marvinquiet

Cellcano

Supervised cell type identification for scATAC-seq data

LRcell

The goal of LRcell is to identify specific sub-cell types that drives the changes observed in a bulk RNA-seq differential gene expression experiment. To achieve this, LRcell utilizes sets of cell marker genes acquired from single-cell RNA-sequencing (scRNA-seq) as indicators for various cell types in the tissue of interest. Next, for each cell type, using its marker genes as indicators, we apply Logistic Regression on the complete set of genes with differential expression p-values to calculate a cell-type significance p-value. Finally, these p-values are compared to predict which one(s) are likely to be responsible for the differential gene expression pattern observed in the bulk RNA-seq experiments.

RefConstruction_supervisedCelltyping

Source code for "Evaluation of some aspects in supervised cell type identification for single-cell RNA-seq: classifier, feature selection, and reference construction".

BART-WEB

Predict functional transcription factors leveraging H3K27ac profiles and ChIP-seq TF binding datasets.

scRNA-seq_celltyping_reference

Exploration on using scRNA-seq datasets as reference, such as what factors might affect reference quality.

marvinquiet

Show my work

bart2

Revised version using adaptive lasso model to predict functional transcription factors from a gene list or a ChIP-seq binding profile.

BART_chipatlas_analysis

Batch generation on ChIP-Atlas result

BARTweb_docker

Docker based, new version of BARTweb

BARTweb_jump

Receive the Amazon SQS Service and trigger the shell script.

BioSPPy

Biosignal Processing in Python

BMI500_hw2

Homework repos for BMI500

BMI500_hw3

HW3-clustering algorithm implement for course BMI500

BSSLecture

Simplified illustration of blind-source separation algorithms

BSSLectureExamplesForStudents

CS584_Final_Project

Class project: from phenotype to genotype.

DEC-keras

Keras implementation for Deep Embedding Clustering (DEC)

deid2020

Class project for de-identification BMI 500 all 2020

IBS574

For IBS574 HW

leetcode_solutions

For leetcode JAVA

LRcellTypeMarkers

This is an external data storage package for LRcell R package using AnnotationHub.

marvinquiet.github.io

Github Pages template for academic personal websites, forked from mmistakes/minimal-mistakes

maupassant-hexo

A simple Hexo theme forked from icylogic.

monocle3

PhysioNet-Cardiovascular-Signal-Toolbox

PhysioNet Cardiovascular Signal Toolbox

pytorch-adda

A PyTorch implementation for Adversarial Discriminative Domain Adaptation

scATAC-adda

Fork from https://github.com/erictzeng/adda

sci-CAR_analysis

Scripts for processing sci-RNA-seq/sci-ATAC-seq/sci-CAR reads processing

SnapATAC

Analysis Pipeline for Single Cell ATAC-seq

Zhaohui-Steve-Qin-lab-page

This is a simple static research lab website template which can be used by college students / professors.