christacaggiano
Postdoctoral fellow studying human genetics and bioinformatics at the Institute for Genomic Health at Mt Sinai. Trying my best.
Los Angeles
Pinned Repositories
algorithms
notes for UCSF BMI 203, winter quarter 2018
causal-inference-reading-list
Some papers I've come across on causal inference
celfie
cfDNA cell type of origin estimation
cell-free-dna-reading-list
Important papers relating to the biology of cell free DNA
ecaviar-in-julia
GWAS-EQTL colocalization written in the Julia programming language
ENCODE_WGBS
a SGE, python, implementation of the ENCODE consortium whole genome bisulfite sequencing pipeline.
IBD
code for analyzing IBD networks
ibd-mapping
Code for IBD mapping in EHR studies of monogenic disease
machine_learning_exercises
Machine learning sample jupyter notebooks
mybaits-probe-design
cfDNA methylation probe design from mybaits targeted sequencing
christacaggiano's Repositories
christacaggiano/cell-free-dna-reading-list
Important papers relating to the biology of cell free DNA
christacaggiano/ENCODE_WGBS
a SGE, python, implementation of the ENCODE consortium whole genome bisulfite sequencing pipeline.
christacaggiano/mybaits-probe-design
cfDNA methylation probe design from mybaits targeted sequencing
christacaggiano/algorithms
notes for UCSF BMI 203, winter quarter 2018
christacaggiano/ecaviar-in-julia
GWAS-EQTL colocalization written in the Julia programming language
christacaggiano/neural-net
Artificial neural network to predict transcription factor binding.
christacaggiano/treeWas-exploration
exploration of TreeWas/TreeWas2 code for the Zaitlen lab. Based on TreeWas developed by McVean Lab @ Oxford.
christacaggiano/genomics_conference_notes
christacaggiano/GWAS-EQTL
analysis for UCSF BMI 206 based on Hormozdiari et al (2016) Am J Hum Genet
christacaggiano/applied_statistics_reading_list
Applied statistics reading list for Zaitlen lab
christacaggiano/awesome-ehr-deeplearning
Curated list of awesome papers for electronic health records(EHR) mining, machine learning, and deep learning.
christacaggiano/bachelor_data
Scraping data from the ABC shows The Bachelor and The Bachelorette.
christacaggiano/cards-against-science
Scientists need to have some fun every now and then; we hope this game is fun (if not, you might just not have any humor).
christacaggiano/caviar
Bioinformatic software to identify causal variants in GWAS and GWAS/eQTL studies.
christacaggiano/images
graphs n stuff mostly for making stable markdown urls
christacaggiano/lung_transplant_cfdna
code for lung transplant cfdna project
christacaggiano/methylation-reference-matrix
generates reference matrix of average beta methylation values
christacaggiano/methylation_processing
simple scripts to process large methylation matrices
christacaggiano/ML-From-Scratch
Machine Learning From Scratch. Bare bones Python implementations of Machine Learning models and algorithms with a focus on transparency and accessibility. Aims to cover everything from Data Mining to Deep Learning.
christacaggiano/pc-confounding
Simulation code for Dahl et al 2017
christacaggiano/pregnancy_cfdna
christacaggiano/pystan_practice
practice exercises in pystan
christacaggiano/selection-of-complex-traits-reading-list
christacaggiano/smith-waterman
python implementation of the smith waterman alignment algorithm
christacaggiano/snakemake_WGBS
Using Snakemake to implement ENCODE WGBS pipeline
christacaggiano/sorting-functions
Basic algorithms/data structures - Quick sort and bubble sort implementation
christacaggiano/TreeWASDir
Repository for our manuscript 'Systematic classification of shared components of genetic risk for common human diseases'.
christacaggiano/unsupervised-clustering
implements k-means clustering and hierarchical clustering from scratch
christacaggiano/Ye_lab
spatial-seq
christacaggiano/zaitlen-lab-website