HaoKuo

ctCNV

A new CNV calling method for DNA-seq data

scDeconv

scDeconv is an R Package to Deconvolve Bulk DNA Methylation Data with scRNA-seq Data in a Multi-omics Manner.

jstest

some test codes

tools

tools for NGS analysis

BayesianOptimization

A Python implementation of global optimization with gaussian processes.

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.).

BIC-RNAseq

Bioinformatics core RNAseq pipeline

BIC-variants_pipeline

BIC@MSKCC Variants Pipeline

bwa-meth

fast and accurate alignment of BS-Seq reads

CfdnaPattern

Pattern Recognition for Cell-free DNA

checkMyIndex

Search for a set of compatible indexes for your sequencing experiment

deepvariant

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

delfi_scripts

enrichR

A hacky little interface to call the Enrichr functional enrichment tool from R.

FREEC-Plot

Plotting outputs of Control-FREEC for targeting sequencing data

h2o-tutorials

Tutorials and training material for the H2O Machine Learning Platform

iCallSV

A Framework to call Structural Variants from NGS based datasets

labs

Rmd source files for the HarvardX series PH525x

MachineLearningTrick

Machine Learning Trick : GBDT_Feature Blending Stacking CascadeForest

Methylation_Analysis

DNA methylation workflow, from beta-values to signatures

MlBayesOpt

R package to tune parameters for machine learning(Support Vector Machine, Random Forest, and Xgboost), using bayesian optimization with gaussian process

Mutation-Analysis

notedown

Markdown <=> IPython Notebook

pandas-cookbook

Recipes for using Python's pandas library

PureCN

Copy number calling and variant classification using targeted short read sequencing

pytorch-book

PyTorch tutorials and fun projects including neural talk, neural style, poem writing, anime generation

reproduce_lucas_wflow

cfDNA_DELFI_LungCancer

RNAseq-workflow

A repository for setting up a RNAseq workflow

SPLICIFY

startbootstrap-resume

A Bootstrap 4 resume/CV theme created by Start Bootstrap