Software

  • CIDR is an R package thay implements an ultrafast and accurate dimensionality reduction and clustering algorithm for single-cell RNA-seq data. The method is described in this Genome Biology paper.
  • Falco is flexible big data framework for fast processing of single-cell RNA-seq data on the cloud. The method is described in this Bioinformatics paper.
  • PBrowse is web-based platform for real-time collaborative exploration and sharing of genomic data. A test server can be found here. The method is described in this Nucleic Acids Research paper.
  • PAD is a web-based bioinformatics tool for analysing transcription factor (TF) co-binding at gene-proximal or distal regulatory elements in mouse embryonic stem cells. A test server can be found here. The method is described in this Bioinformatics paper.
  • XGSA is an R package that implements our statistical method for cross-species gene set analysis. A full description of the method can be found in this Bioinformatics paper.
  • ENCODE-X Cross-species chromatin data browser is an online portal for ENCODE and modENCODE chromatin datasets. A full description of the data can be found in our Nature paper.
  • hiHMM is a new Bayesian non-parametric method to jointly infer chromatin state maps in multiple genomes (different cell types, developmental stages, even multiple species) using genome-wide histone modification data.
  • ToothCODE is an online portal of embryonic mouse tooth development data generated by the tooth regeneration team of SysCODE.
  • iSyTE is an integrated systems tool for eye gene discovery.
  • SeqVis is a stand-alone, platform-independent Java application developed with the aim to facilitate analysis and 3D visualization of compositional heterogeneity in species-rich alignments of nucleotide sequences.
  • DVA is a R script that performs differential variability analysis. A full description of this method can be found in this Bioinformatics paper.

Datasets

  • Antibody microarray of patients with Systemic Lupus Erythematosus (GEO)
  • Histone modification and gene expression in dosage compensation of Drosophila melanogaster (GEO)
  • Developmental timecourse of mouse ocular lens and whole embryo control (GEO)
  • Gene expression during embryonic mouse molar tooth development (GEO)