Wenjing Ma's repositories
HippoOrganoid_analysis_pipeline
The analysis code for analyzing Hippocampus Organoid
marvinquiet
Show my work
marvinquiet.github.io
Github Pages template for academic personal websites, forked from mmistakes/minimal-mistakes
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".
scRNA-seq_celltyping_reference
Exploration on using scRNA-seq datasets as reference, such as what factors might affect reference quality.
scATAC-adda
Fork from https://github.com/erictzeng/adda
LRcellTypeMarkers
This is an external data storage package for LRcell R package using AnnotationHub.
SnapATAC
Analysis Pipeline for Single Cell ATAC-seq
BSSLecture
Simplified illustration of blind-source separation algorithms
deid2020
Class project for de-identification BMI 500 all 2020
BMI500_hw3
HW3-clustering algorithm implement for course BMI500
BMI500_hw2
Homework repos for BMI500
PhysioNet-Cardiovascular-Signal-Toolbox
PhysioNet Cardiovascular Signal Toolbox
BioSPPy
Biosignal Processing in Python
CS584_Final_Project
Class project: from phenotype to genotype.
BART_chipatlas_analysis
Batch generation on ChIP-Atlas result
DEC-keras
Keras implementation for Deep Embedding Clustering (DEC)
IBS574
For IBS574 HW
Zhaohui-Steve-Qin-lab-page
This is a simple static research lab website template which can be used by college students / professors.
bart2
Revised version using adaptive lasso model to predict functional transcription factors from a gene list or a ChIP-seq binding profile.
BARTweb_docker
Docker based, new version of BARTweb
BARTweb_jump
Receive the Amazon SQS Service and trigger the shell script.
sci-CAR_analysis
Scripts for processing sci-RNA-seq/sci-ATAC-seq/sci-CAR reads processing
pytorch-adda
A PyTorch implementation for Adversarial Discriminative Domain Adaptation
maupassant-hexo
A simple Hexo theme forked from icylogic.