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/seqviz
DNA sequence viewer supporting custom, GenBank, FASTA, NCBI accession, and iGEM input.
liupfskygre/MetaCHIP
Horizontal gene transfer (HGT) identification pipeline
liupfskygre/pangenomics
Scripts and utilities for pangenomic/phylogenomic analysis of prokaryotic genomes. Scripts for the analysis of genomic features such as C-ARSC, N-ARSC, and intergenic spacer lengths are also included.
liupfskygre/keras
Deep Learning for humans
liupfskygre/FUNGuild
FUNGuild: parsing OTUs into functional guilds
liupfskygre/CAP2
liupfskygre/gatk
Official code repository for GATK versions 4 and up
liupfskygre/metagenomics-workshop-1
Metagenomics Workshop
liupfskygre/Coelho2021_GMGCv1
liupfskygre/viralrecall
Detection of NCLDV signatures in 'omic data
liupfskygre/CrisprOpenDB
liupfskygre/R-statistics-ecology
statistics and ecology related topic and scripts
liupfskygre/MARVEL
MARVEL: Metagenomic Analyses and Retrieval of Viral ELements
liupfskygre/What_the_Phage
WtP: Phage identification via nextflow and docker or singularity
liupfskygre/rnaseqc
Fast, efficient RNA-Seq metrics for quality control and process optimization
liupfskygre/MGV
Supporting code for uncultivated gut virus manuscript
liupfskygre/mmgenome2
Tools for extracting individual genomes from metagenomes
liupfskygre/vamb
Variational autoencoder for metagenomic binning
liupfskygre/vpf-tools
Virus Protein Family tools
liupfskygre/microeco
An R package for data analysis in microbial community ecology
liupfskygre/run_dbcan
Run_dbcan V2, using genomes/metagenomes/proteomes of any assembled organisms (prokaryotes, fungi, plants, animals, viruses) to search for CAZymes.
liupfskygre/ggsci
🦄 Scientific journal and sci-fi themed color palettes for ggplot2
liupfskygre/ggupset
Combination matrix axis for 'ggplot2' to create 'UpSet' plots
liupfskygre/R-plot-sda
plotting, statistics and R
liupfskygre/gdown
Download a large file from Google Drive (curl/wget fails because of the security notice).
liupfskygre/NetCoMi
Network Comparison for Microbial Compositional Data
liupfskygre/ggvenn
Venn Diagram by ggplot2, with really easy-to-use API.
liupfskygre/virmap
liupfskygre/PropagAtE
liupfskygre/mOTUs_v2
motus - a tool for marker gene-based OTU (mOTU) profiling