Tools to make an R developer's life easier

Convert statistical analysis objects from R into tidy format

An R 📦 to make testing 😀

Packrat is a dependency management system for R

Differential analysis of RNA-Seq

Create timecourse "fish plots" that show changes in the clonal architecture of tumors

Bioconductor package "ballgown", devel version. Isoform-level differential expression analysis in R.

Inferring and visualizing clonal evolution in multi-sample cancer sequencing

deconstructSigs

Algorithm to implement Fraction and Copy number Estimate from Tumor/normal Sequencing.

Copy number calling and variant classification using targeted short read sequencing

An R package for inferring the subclonal architecture of tumors

Analysis pipeline for cancer sequencing data

Bioconductor package "polyester", devel version. RNA-seq read simulator.

BatchJobs: Batch computing with R

Locus Overlap Analysis: Enrichment of Genomic Ranges

Visualization and annotation of CNVs from population-scale whole-genome sequencing data

Accessing Intra-Tumor Heterogeneity and Tracking Longitudinal and Spatial Clonal Evolutionary History by Next-Generation Sequencing.

Somatic copy variant caller (CNV) for next generation sequencing

Amelia: A Package for Missing Data

MIP based joint inference of copy number and rearrangement state in cancer whole genome sequence data.

QDNAseq package for Bioconductor

Bayesian mixture models for estimating and clustering cancer cell fractions

Abbreviate strings to short, unique identifiers

Callable Cancer Loci - assessment of sequencing coverage for actionable and pathogenic loci in cancer

Quick Read Quality Control

Exploration, clustering, visualization and classification of DNA damage patterns

R tools to interact with hap.py output

Deprecated, see https://labsyspharm.github.io/rnaseq/