Pinned Repositories
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
cm_pipeline
Pipeline that uses an improved version of CM for generating well-connected clusters
ColabFold
Copy of colabfold. Adding options to realign the retrieved sequences from MMSeqs2
CS125Fall20QuizPrep
A repo where I will post questions that summarize prior week's contents to help students prepare for the next week's quiz.
EMMA
an ensemble usage of MAFFT-linsi --add on large datasets
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
VireTap
A 03-713 Bioinformatics Practicum project. It focuses on virus transcriptome detection of a given diseased model (i.e. human cancer) using RNA-seq data, and in the future, some further analyses including SNP analysis etc.
WITCH
WITCH is a multiple sequence alignment method that uses multiple weighted HMMs to align unaligned sequences and find consensuses.
c5shen's Repositories
c5shen/WITCH
WITCH is a multiple sequence alignment method that uses multiple weighted HMMs to align unaligned sequences and find consensuses.
c5shen/EMMA
an ensemble usage of MAFFT-linsi --add on large datasets
c5shen/GPU-BLAST-plus
A class project for CS508 from UIUC to implement the classic BLAST algorithm using different GPU computing techniques.
c5shen/CS125Fall20QuizPrep
A repo where I will post questions that summarize prior week's contents to help students prepare for the next week's quiz.
c5shen/VireTap
A 03-713 Bioinformatics Practicum project. It focuses on virus transcriptome detection of a given diseased model (i.e. human cancer) using RNA-seq data, and in the future, some further analyses including SNP analysis etc.
c5shen/kmSortFile
k-means clustering sorting to heatmap display
c5shen/cm_pipeline
Pipeline that uses an improved version of CM for generating well-connected clusters
c5shen/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).
c5shen/BSCAMPP_code
New Code for EPA-ng-BSCAMPP
c5shen/ColabFold
Copy of colabfold. Adding options to realign the retrieved sequences from MMSeqs2
c5shen/CommonLibSSE-NG
This is a reverse engineered library for Skyrim Special Edition and Skyrim VR.
c5shen/connectivity-modifier
better community detection through small cuts
c5shen/constrained-INC
A copy of constrained-INC (INC) from steven-le-thien
c5shen/contrained-MAGUS
Graph Clustering Merger
c5shen/crucible
c5shen/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.
c5shen/DEPP
c5shen/HMMerge
c5shen/learnMSA
Learning and Aligning Large Protein Families (MSA-HMM)
c5shen/llm.c
LLM training in simple, raw C/CUDA
c5shen/MAGUS-legacy
A legacy version of MAGUS that I will personally work on
c5shen/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).
c5shen/njmerge
A tool for divide-and-conquer tree estimation via a shared distance matrix
c5shen/Novelty
Codes for computing novelty indicators.
c5shen/OrthoFinder
Phylogenetic orthology inference for comparative genomics
c5shen/PLUSplacer
c5shen/sepp
Ensemble of HMM methods (SEPP, TIPP, UPP)
c5shen/soulsy
A minimal Souls-like HUD for Skyrim AE & SE. SKSE plugin.