Q-KIM

AlphaGo

A replication of DeepMind's 2016 Nature publication, "Mastering the game of Go with deep neural networks and tree search," details of which can be found on their website.

appliedgenomics2018

Materials for Spring 2018 Applied Genomics Course

ascat

ASCAT copy number R package

ASE_PO

awesome-single-cell

List of software packages for single-cell data analysis, including RNA-seq, ATAC-seq, etc.

bioinformatics

Utilities written for bioinformatics

bioruby-vcf

Smart VCF parser

ComplexHeatmap

make complex heatmaps as well as self define annotation graphics

eQTL-Brain

eQTL (single and Meta analysis of Brain tissue)

gtex-1

GTEx analysis scripts

impute

Phasing and imputation of multiple data sets

impute-tools

Scripts to facilitate imputation of genotypes and subsequent QC.

inferCNV

Inferring CNV from Single-Cell RNA-Seq

leafcutter

LeafCutter: Annotation-free quantification of RNA splicing. Yang I Li, David A Knowles, Jonathan K Pritchard.

maftools

Summarize, Analyze and Visualize MAF files from TCGA or in house studies.

pan-cancer-drug-response

DrugResponseAnalysis through the pan-cancer view

pcaReduce

PrediXcan

Code for the in-dev PrediXcan Project

PyClone

Group project for group 2 in course DD2434 - Machine Learning, Advanced Course at KTH.

rasqual

Robust Allele Specific Quantification and quality controL

rnaseq_tutorial

Informatics for RNA-seq: A web resource for analysis on the cloud. Educational tutorials and working pipelines for RNA-seq analysis including an introduction to: cloud computing, critical file formats, reference genomes, gene annotation, expression, differential expression, alternative splicing, data visualization, and interpretation.

rPGA

scLVM

scLVM is a modelling framework for single-cell RNA-seq data that can be used to dissect the observed heterogeneity into different sources, thereby allowing for the correction of confounding sources of variation.

scMT-seq

SCUMIKit

A pipeline for processing UMI-tagged single cell RNA-Seq data

tagteam

Enhanced Social Tagging for Academic Communities

THetA

Tumor Heterogeneity Analysis (THetA) is an algorithm that estimates the tumor purity and clonal/subclonal copy number aberrations directly from high-throughput DNA sequencing data. Please note that the latest release is now called THetA2.

VarDict

VarDict

Viral-Track

WASP

WASP: allele-specific pipeline for unbiased read mapping and molecular QTL discovery