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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Partek Genomics Suite Resource Report Resource Website 50+ mentions |
Partek Genomics Suite (RRID:SCR_011860) | Partek Genomics Suite | commercial organization, software resource | A comprehensive suite of advanced statistics and interactive data visualization specifically designed to reliably extract biological signals from noisy data. | is listed by: OMICtools | Commercial license | OMICS_01133 | SCR_011860 | 2026-08-08 12:06:06 | 76 | |||||||||
|
CGDB Resource Report Resource Website 10+ mentions |
CGDB (RRID:SCR_011959) | CGDB | data or information resource, data set | A database of membrane protein/lipid interactions by coarse-grained molecular dynamics simulations. | protein, image, coarse-grained, molecular dynamics, membrane protein |
is listed by: OMICtools has parent organization: University of Oxford; Oxford; United Kingdom |
BBSRC | PMID:18937097 PMID:18208379 |
Acknowledgement requested | OMICS_01608 | SCR_011959 | Coarse Grained Database, Coarse-Grained Database, CG Database | 2026-08-08 12:06:15 | 32 | |||||
|
Duplicate reads removal Resource Report Resource Website |
Duplicate reads removal (RRID:SCR_000231) | Duplicate reads removal | commercial organization, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Plug-in tool to filter out duplicate reads that is specifically well-suited to handle those coming from PCR amplification errors which can have a negative effect because a certain sequence is represented in artificially high numbers. | pcr amplification, duplicate, read | is listed by: OMICtools | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02101 | SCR_000231 | 2026-08-08 12:05:43 | 0 | ||||||||
|
Lab7 Resource Report Resource Website |
Lab7 (RRID:SCR_001210) | Lab7 | commercial organization, software resource | Software to address all aspects of Next Generation Sequencing data workflow. | next-generation sequencing | is listed by: OMICtools | Commerical | OMICS_02132 | SCR_001210 | Lab7 Systems | 2026-08-08 12:05:45 | 0 | |||||||
|
Omixon Target HLA Typing Resource Report Resource Website 1+ mentions |
Omixon Target HLA Typing (RRID:SCR_001206) | Omixon Target HLA | commercial organization, software resource | An optional module in the Omixon Target application suite for HLA typing using NGS (next-generation sequencing) data that gives high resolution results with whole genome, exome or very targeted DNA data, or with RNA seq data. | whole genome, exome, target dna, rna-seq, hla allele, hla, allele, next-generation sequencing |
is listed by: OMICtools has parent organization: Omixon Target Data Analysis |
License required | OMICS_02142 | SCR_001206 | 2026-08-08 12:05:39 | 1 | ||||||||
|
SNP and Variation Suite SNP Analysis Resource Report Resource Website 1+ mentions |
SNP and Variation Suite SNP Analysis (RRID:SCR_001285) | SVS SNP Analysis | software resource | SNP Analysis software for basic to advanced analyses that incorporates a number of intuitive workflows to lead you beyond single marker associations. With support for case-control and quantitative traits, whole genome and candidate gene data, you can run a breadth of statistical tests under several genetic models. Advanced regression can further help elucidate even the most complex gene-gene and gene-environment interactions. | single nucleotide polymorphism, linkage disequilibrium, haplotype, homozygosity |
is listed by: OMICtools has parent organization: Golden Helix Incorporated |
Restricted | OMICS_02052 | SCR_001285 | SNP and Variation Suite: SNP Analysis, SNP Package of SVS 7, SNP & Variation Suite (SVS) SNP Analysis, SNP & Variation Suite SNP Analysis, SNP & Variation Suite: SNP Analysis | 2026-08-08 12:05:46 | 1 | |||||||
|
VectorFriends Resource Report Resource Website |
VectorFriends (RRID:SCR_001230) | VectorFriends | commercial organization, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 18,2025. Sequence analysis software for molecular biologists. | cloning, isothermal assembly, pcr, primer design, data management, sequence analysis, sequence, analysis, primer, windows, mac os | is listed by: OMICtools | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02113 | SCR_001230 | 2026-08-08 12:05:39 | 0 | ||||||||
|
Anchored Assembly Resource Report Resource Website |
Anchored Assembly (RRID:SCR_001188) | Anchored Assembly | commercial organization, software resource | Analysis pipeline that accurately detects and maps variations that are often missed by standard analysis algorithms. It uses direct de novo read overlap assembly to accurately detect and characterize SNPs (single nucleotide polymorphisms), indels, and SVs (structural variations). The pipeline uses existing Illumina HiSeq data and does not require additional library preparation. The algorithm is optimized for projects with at least 20x coverage per chromosome set (i.e. 40x for diploid). | variation, structural variation, single nucleotide polymorphism |
is listed by: OMICtools has parent organization: Spiral Genetics Incorporated |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02167 | SCR_001188 | 2026-08-08 12:05:45 | 0 | ||||||||
|
OmicsOffice for NGS SeqSolve Resource Report Resource Website |
OmicsOffice for NGS SeqSolve (RRID:SCR_001222) | OmicsOffice for NGS | commercial organization, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 18,2025. Software for secondary and tertiary analysis of Next Generation Sequencing (NGS) data. | next-generation sequencing, rna-seq, chip-seq, transcript, alternative splicing, variant, mirna, non-coding rna expression, genome, differential expression, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:20671709 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:seqsolve, OMICS_02111 | https://bio.tools/seqsolve | SCR_001222 | OmicsOffice for NGS (SeqSolve), SeqSolve | 2026-08-08 12:05:45 | 0 | |||||
|
Methyl-Analyzer Resource Report Resource Website |
Methyl-Analyzer (RRID:SCR_000318) | software resource, source code | A data analysis pipeline for the Methyl-MAPS method. | methyl maps, data analysis, python, pipeline | is listed by: OMICtools | PMID:21685051 | Free, Available for download, Freely available | OMICS_00617 | SCR_000318 | 2026-08-08 12:05:37 | 0 | ||||||||
|
CGH Fusion Resource Report Resource Website |
CGH Fusion (RRID:SCR_000295) | CGH Fusion | commercial organization, software resource | Software for DNA Copy Number and loss of heterozygosity (LOH) analysis designed with high-throughput diagnostic laboratories in mind. | array, comparative genomic hybridization, snp, cytogenetics | is listed by: OMICtools | Restricted | OMICS_02049 | SCR_000295 | 2026-08-08 12:05:43 | 0 | ||||||||
|
Screensaver Resource Report Resource Website 1+ mentions |
Screensaver (RRID:SCR_000297) | software resource, collaboration tool, source code | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Software for a Lab Information Management System (LIMS) for high-throughput screening of small molecule and RNAi biological assays. | open source, lab information management system, lims, biological assay | is listed by: OMICtools | PMID:20482787 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02556 | SCR_000297 | 2026-08-08 12:05:37 | 1 | ||||||||
|
GeneWays Resource Report Resource Website |
GeneWays (RRID:SCR_000572) | Geneways | service resource | System for automatically extracting, analzying, visualizing and integrating molecular pathway data from the research literature. System focuses on interactions between molecular substances and actions, providing a graphical consensus view on the collected information. GeneWays is designed as open platform, allowing researchers to query, review and critique integrated information. | pathway, molecule, literature, natural language processing, gene, protein, interaction, database |
is listed by: OMICtools has parent organization: Argonne National Laboratory has parent organization: Columbia University; New York; USA |
NSF ; DOE ; NIGMS GM61372 |
PMID:15016385 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-30019, SCR_008368, OMICS_01182 | http://anya.igsb.anl.gov/genewaysApp | SCR_000572 | GeneWays: A System for Extracting Analyzing Visualizing and Integrating Molecular Pathway Data, GeneWays: A System for Extracting Analyzing Visualizing Integrating Molecular Pathway Data | 2026-08-08 12:05:44 | 0 | ||||
|
ReCount - A multi-experiment resource of analysis-ready RNA-seq gene count datasets Resource Report Resource Website 10+ mentions |
ReCount - A multi-experiment resource of analysis-ready RNA-seq gene count datasets (RRID:SCR_001774) | ReCount | data or information resource, data set | RNA-seq gene count datasets built using the raw data from 18 different studies. The raw sequencing data (.fastq files) were processed with Myrna to obtain tables of counts for each gene. For ease of statistical analysis, they combined each count table with sample phenotype data to form an R object of class ExpressionSet. The count tables, ExpressionSets, and phenotype tables are ready to use and freely available. By taking care of several preprocessing steps and combining many datasets into one easily-accessible website, we make finding and analyzing RNA-seq data considerably more straightforward. | rna-seq, gene count, gene, phenotype, r |
is listed by: OMICtools is related to: Myrna has parent organization: SourceForge has parent organization: Johns Hopkins Bloomberg School of Public Health; Maryland; USA |
NIGMS T32GM074906 | PMID:22087737 | Free, Available for download, Freely available | OMICS_01953 | SCR_001774 | 2026-08-08 12:05:46 | 35 | ||||||
|
ZOOM Resource Report Resource Website 100+ mentions |
ZOOM (RRID:SCR_002175) | ZOOM | commercial organization, software resource | Software to map the Illumina/Solexa reads of 15x coverage of a human genome to the reference human genome in one CPU-day, allowing two mismatches, at full sensitivity. | next-generation sequencing, illumina, solexa, reference genome, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:18684737 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01852, biotools:zoom | https://bio.tools/zoom | SCR_002175 | ZOOM: Next Gen Sequencing | 2026-08-08 12:05:47 | 278 | |||||
|
qBasePLUS Resource Report Resource Website 100+ mentions |
qBasePLUS (RRID:SCR_003370) | qbase+ | commercial organization, software resource | Software program for quantitative PCR (qPCR) data analysis based on geNorm and qBase technology. | real-time quantitative pcr |
is listed by: OMICtools is listed by: SoftCite is related to: geNORM has parent organization: Biogazelle |
PMID:17291332 | Free, Available for download, Freely available | OMICS_02320 | https://biogazelle-qbaseplus.software.informer.com/2.0/ | http://medgen.ugent.be/qbase/ | SCR_003370 | 2026-08-08 12:05:48 | 344 | |||||
|
PANDAseq Resource Report Resource Website 500+ mentions |
PANDAseq (RRID:SCR_002705) | software resource, source code | Software program to align Illumina reads, optionally with PCR primers embedded in the sequence, and reconstruct an overlapping sequence. | standalone software, unix/linux, mac os x, windows, c | is listed by: OMICtools | PMID:22333067 | Free, Available for download, Freely available | OMICS_05255 | SCR_002705 | PAired-eND Assembler for DNA sequences | 2026-08-08 12:05:43 | 720 | |||||||
|
FastPCR Resource Report Resource Website 50+ mentions |
FastPCR (RRID:SCR_003155) | FastPCR | commercial organization, software resource | Software tool for PCR primers or probe design, in silico PCR, oligonucleotide assembly and analyses, alignment and repeat searching. | probe design, probe, windows, pcr primer | is listed by: OMICtools | PMID:24395370 | Free, Available for download, Freely available | OMICS_02336 | SCR_003155 | 2026-08-08 12:05:48 | 93 |
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