Software

The Bioinformatics team focuses on the development of software for analysis, quality control and visualization of biological data relevant to our work at the LMS. All software developed is publically available through our GitHub site or Bioconductor. We currently maintain two analysis pipelines (ChIP-seq and RNA-seq) to allow for the rapid and reproducible analysis of these common data types. We also developed and maintain four Bioconductor packages within the team: ChIPQC, tracktables, Soggi, basecallQC in addition to Java packages, VisRseq, ChAsE, and ALEA.

  • Developed by Tom Carroll, previously Head of Bioinformatics at the LMS and currently at ‎The Rockefeller University , with Rory Stark, Wei Liu and Ines de Santiago at CRUK. ChIPQC provides a set of tools for the evaluation of ChIP-seq, MNAse-seq and ChIP-exo quality.
  • Bioconductor Site:- Link
  • Bioconductor talk/course on ChIPQC:- Link
  • Related paper:- Link
  • Developed by Sanjay Khadayate, MRC London Institute of Medical Sciences and Tom Carroll, tracktables provides tools to create dynamic genome browser linked (IGV) HTML reports from BAM, bigwigs and interval files as well as many Bioconductor objects.
  • Bioconductor Site:- Link
  • Github Site:- Link
  • Developed by Gopuraja Dharmalingam, MRC London Institute of Medical Sciences and Tom Carroll, soGGi (summarising over grouped genomic intervals) provides tools to summarise and visualise signal, motifs and conservation over genomic ranges using GGplot2.
  • Bioconductor Site:- Link
  • Github Site:- Link
  • Developed by Tom Carroll and Marian Dore, MRC London Institute of Medical Sciences, basecallQC package provides tools to work with Illumina basecalling and demultiplexing input and output files (bcl2Fastq versions >= 2.1.7).
  • Bioconductor Site:- Link
  • Github Site:- Link
  • Developed by Mohammad Karimi from LMS, Hamid Younesy and other collaborators from University of British Columbia and Simon Fraser University, VisRseq is a framework for analysis of sequencing datasets that provides computationally rich and accessible tools for integrative and interactive analyses without requiring programming expertise.
  • Github Site:- Link
  • Related paper:- Link
  • Developed by Mohammad Karimi from LMS, Hamid Younesy and other collaborators from University of British Columbia and Simon Fraser University, ChAsE is a cross-platform desktop application for interactive visualization, exploration and clustering of epigenomic data such as ChIP-seq experiments.
  • Github Site:- Link
  • Related paper:- Link
  • Developed by Mohammad Karimi from LMS, Hamid Younesy and other collaborators from University of British Columbia and Simon Fraser University, ALEA is a computational toolbox for allele-specific (AS) epigenomics analysis, which incorporates allelic variation data within existing resources, allowing for the identification of significant associations between epigenetic modifications and specific allelic variants in human and mouse cells.
  • Github Site:- Link
  • Related paper:- Link
  • Developed by Mohammad Karimi from LMS, Julien Richard Albert and other collaborators from University of British Columbia and Simon Fraser University, MEA is an INDEL-aware Methylomic and Epigenomic Allele-specific analysis pipeline which enables user-friendly data exploration, visualization and interpretation of allelic imbalance.
  • Github Site:- Link
  • Related paper:- Link
  • Developed by Mohammad Karimi from LMS, Artem Babaian and other collaborators from University of British Columbia, LIONS is a software suite to analyze paired-end RNA-seq data for detecting and quantifying significant Tranposable Element (TE)-contributions to a transcriptome. The LIONS suite serves as a platform for TE RNA-seq analysis and can be applied to a broad set of data sets for the study of development, stress treatments, aging and cancer.
  • Github Site:- Link
  • Related paper: under review in bioinformatics