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/metascan
Metabolic scanning and annotation of Metagenomes
liupfskygre/Metagenome_Assembly
liupfskygre/serratus
Ultra-deep search for novel viruses
liupfskygre/iceberg
❄️🐻 Climate change and cross-species viral transmission
liupfskygre/CHERRY
Host prediction
liupfskygre/ImageGP
liupfskygre/Cenote-Taker2
Cenote-Taker2: Discover and Annotate Divergent Viral Contigs
liupfskygre/metapop
A pipeline for the macro- and micro-diversity analyses and visualization of metagenomic-derived populations
liupfskygre/CoolBox
Jupyter notebook based genomic data visualization toolkit.
liupfskygre/iDIRECT
liupfskygre/parallel-meta-suite
liupfskygre/PhaGCN
GCN classifier for phage taxanomy classification
liupfskygre/pymol-open-source
Open-source foundation of the user-sponsored PyMOL molecular visualization system.
liupfskygre/mamba
The Fast Cross-Platform Package Manager
liupfskygre/RoseTTAFold
This package contains deep learning models and related scripts for RoseTTAFold
liupfskygre/bedtools2
bedtools - the swiss army knife for genome arithmetic
liupfskygre/carveme
CarveMe: genome-scale metabolic model reconstruction
liupfskygre/PlasForest
A random forest classifier to identify contigs of plasmid origin in contig and scaffold genomes
liupfskygre/zoonotic_rank
Code and data used in Mollentze et al. (2021) "Identifying and prioritizing potential human-infecting viruses from their genome sequences".
liupfskygre/matrixStats
R package: Methods that Apply to Rows and Columns of Matrices (and to Vectors)
liupfskygre/NetworkNullHPC
OTU co-occurrence network inferrence base on null model for HPC
liupfskygre/virus_in_metagenome
log of virus-phage analysis in metagenomes contigs, collaboration with Josue
liupfskygre/alphafold
Open source code for AlphaFold.
liupfskygre/R_plot_ggplot2_examples
R scripts for viz and plot, collection
liupfskygre/CAT
CAT/BAT: tool for taxonomic classification of contigs and metagenome-assembled genomes (MAGs)
liupfskygre/cgview
CGView is a Java package for generating high-quality, zoomable maps of circular genomes.
liupfskygre/plyranges
A grammar of genomic data transformation
liupfskygre/VAPiD
VAPiD: Viral Annotation and Identification Pipeline
liupfskygre/OWC_metaT_analysis2019
metaT_analysis of the OWC wetland dataset, 2019, mapping, quantification,
liupfskygre/CRISPRidentify