Our services

What we can help you with

These are examples of bioinformatic analyses that we perform.

RNA-seq

  • Quality control
  • Sequence alignment
  • Differential gene expression
  • GSEA/gene ontology
  • Allele-specific expression
  • Isoform-level analysis
  • RNA editing analysis
  • CAGE analysis
  • Small RNA analysis (e.g., microRNAs)

Epigenetics/ChIP-Seq

  • DNase-seq
  • FAIRE-seq
  • Peak calling, hidden-markov models
  • Mapping DNA binding proteins
  • Novel transcriptor factor binding sites
  • Motif discovery

Network analysis

  • Co-expression networks
  • Differential module usage
  • Various gene set enrichment strategies
  • Meta-correlations
  • Cytoscape visualization models
  • Discovery of hub genes

Genome-wide association studies

  • Imputing genotypes
  • Association analysis
  • Genomic inflation
  • Mixed linear models
  • cis/trans interactions

Microbiome, meta-genomics, and environmental genetics

  • 16S rRNA analysis
  • Taxonomy determination
  • Meta-genome assembly
  • alpha/beta diversity, Shannon index

Quantitative trait loci

  • Genotype
  • Association analysis
  • Meta-analysis
  • Adjustment of covariates
  • Adjustment of batch effects
  • Multivariate linear regression

De novo assembly of genomes

  • Annotation of genomes
  • Comparative genomics
  • BLAST-based gene analysis
  • Gene-family analysis
  • Repeat analysis
  • Homology analysis

Variant calling from whole genome data

  • Single nucleotide polymorphisms
  • Insertions and deletions
  • Copy number variations
  • Large rearrangements

Phylogenetic analysis of microbial genetics

  • Multiple-sequence alignment
  • Neighbor-joining/maximum likelihood trees
  • Bootstrapping quality scores
  • Interpretation and visualization of large taxonomies

Graphics and visualization

  • Circos plots
  • Chromosome-wide plots
  • LocusZoom plots
  • Scatter plots

Machine learning

  • Feature selection
  • Algorithm training
  • Model selection and evaluation
  • Receiver Operating Characteristics
  • Sensitivity/Specificity/F1 metrics

General statistics

  • Frequentist and Bayesian statistics
  • Power calculations
  • Non-parametric statistics
  • Multiple correction, false discovery rate adjustments, family-wise error rates
  • Dimensionality reduction approaches (e.g., PCA, t-SNE)
  • Empirical distributions
  • Correlations

In addition, we also can help our with general statistical analysis (for example, power calculations for grant preparation), not necessarily restricted to biological data.