cnv-caller

A cnv, snv and clonality caller.

cnvworkshopebi

hands-on for NGS/SNParray CNV call trainning

cocoanlab.github.io

Build a beautiful and simple website in literally minutes. Demo at http://deanattali.com/beautiful-jekyll

complexheatmap

make complex heatmaps as well as self define annotation graphics

copynumbr

An R package for copy number data (aCGH, SNP arrays)

d3network

Tools for creating D3 JavaScript network graphs from R.

deconstructsigs

deconstructSigs

deconvolution2016

Simulation code and manuscript files for Aaron and Karsten's deconvolution paper.

deepmedic

Efficient Multi-Scale 3D Convolutional Neural Network for Brain Lesion Segmentation

deeptools

Tools to process and analyze deep sequencing data.

delly

DELLY2: Structural variant discovery by integrated paired-end and split-read analysis

derfinder

R package for DER Finder, a method for differential expression analysis of RNA-seq data

devmeth450k

Supplementary Code for "Mapping DNA methylation across development, genotype, and schizophrenia in the human frontal cortex"

diff_splice_paper

Code for differential splicing comparison paper (Soneson, Matthes, et al.)

director

drimseq_paper_analyses

dygraphs

R interface to dygraphs

egonet

Subnetwork selection from large-scale biological network based on gene expression data

epicseg

Chromatin segmentation in R

epitopefinder

Python package for mapping epitopes to sequences

erythroid_ir_analysis

Intron retention analysis for erythroid development (RNA-Seq)

eventpointer

R package to identify alternative splicing events using junction microarrays

example

example

fishplot

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

fluff

Fluff is a Python package that contains several scripts to produce pretty, publication-quality figures for next-generation sequencing experiments.

focalcall

R-package for the detection and annotation of focal CNAs

fred2

Python-based framework for computational immunomics

genefuse

Gene fusion detection and visualization

genesets

Gene Sets as R Environments

ggbrain

Helper functions for making brain image figures with ggplot