SVDetect is a application for the isolation and the type prediction of intra- and inter-chromosomal rearrangements from paired-end/mate-pair sequencing data provided by the high-throughput sequencing technologies.
KGGSeq (Genomic and Genetic studies using Sequence data) is a software platform constituted of Bioinformatics and statistical genetics functions making use of valuable biologic resources and knowledge for sequencing-based genetic mapping of variants/genes responsible for human diseases/traits. Simply, KGGSeq is like a fishing rod facilitating geneticists to fish the genetic determinants of human diseases/traits in the big sea of DNA sequences. Compared with other genetic tools like plink/seq, KGGSeq paid more attention downstream analysis of genetic mapping. Currently, a comprehensive and efficient framework was newly implemented on KGGSeq to filter and prioritize genetic variants from whole exome sequencing data.
KGGSEE is a standalone Java tool for knowledge-based secondary analyses of genomic and genetic association summary statistics of complex phenotypes by integrating gene expression and related data. It has four major integrative analyses, 1) unconditional gene-based association guided by expression quantitative trait loci (eQTLs), 2) conditional gene-based association guided by selective expression in tissues or cell types, 3) estimation of phenotype-associated tissues or cell-type based on gene expression in single-cell or bulk cells of different tissues, and 4) causal gene inference for complex diseases and/or traits based-on multiple eQTL.
1. Xue C., et al. A global overview of single-cell type selectivity and pleiotropy in complex diseases and traits. In Submission (For estimation of phenotype-associated tissues or cell-type based on gene expression in single-cell or bulk cells of different tissues)
2. Jiang L., et al. Systematic comparative analysis of Mendelian randomization methods for inferring causal genes of complex phenotypes and the application to psychiatric diseases. In Submission (For causal gene inference for complex diseases and/or traits based-on multiple eQTL)
3. Li X.Y., et al. Gene-based association guided by eQTL. In Submission (For unconditional and condition gene-based association guided by eQTL)
GenePattern is a powerful genomic analysis platform that provides access to more than 125 tools for gene expression analysis, proteomics, SNP analysis and common data processing tasks. A web-based interface provides easy access to these tools and allows the creation of multi-step analysis pipelines that enable reproducible in silico research.
GenePattern provides access to a broad array of computational methods used to analyze genomic data. Its extendable architecture makes it easy for computational biologists to add analysis and visualization modules, which ensures that GenePattern users have access to new computational methods on a regular basis.