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deepvariant

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

evofreq

Evolutionary frequency visualization tool of temporal data

examples-r

Analysis examples based on the ISB-CGC hosted TCGA data, using R and R Markdown.

firebrowser

An R client for broads firehose pipeline, providing TCGA data sets

fishplot

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

gatk

Official code repository for GATK versions 4 and up

genomicdata_visualization

getting-started-with-genomics-tools-and-resources

Unix, R and python tools for genomics and data science

ginkgo

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

hadoop-bam

Hadoop-BAM is a Java library for the manipulation of files in common bioinformatics formats using the Hadoop MapReduce framework

hmftools

Various utility tools for working with genomics data

infercnv

Inferring CNV from Single-Cell RNA-Seq

lab_scripts

Consolidated scripts used by the Morin lab

microbial_bioinformatics

Collection of the some of the most famous microbial genome data analysis tools.

mlr

mlr: Machine Learning in R

ncr_notebooks

ngs-pipelines

oncosnpseq

OncoSNP-SEQ

pyclone

Probabilistic model for inferring clonal population structure from deep NGS sequencing.

pysyft

A library for encrypted, privacy preserving machine learning

python-data-science

Python3 teaching materials for data science (2 days)

readdepth

R package for inferring copy number from read depth

rna-seq

rna-seq-qc

Rna-seq pipeline, From FASTQ to differential expression analysis...

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.

scclust

Package: Segmentation and Clustering of Single Cell Sequencing Copy Number Profiles

sciclone

An R package for inferring the subclonal architecture of tumors

scnv

Single-cell Genome-wide CNV profiling

scripts

seurat

R toolkit for single cell genomics