Priya Vijay

DISCO is a platform for the analysis of alternative splicing in single-cell RNA-seq or any other large-scale RNA-seq study (best suited for hundreds of samples). It performs non-parametric statistical testing and visualization for computing distributions of isoforms or other alternative splicing events.

Paul Zumbo, Sheng Li

r-make is inspired by Solexa’s original pipeline. Solexa’s original pipeline (and Illumina’s current implementation of it) is powered by make. make automates the building of large, complicated processes by traversing dependency chains, allowing for unguided parallelization by abstraction. r-make picks up where Illumina leaves off. 

Alexa McIntyre

Prediction of base modifications from differences between measured and expected currents in nanopore data.

Yogesh Saletore

A moving-window, peak-finding algorithm for Methylated RNA Immunoprecipitation (MeRIP) data sets. 

Altuna Akalin

methylKit is an R package for DNA methylation analysis and annotation from high-throughput bisulfite sequencing. The package is designed to deal with sequencing data from RRBS and its variants, but also target-capture methods such as Agilent SureSelect methyl-seq. It can potentially handle whole-genome bisulfite sequencing data if proper input format is provided.

Sheng Li

Comprehensive DMR analysis based on bimodal normal distribution model and weighted cost function for regional methylation analysis optimization. It captures the regional methylation modification by taking the spatial distribution of CpGs into account for the enrichment DNA methylation sequencing data so as to optimize the definition of the empirical regions. Combined with the dependent adjustment for regional p-value combination and DMR annotation.

N/A

methylKit is an R package for DNA methylation analysis and annotation from high-throughput bisulfite sequencing. The package is designed to deal with sequencing data from RRBS and its variants, but also target-capture methods such as Agilent SureSelect methyl-seq. It can potentially handle whole-genome bisulfite sequencing data if proper input format is provided.

Sheng Li

Scripts for data analysis in relapsed AML study.

Altuna Akalin, Vedran Franke

An R package for genomic feature analysis and annotation by extending bioconductor packages.

Christopher E. Mason, Stephan Sanders

This program is designed to simplify all stages of predicting and analyzing CNVs, from running prediction algorithms and combining their results to visualizing the raw data and designing qPCR primers for confirmation