Pinned Repositories
awesome
Awesome resources on Bioinformatics, data science, machine learning, programming language (Python, Golang, R, Perl) and miscellaneous stuff.
awesome-1
:sunglasses: Curated list of awesome lists
Awesome-Bioinformatics
A curated list of awesome Bioinformatics libraries and software.
combat.py
python / numpy / pandas / patsy version of ComBat for removing batch effects.
ctCNV
A new CNV calling method for DNA-seq data
jstest
some test codes
MB
molecular barcode pipeline
NGS-pipeline
GATK and VARSCAN analysis pipeline
scDeconv
scDeconv is an R Package to Deconvolve Bulk DNA Methylation Data with scRNA-seq Data in a Multi-omics Manner.
tools
tools for NGS analysis
HaoKuo's Repositories
HaoKuo/ctCNV
A new CNV calling method for DNA-seq data
HaoKuo/scDeconv
scDeconv is an R Package to Deconvolve Bulk DNA Methylation Data with scRNA-seq Data in a Multi-omics Manner.
HaoKuo/jstest
some test codes
HaoKuo/tools
tools for NGS analysis
HaoKuo/BayesianOptimization
A Python implementation of global optimization with gaussian processes.
HaoKuo/benchm-ml
A minimal benchmark for scalability, speed and accuracy of commonly used open source implementations (R packages, Python scikit-learn, H2O, xgboost, Spark MLlib etc.) of the top machine learning algorithms for binary classification (random forests, gradient boosted trees, deep neural networks etc.).
HaoKuo/BIC-RNAseq
Bioinformatics core RNAseq pipeline
HaoKuo/BIC-variants_pipeline
BIC@MSKCC Variants Pipeline
HaoKuo/bwa-meth
fast and accurate alignment of BS-Seq reads
HaoKuo/CfdnaPattern
Pattern Recognition for Cell-free DNA
HaoKuo/checkMyIndex
Search for a set of compatible indexes for your sequencing experiment
HaoKuo/deepvariant
DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
HaoKuo/delfi_scripts
HaoKuo/enrichR
A hacky little interface to call the Enrichr functional enrichment tool from R.
HaoKuo/FREEC-Plot
Plotting outputs of Control-FREEC for targeting sequencing data
HaoKuo/h2o-tutorials
Tutorials and training material for the H2O Machine Learning Platform
HaoKuo/iCallSV
A Framework to call Structural Variants from NGS based datasets
HaoKuo/labs
Rmd source files for the HarvardX series PH525x
HaoKuo/MachineLearningTrick
Machine Learning Trick : GBDT_Feature Blending Stacking CascadeForest
HaoKuo/Methylation_Analysis
DNA methylation workflow, from beta-values to signatures
HaoKuo/MlBayesOpt
R package to tune parameters for machine learning(Support Vector Machine, Random Forest, and Xgboost), using bayesian optimization with gaussian process
HaoKuo/Mutation-Analysis
HaoKuo/notedown
Markdown <=> IPython Notebook
HaoKuo/pandas-cookbook
Recipes for using Python's pandas library
HaoKuo/PureCN
Copy number calling and variant classification using targeted short read sequencing
HaoKuo/pytorch-book
PyTorch tutorials and fun projects including neural talk, neural style, poem writing, anime generation
HaoKuo/reproduce_lucas_wflow
cfDNA_DELFI_LungCancer
HaoKuo/RNAseq-workflow
A repository for setting up a RNAseq workflow
HaoKuo/SPLICIFY
HaoKuo/startbootstrap-resume
A Bootstrap 4 resume/CV theme created by Start Bootstrap