christacaggiano/cell-free-dna-reading-list

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christacaggiano/cell-free-dna-reading-list

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Important papers relating to the biology of cell free DNA

celfie

cfDNA cell type of origin estimation

Jupyter Notebook

ENCODE_WGBS

a SGE, python, implementation of the ENCODE consortium whole genome bisulfite sequencing pipeline.

mybaits-probe-design

cfDNA methylation probe design from mybaits targeted sequencing

IBD

code for analyzing IBD networks

Jupyter Notebook

algorithms

notes for UCSF BMI 203, winter quarter 2018

treeWas-exploration

exploration of TreeWas/TreeWas2 code for the Zaitlen lab. Based on TreeWas developed by McVean Lab @ Oxford.

causal-inference-reading-list

Some papers I've come across on causal inference

ecaviar-in-julia

GWAS-EQTL colocalization written in the Julia programming language

neural-net

Artificial neural network to predict transcription factor binding.

C

C code written for Brandeis course Data Structures and Algorithms

genomics_conference_notes

Circle_RNA

Circle RNA exploration

machine_learning_exercises

Machine learning sample jupyter notebooks

Jupyter Notebook

exome_processing_pipeline

simple pipeline for processing exome sequencing data using BWA and GATK4

process-methylation