wisekh6 Goto Github PK

chia_rep

chip-seq-analysis

ChIP-seq analysis notes from Tommy Tang

chm13

Ultra-long reads for CHM13 genome assembly

circularplot

classweb

Template for class websites

cloud-computing-for-genomics

cn_learn

CN-Learn

coder

ChrOmothripsis DiscovEry through Rearrangements

computational-genomics-project

A systematic analysis of four tumor-purity-estimating methods on about 7500 patients across 15 cancer types from The Cancer Genome Atlas (TCGA).

configs

Config files used to define parameters specific to compute environments at different Institutions

conusig

COpy NUmber SIGnatures

copy-number-analysis

Explore, compare, and evaluate Bioconductor packages related to genomic copy number analysis

copycat

Copycat is a simple script to capture and bin the read coverage across a genome from a bam file of read alignments. It relies on bedtools to get coverage for each individual nucleotide in the genome using bedtools genomecov, then bins and organizes these coverage values into 10kb bins and outputs the coverage information in a .csv format (for upload to SplitThreader) and in a .seg format (for viewing the copy number profile in IGV)

coursework

Help Manage Barry's Courses

curriculum_contribution

guidelines for contributing to fredhutch.io courses

cycleviz

cycleviz-1

Visualize outputs of AmpliconArchitect and AmpliconReconstructor in Circos-style images.

debrowser

Differential Count Data Analysis Toolbox

deep-neural-networks-healthcare

Tangible and Practical Deep Learning Projects Repository for Healthcare such as Cancer, Drug Discovery, Genomic and More

deeplearning-biology

A list of deep learning implementations in biology

dirichletprocessmixturemodel

The Dirichlet Process Gaussian Mixture Model provides a fully Bayesian analysis for the inference of clusters and their parameters.

dna-methylation-analysis

my notes on DNA methylation analysis (arrays and sequencing data)

dna-seq-analysis

my notes on whole exome and whole genome sequencing analysis

dna-seq-gatk-variant-calling

This Snakemake pipeline implements the GATK best-practices workflow

dnanexus_ngsapp

Dockerfile for DNA Nexus NGS tools

docker-workshop

A two-hour Docker workshop for DockerDC

dolphinnext

A graphical user interface for distributed data processing of high throughput genomics

dpclust

Dirichlet Process based methods for subclonal reconstruction of tumours

dpclustering.jl

Dirichilet process clustering for cancer sequencing data

dsde-deep-learning

DSDE Deep Learning Club