q-kim Goto Github PK

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

capseg

CapSeg - Copy Number from Exome Sequencing

cgat

CGAT - Computational Genomics Analysis Tools

clonehd

High-definition reconstruction of clonal composition from next-generation sequencing data

clonevol

Inferring and visualizing clonal evolution in multi-sample cancer sequencing

complexheatmap

make complex heatmaps as well as self define annotation graphics

d3e

Discrete Distributional Differential Expression

derfinder

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

docs

Documentation for all of the googlegenomics repositories.

eqtl-brain

eQTL (single and Meta analysis of Brain tissue)

gatk

Daniel Klevebring's GATK Repository: contains the core MIT-licensed GATK framework, and custom tools, free for all uses.

ginkgo

Cloud-based single-cell copy-number variation analysis tool

gtex

eQTL Detection from GTEx data

gtex-1

GTEx analysis scripts

igv

Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations

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

jvarkit

Java utilities for Bioinformatics

laggingstrand

Exploring the relationships between DNA replication and mutation.

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

paper-rgasp3-cov

RGASP3 coverage statistics pipeline