Pinned Repositories
amplicon
Statistics and visualization for amplicon data
bcbb
Incubator for useful bioinformatics code, primarily in Python and R
Community-assembly-processes-and-species-coexistences-of-agricultural-soils-microbiome
Methanoliparum_MS_code
OWC_metaT_analysis2019
metaT_analysis of the OWC wetland dataset, 2019, mapping, quantification,
SgVG_supraglacial_virome
scripts for the GGV projects
Tools-Microbiome-Analysis
A list of R environment based tools for microbiome data exploration, statistical analysis and visualization
virus_in_metagenome
log of virus-phage analysis in metagenomes contigs, collaboration with Josue
liupfskygre's Repositories
liupfskygre/SgVG_supraglacial_virome
scripts for the GGV projects
liupfskygre/BASALT
liupfskygre/bindash
Fast and precise comparison of genomes and metagenomes (in the order of terabytes) on a typical personal laptop
liupfskygre/bioinformatics-snakemake-pipelines
Collection of Snakemake pipeline for commin bioinformatics tasks
liupfskygre/Bracken
Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.
liupfskygre/cobra
A tool to raise the quality of viral genomes assembled from short-read metagenomes via resolving and joining of contigs fragmented during de novo assembly.
liupfskygre/CRISPRCasTyper
CCTyper: Automatic detection and subtyping of CRISPR-Cas operons
liupfskygre/EasyAmplicon
Easy Amplicon data analysis pipeline
liupfskygre/FastAAI
liupfskygre/gapseq
Informed prediction and analysis of bacterial metabolic pathways and genome-scale networks
liupfskygre/genomescope2.0
Reference-free profiling of polyploid genomes
liupfskygre/gggenomes
A grammar of graphics for comparative genomics
liupfskygre/hdWGCNA
High dimensional weighted gene co-expression network analysis
liupfskygre/hh-suite
Remote protein homology detection suite.
liupfskygre/KEGGCharter
A tool for representing genomic potential and transcriptomic expression into KEGG pathways
liupfskygre/LucaProt
LucaProt: A novel deep learning framework that incorporates protein amino acid sequence and structure information to predict protein function.
liupfskygre/metaGEM
:gem: An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data
liupfskygre/Metagenome_Assembly
liupfskygre/metascan
Metabolic scanning and annotation of Metagenomes
liupfskygre/MLP_oil_virus_analysis
virus analysis of MLP oil degradation
liupfskygre/oneliners
Useful bash one-liners for bioinformatics.
liupfskygre/PhaGCN2.0
liupfskygre/PPanGGOLiN
Build a partitioned pangenome graph from microbial genomes
liupfskygre/qcmi
To explore biotic associations of microbes at the community level. See the detailed package tutorial (https://joshualiuxu.github.io/).
liupfskygre/RCrashCourse_Book
A GitBook version of the R Crash Course self-tutorials: https://colauttilab.github.io/RCrashCourse
liupfskygre/riboviria.org
Source code for riboviria.org
liupfskygre/serratus
Ultra-deep search for novel viruses
liupfskygre/taxonium
A tool for exploring very large trees in the browser
liupfskygre/taxonkit
A Practical and Efficient NCBI Taxonomy Toolkit, also supports creating NCBI-style taxdump files for custom taxonomies like GTDB/ICTV
liupfskygre/Wu_dn_pure_culture