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ambigram

Detecting complex breakage-fusion-bridge genome rearrangement with Ambigram

ambigram_paper

Ambigram experiment materials: rundown, data, scripts...

bi-matching

cernatax

Detecting ceRNA network mRNA-miRNA-lncRNA triplet axis

cnahap

A germline haplotyping method using tumor allele-specific copy number alteration.

cov_simulation

crustdb_api

crustdb_web

crux

Migrated from old gitlab repository

deephost

This is the repository for DeepHost, a phage host prediction tool.

deeptape-1.0

DeepTAPE is an advanced deep learning tool designed to provide reference diagnostics for SLE, leveraging pre-trained models and supporting custom training within its framework.

fusesv

tools for oncovirus analysis from NGS data

gcnframe

This is a python package for genomics study with a GCN framework.

graphage

This is the repository for GraphPhage, a phage analysis tool that integrates phage and ICE discrimination, phage integration site prediction, phage lifestyle prediction, and phage host prediction.

gutmeta_analysis_scripts

interaction-redundancy

Deciphering microbial interactions with functional redundancy in human microbial community with partial information decomposition.

localhaplotypesolver

localhgt

Detect complete horizontal gene transfer (HGT) event rapidly and accurately from complex metagenomics data.

mam

An in silico approach for predicting the MHC-I-peptide binding affinity, extracting binding motifs, and generating new peptides with high affinity

mhc

mrna

palace

A tool to assemble high-quality phages from metagenomes.

phagescope

PhageScope: a well-annotated bacteriophage database with automatic analysis and visualization

plasmid_api

plasmid_web

pstrain

pstrain-tracer

reptime

A tool for calculating replication timing of WGS data