ArticleBMC bioinformatics2011
SeqGene: a comprehensive software solution for mining exome- and transcriptome- sequencing data.
Article in BMC bioinformatics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- CONY: A Bayesian procedure for detecting copy number variations from sequencing read depths.Scientific reports · 2020Article
- Comprehensive Outline of Whole Exome Sequencing Data Analysis Tools Available in Clinical Oncology.Cancers · 2019Review
- An accurate and powerful method for copy number variation detection.Bioinformatics (Oxford, England) · 2019Article
- The developmental and genetic basis of 'clubfoot' in the peroneal muscular atrophy mutant mouse.Development (Cambridge, England) · 2018Article
- Elucidating and mining the Tulipa and Lilium transcriptomes.Plant molecular biology · 2016Article
- BRD4 is a histone acetyltransferase that evicts nucleosomes from chromatin.Nature structural & molecular biology · 2016Article
- VDAP-GUI: a user-friendly pipeline for variant discovery and annotation of raw next-generation sequencing data.3 Biotech · 2016Article
- Evaluation of somatic copy number estimation tools for whole-exome sequencing data.Briefings in bioinformatics · 2016Article
- SpinachDB: A Well-Characterized Genomic Database for Gene Family Classification and SNP Information of Spinach.PloS one · 2016Article
- Genomic analysis of mycosis fungoides and Sézary syndrome identifies recurrent alterations in TNFR2.Nature genetics · 2015Article
- Mutated genes and driver pathways involved in myelodysplastic syndromes—a transcriptome sequencing based approach.Molecular bioSystems · 2015Article
- Natural variability of minimotifs in 1092 people indicates that minimotifs are targets of evolution.Nucleic acids research · 2015Article
- Recurrent point mutations in the kinetochore gene KNSTRN in cutaneous squamous cell carcinoma.Nature genetics · 2014Article
- Performance comparison of SNP detection tools with illumina exome sequencing data--an assessment using both family pedigree information and sample-matched SNP array data.Nucleic acids research · 2014Article
- Article
- An integrated SNP mining and utilization (ISMU) pipeline for next generation sequencing data.PloS one · 2014Article
- Genetic and genomic analyses of musculoskeletal differences between BEH and BEL strains.Physiological genomics · 2013Article
- Mosaic activating RAS mutations in nevus sebaceus and nevus sebaceus syndrome.The Journal of investigative dermatology · 2013Article
- Current analysis platforms and methods for detecting copy number variation.Physiological genomics · 2013Review
- WEP: a high-performance analysis pipeline for whole-exome data.BMC bioinformatics · 2013Article
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1 author.
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Abstract
backgroundThe popularity of massively parallel exome and transcriptome sequencing projects demands new data mining tools with a comprehensive set of features to support a wide range of analysis tasks.
resultsSeqGene, a new data mining tool, supports mutation detection and annotation, dbSNP and 1000 Genome data integration, RNA-Seq expression quantification, mutation and coverage visualization, allele specific expression (ASE), differentially expressed genes (DEGs) identification, copy number variation (CNV) analysis, and gene expression quantitative trait loci (eQTLs) detection. We also developed novel methods for testing the association between SNP and expression and identifying genotype-controlled DEGs. We showed that the results generated from SeqGene compares favourably to other existing methods in our case studies.
conclusionSeqGene is designed as a general-purpose software package. It supports both paired-end reads and single reads generated on most sequencing platforms; it runs on all major types of computers; it supports arbitrary genome assemblies for arbitrary organisms; and it scales well to support both large and small scale sequencing projects. The software homepage is http://seqgene.sourceforge.net.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.