line, c++, python |
is listed by: OMICtools has parent organization: SourceForge |
Free, Available for download, Freely available | OMICS_00457 | SCR_001092 | SciCrunch Registry | 2026-10-17 01:24:48 | 0 | ||||||||
|
Breakway Resource Report Resource Website |
Breakway (RRID:SCR_001180) | Breakway | software resource | A suite of software programs that take aligned genomic data and report structural variation breakpoints. Features include: * Takes in BAM formatted input, the current standard for genomic alignments. * Compatible with standard output from major alignment algorithms such as BFAST, BWA, MAQ, et cetera. * Capable of analyzing data from any major platform--Solexa, SOLiD, 454, et cetera. * Empirically identifies structural variation breakpoints. * Highly specific analysis generates very few false positives. * Includes a suite of downstream tools for annotating identified breakpoints and reducing false positives. | genome, structural variation, breakpoint |
is listed by: OMICtools has parent organization: SourceForge has parent organization: University of California at Los Angeles; California; USA |
PMID:20126413 | Free, Available for download, Freely available | OMICS_02176 | SCR_001180 | SciCrunch Registry | Breakway: Identify Structural Variations in Genomic Data | 2026-10-17 01:25:01 | 0 | ||||||
|
ChIP-seq Resource Report Resource Website 5000+ mentions |
ChIP-seq (RRID:SCR_001237) | ChIP-seq | data analysis software, data processing software, software application, software resource, software toolkit | Set of software modules for performing common ChIP-seq data analysis tasks across the whole genome, including positional correlation analysis, peak detection, and genome partitioning into signal-rich and signal-poor regions. The tools are designed to be simple, fast and highly modular. Each program carries out a well-defined data processing procedure that can potentially fit into a pipeline framework. ChIP-Seq is also freely available on a Web interface. | high-throughput sequencing, chromatin immuno precipitation, chip-seq, genome, c |
is listed by: OMICtools has parent organization: SourceForge has parent organization: Ecole Polytechnique Federale de Lausanne; Lausanne; Switzerland has parent organization: SIB Swiss Institute of Bioinformatics |
PMID:27863463 | Free, Available for download, Freely available | OMICS_02103 | https://epd.expasy.org/chipseq/, https://chip-seq.sourceforge.net/ | SCR_001237 | SciCrunch Registry | ChIP-seq - Tools for the analysis of ChIP-seq data | 2026-10-17 01:24:50 | 8035 |
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