NGS analytics (Total)

• FASTQ, Post alignment QC
• Alignment to genome using OSA
• Gene and Transcript counting using RSEM algorithm
• Exon, exon junction counting
• Post counting normalization methods
• Mutation detection and annotation
• Alternative splicing analysis
• Differential analysis using DESeq
• Fusion detection using FusionMap
• Copy Number detection and segmentation algorithm

DNA-Seq analysis

• FASTQ QC
• Alignment to genome using OSA
• Post-alignment QC
• Fusion Detection using FusionMap
• Mutation detection and annotation
• Somatic mutation detection algorithm
• Copy number detection and segmentation algorithm
• Targeted sequencing analysis
• Run external tools (BWA, Bowtie, GATK and more)

RNA-Seq analysis

• FASTQ QC
• Alignment to genome using OSA
• Post-alignment QC
• Gene and transcript counting using RSEM.algorithm
• Exon counting
• Exon junction counting
• Post-counting normalization methods
• Mutation detection and annotation
• Alternative splicing analysis
• Differential anlysis using DESeq
• Fusion detection using FusionMap
• Run external tools (Tophat, Cufflinks, and more)
• Single-cell genomics (scRNA-seq)

Gene expressiAon

• Generic platform importing (Affymetrix, Illumina, Agilent, Nanostring, Generic platform)
• Normalization modules (RMA, GCRMA, MAS5, OmicSoft Signal Extraction)
• QC and pattern modules
• Clustering (Hierarchical, K-means, PAM, SOM, NMF)
• Correlation to covariates
• Prediction and classification
• Statistics (T-Test, ANOVA etc.)

Copy number

• Affymetrix, Illumina, Agilent platform
• Log2 ratio generation
• B Allele frequency
• Built in segmentation algorithm
• Summarize at gene or segment levels
• Compatible with genome browser
• Integration with expression data

Genotyping/GWAS

• QC
• Imputation
• Pattern eetection
• Single and two marker association
• Quantified traits
• Binary traits
• Categorical traits
• Survival traits
• Repeated measure traits