Pinned Repositories
10x-scATAC-2019
Publication Page for Satpathy*, Granja* et al 2019
affymetrix-power-tools
AfterQC
Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data
alfred
BAM Statistics, Feature Counting and Annotation
alpine
Modeling and correcting fragment sequence bias for RNA-seq
combat.py
python / numpy / pandas / patsy version of ComBat for removing batch effects.
hrk2109's Repositories
hrk2109/10x-scATAC-2019
Publication Page for Satpathy*, Granja* et al 2019
hrk2109/amazon-sagemaker-examples
Example notebooks that show how to apply machine learning, deep learning and reinforcement learning in Amazon SageMaker
hrk2109/atropos
An NGS read trimming tool that is specific, sensitive, and speedy. (production)
hrk2109/build-your-own-x
🤓 Build your own (insert technology here)
hrk2109/CAR-T
Clonal kinetics and single-cell transcriptional profiling of adoptively transferred CD19-specific CD8+ CAR-T cells
hrk2109/coding-interview-university
A complete computer science study plan to become a software engineer.
hrk2109/covid19_sc
Processing workflow for COVID-19 single cell data
hrk2109/CRIS.py
Analyze NGS data for CRISPR (or any engineered endonuclease) activity and screen for clones. Screen for NHEJ or multiple HDR events concurrently.
hrk2109/CytoExploreR
Interactive Cytometry Data Analysis
hrk2109/developer-roadmap
Roadmap to becoming a web developer in 2020
hrk2109/drnet
💉📈 Dose response networks (DRNets) are a method for learning to estimate individual dose-response curves for multiple parametric treatments from observational data using neural networks.
hrk2109/ecTMB
hrk2109/gitignore
A collection of useful .gitignore templates
hrk2109/impute-me
This is the code behind the www.impute.me site. It contains algorithms for personal genome analysis, including imputation and polygenic risk score calculation
hrk2109/incubator-mxnet
Lightweight, Portable, Flexible Distributed/Mobile Deep Learning with Dynamic, Mutation-aware Dataflow Dep Scheduler; for Python, R, Julia, Scala, Go, Javascript and more
hrk2109/javascript-algorithms
📝 Algorithms and data structures implemented in JavaScript with explanations and links to further readings
hrk2109/matchSCore2
hrk2109/ohmyzsh
🙃 A delightful community-driven (with 1500+ contributors) framework for managing your zsh configuration. Includes 200+ optional plugins (rails, git, OSX, hub, capistrano, brew, ant, php, python, etc), over 140 themes to spice up your morning, and an auto-update tool so that makes it easy to keep up with the latest updates from the community.
hrk2109/PHATE
PHATE (Potential of Heat-diffusion for Affinity-based Transition Embedding) is a tool for visualizing high dimensional data.
hrk2109/PhenoGraph
Subpopulation detection in high-dimensional single-cell data
hrk2109/public-apis
A collective list of free APIs for use in software and web development.
hrk2109/SB_neoantigen_Models
hrk2109/scRNA-tools
Table of software for the analysis of single-cell RNA-seq data.
hrk2109/sentieon-nextflow
A nextflow-based workflow for aligning a DNA sample using the Sentieon tool set
hrk2109/signac
An analytics package for single cell data
hrk2109/system-design-primer
Learn how to design large-scale systems. Prep for the system design interview. Includes Anki flashcards.
hrk2109/the-art-of-command-line
Master the command line, in one page
hrk2109/umis
Tools for processing UMI RNA-tag data
hrk2109/xsv
A fast CSV command line toolkit written in Rust.
hrk2109/zUMIs
zUMIs: A fast and flexible pipeline to process RNA sequencing data with UMIs