cchen22

cchen22's Stars

• vib-singlecell-nf/vsn-pipelines

  A repository of pipelines for single-cell data in Nextflow DSL2

  Language:Nextflow7532

• BioMedicalBigDataMiningLab/GraphCDR

  GraphCDR: A graph neural network method with contrastive learning for cancer drug response prediction

  259

• sajuukLyu/projectLSI

  Project bulk/single-cell RNA-seq data to given LSI space

  Language:R112

• obophenotype/cell-ontology-training

  Training session for the Cell Ontology

  72

• NKI-CCB/TANDEM

  A two-stage regression method that can be used when various input data types are correlated, for example gene expression and methylation in drug response prediction. In the first stage it uses the upstream features (such as methylation) to predict the response variable (such as drug response), and in the second stage it uses the downstream features (such as gene expression) to predict the residuals of the first stage. In our manuscript (Aben et al., 2016), we show that using TANDEM prevents the model from being dominated by gene expression and that the features selected by TANDEM are more interpretable.

  Language:R4

• Ming-Lian/NGS-analysis

  二代测序数据分析

  354164

• gersteinlab/UMG

  A network propagation method to prioritize long tail genes in cancer

  Language:Python3

• stan-dev/projpred

  Projection predictive variable selection

  Language:R11025

• yao-yl/Multimodal-stacking-code

  replication code and data for the paper "The Curse and Blessing of Multimodal Posteriors: Inference From Non-Mixing Parallel Computations"

  Language:HTML6

• rgiordan/StanSensitivity

  Tools for automatically generating local sensitivity measures in Stan.

  Language:R354

• majianthu/transferentropy

  Code for the paper "Estimating Transfer Entropy via Copula Entropy"

  Language:R4013

• majianthu/copent

  R package for estimating copula entropy (mutual information), transfer entropy (conditional mutual information), and the statistic for multivariate normality test and two-sample test

  Language:R4110

• R-Stefano/Grid-Cells

  Implementation of Vector Based Navigation using Grid-like cells using Tensorflow and Numpy

  Language:Python337

• cbongiorno/pednav

  Language:Python171

• jrnold/docker-stan

  Dockerfiles with rstan and CmdStan

  Language:Makefile2411

• qiyuangong/leetcode

  Python & JAVA Solutions for Leetcode

  Language:Python5.2k1.5k

• pyro-ppl/pyro

  Deep universal probabilistic programming with Python and PyTorch

  Language:Python8.6k984

• hbctraining/Intro-to-rnaseq-hpc-O2

  This repository has teaching materials for a 2 and 3-day Introduction to RNA-sequencing data analysis workshop using the O2 Cluster

  Language:HTML16589

• KunKuang/Differentiated-Confounder-Balancing

  The source code of our DCB algorithm in KDD17 paper: Estimating Treatment Effect in the Wild via Differentiated Confounder Balancing

  Language:Matlab10

• bowang-lab/BIONIC

  Biological Network Integration using Convolutions

  Language:Python594

• schulter/EMOGI

  An explainable multi-omics graph integration method based on graph convolutional networks to predict cancer genes.

  Language:Jupyter Notebook14432

• KrishnaswamyLab/SingleCellWorkshop

  Language:Jupyter Notebook8835

• jwasham/coding-interview-university

  A complete computer science study plan to become a software engineer.

  309k77.3k

• mskcc/RNAseqDB

  Language:Perl14041

• theislab/single-cell-tutorial

  Single cell current best practices tutorial case study for the paper:Luecken and Theis, "Current best practices in single-cell RNA-seq analysis: a tutorial"

  Language:Jupyter Notebook1.4k466

• shap/shap

  A game theoretic approach to explain the output of any machine learning model.

  Language:Jupyter Notebook23.1k3.3k

• cole-trapnell-lab/sci-plex

  repository containing analysis scripts and auxiliary files

  Language:R302

• Roy-lab/merlin-p

  A prior-based integrative framework for functional transcriptional regulatory network inference (Fotuhi Siahpirani & Roy, Nucleic Acids Research 2017)

  Language:C56

• califano-lab/ARACNe-AP

  Network Reverse Engineering through AP inference of Mutual Information

  Language:Java8124

• NVIDIA-Genomics-Research/rapids-single-cell-examples

  Examples of single-cell genomic analysis accelerated with RAPIDS

  Language:Jupyter Notebook32769