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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
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 | FunctSNP - Linking SNPs to functional knowledge | 2026-09-12 12:55:08 | 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 | LIMS for proteomics | 2026-09-12 12:55:06 | 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 | 2026-09-12 12:55:11 | 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 | The OpenMS Proteomics Pipeline Assistant, TOPP Pipeline Assistant | 2026-09-12 12:55:11 | 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 | 2026-09-12 12:55:11 | 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 | Reprever: resolving low-copy duplicated sequences using template drive | 2026-09-12 12:55:10 | 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 | Viral Recombination Mapper | 2026-09-12 12:55:11 | 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 | VariantMaster - Extract causative variants for monogenic and sporadic genetic diseases | 2026-09-12 12:55:11 | 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 | 2026-09-12 12:55:13 | 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 | Short Read Micro re-Aligner | 2026-09-12 12:55:13 | 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 | 2026-09-12 12:55:13 | 1 | ||||||||
|
miRDeep* Resource Report Resource Website 10+ mentions |
miRDeep* (RRID:SCR_012960) | miRDeep* | software resource | An integrated application software tool for miRNA identification from RNA sequencing data. |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23221645 | GNU General Public License, v3, Acknowledgement requested | OMICS_00374 | SCR_012960 | 2026-09-12 12:57:56 | 23 | ||||||||
|
Trowel Resource Report Resource Website 1+ mentions |
Trowel (RRID:SCR_012890) | Trowel | software resource | An error correction module for Illumina sequencing reads, which is based on the k-mer spectrum approach. | c++, illumina, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
Apache License | OMICS_01111, biotools:trowel | https://bio.tools/trowel/ | SCR_012890 | Trowel - Error Correction Module for Illumina Sequencing Reads, Trowel - Sequencing Error Corrector | 2026-09-12 12:57:54 | 5 | ||||||
|
Onco-STS Resource Report Resource Website |
Onco-STS (RRID:SCR_012990) | Onco-STS | software resource | Software for a web-based Laboratory Information Management System for sample and analysis tracking in oncogenomic experiments. |
is listed by: OMICtools has parent organization: SourceForge |
GNU General Public License, v3 | OMICS_01008 | SCR_012990 | Onco-STS - A web-based Laboratory Information Management System | 2026-09-12 12:57:56 | 0 | ||||||||
|
NxGview Resource Report Resource Website |
NxGview (RRID:SCR_012994) | NxGview | software resource | A virtual software pipeline that contains several PERL modules for processing next generation sequencing data. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_01065 | SCR_012994 | 2026-09-12 12:57:57 | 0 | ||||||||||
|
Bamformatics Resource Report Resource Website 1+ mentions |
Bamformatics (RRID:SCR_013041) | Bamformatics | software resource | Software that provides a coherent and consistent approach to analysis of high-throughput sequencing data. | matlab |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00283 | SCR_013041 | Bamformatics - Toolkit and GUI for sequencing data analysis | 2026-09-12 12:57:58 | 1 | ||||||||
|
BSmapper Resource Report Resource Website |
BSmapper (RRID:SCR_012998) | BSmapper | software resource | Sequence mapper for bisulfite sequencing reads for DNA methylation studies. |
is listed by: OMICtools has parent organization: SourceForge |
GNU General Public License, v3 | OMICS_00580 | SCR_012998 | 2026-09-12 12:57:57 | 0 | |||||||||
|
MendelScan Resource Report Resource Website 1+ mentions |
MendelScan (RRID:SCR_013053) | MendelScan | software resource | A software tool for prioritizing candidate variants in family-based studies of inherited disease. | matlab |
is listed by: OMICtools has parent organization: SourceForge |
GNU General Public License, v2 | OMICS_00065 | SCR_013053 | MendelScan - Variant scoring and linkage mapping for family exome sequencing | 2026-09-12 12:57:58 | 4 | |||||||
|
ProbeSelect Resource Report Resource Website 1+ mentions |
ProbeSelect (RRID:SCR_012965) | ProbeSelect | software resource | Software for selecting probes in heterogenous transcriptional sets. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00836 | SCR_012965 | ProbeSelect - Selecting probes in heterogenous transcriptional sets | 2026-09-12 12:57:56 | 5 | |||||||||
|
SeqGenome Browser Resource Report Resource Website |
SeqGenome Browser (RRID:SCR_012970) | SeqGenome Browser | software resource | Mini cross-platform local genome browser software designed for visualizing next-generation sequencing data. | c++ |
is listed by: OMICtools has parent organization: SourceForge |
GNU General Public License, v2 | OMICS_00924 | SCR_012970 | 2026-09-12 12:57:56 | 0 |
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The data sets included in this resource are published in Kravitz et al, 2012. Distinct roles for direct and indirect pathway striatal neurons in reinforcement (Nat. Neurosci).
