pytenn2014_tutorial

PyTennessee 2014: Statistical Data Analysis in Python

qqman

R code for creating Manhattan plots and Q-Q plots for GWAS

quantumclone

Clonal reconstruction from HTS data

r_ex

rdiff

Tests for Differential RNA Isoform Expression

rep-res-book

Source code files for the book Reproducible Research with R/RStudio

repo

repseq-tutorial

Rep-Seq data analysis tutorial

resprog

Program directory RESPONSIFY

rmi

R in medical imaging

rmodules

A R statistical analysis module plugin for tranSMART

rna-seq-diff-exprn

RNA-Sequencing data differential expression analysis pipeline. Performs: genome coverage (via bedtools and HTSeq), generates Circos code and plots, differential expression (via DESeq and NOISeq), structural variant detection (e.g. fusion genes, via SVDetect) and differential exon usage (via DEXSeq).

rnaseq_tutorial

An educational tutorial and working demonstration pipeline for RNA-seq analysis including an introduction to: cloud computing, next generation sequence file formats, reference genomes, gene annotation, expression analysis, differential expression analysis, alternative splicing analysis, data visualization, and interpretation.

rniftyreg

An R interface to the NiftyReg medical image registration library

rthreejs

Three.js widgets for R and shiny

scater

Single cell analysis tools for expression from RNA-seq in R

scater_tutorials_open_data

A set of tutorials using the scater package to QC publicly available single-cell expression data sets

sccantutorial

introduction to sccan statistical studies

schism

Subclonal Hierarchy Inference from Somatic Mutations

sciclone

An R package for inferring the subclonal architecture of tumors

scmt-seq

scripts

scrna-seq_papers

A list of single-cell RNA-Seq papers from our reading group

shinyheatmap

Create user-friendly, highly customizable static and interactive biological heatmaps in a web browser

sj2psi

Convert RNA-STAR aligner "SJ.out.tab" files to "Percent spliced-in" (Psi) scores

smartas

Jupyter notebook of the smartas project.

snpchip

This package defines methods for visualizing high-throughput SNP array data for copy number applications

splitthreader

Explore rearrangements and copy-number amplifications in a cancer genome

squid

statistical-analysis-python-tutorial

Statistical Data Analysis in Python