Chengze Shen's repositories
CS125Fall20QuizPrep
A repo where I will post questions that summarize prior week's contents to help students prepare for the next week's quiz.
GPU-BLAST-plus
A class project for CS508 from UIUC to implement the classic BLAST algorithm using different GPU computing techniques.
kmSortFile
k-means clustering sorting to heatmap display
cm_pipeline
Pipeline that uses an improved version of CM for generating well-connected clusters
ATMerger
A standalone alignment merging tool that utilizes transitivity that merges a set of overlapping alignments. The original implementation comes from PASTA and UPP (see README).
BSCAMPP_code
New Code for EPA-ng-BSCAMPP
ColabFold
Copy of colabfold. Adding options to realign the retrieved sequences from MMSeqs2
CommonLibSSE-NG
This is a reverse engineered library for Skyrim Special Edition and Skyrim VR.
connectivity-modifier
better community detection through small cuts
constrained-INC
A copy of constrained-INC (INC) from steven-le-thien
contrained-MAGUS
Graph Clustering Merger
CS598FinalProject
Git repo for the CS598 final project. This is a simple modification to the ILP version of PhISCS, where we allow the model to handle ISA (infinite site assumption) violations implicitly.
learnMSA
Learning and Aligning Large Protein Families (MSA-HMM)
MAGUS-legacy
A legacy version of MAGUS that I will personally work on
my-deep-learning-collection
A collection of deep learning implementations, including MLP, CNN, RNN. Additionally, a new CNN approach for solving PDEs are provided (GACNN).
njmerge
A tool for divide-and-conquer tree estimation via a shared distance matrix
Novelty
Codes for computing novelty indicators.
OrthoFinder
Phylogenetic orthology inference for comparative genomics
sepp
Ensemble of HMM methods (SEPP, TIPP, UPP)
soulsy
A minimal Souls-like HUD for Skyrim AE & SE. SKSE plugin.