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/blast-QC
A Quality Control filter and parser for NCBI BLAST XML results.
liupfskygre/OWC_MAGs_Genome_annotation
May use DRAM et al. tools to annotate genomes or MAGs
liupfskygre/dataviz
A book covering the fundamentals of data visualization
liupfskygre/PhiSpy
Prediction of prophages from bacterial genomes
liupfskygre/VirMiner
Scripts to quality control for metagenomic raw data, including removing the adapters, low quality reads, bases or PCR duplicates
liupfskygre/MicrobiomeStatPlot
Interpretation and visualization of microbiome charts
liupfskygre/functional-dark-side.github.io
liupfskygre/homebrew-arb
Homebrew tap for formulae to build ARB (http://www.arb-home.de) and related software.
liupfskygre/Note
liupfskygre/MDM
Workflow and package for network approach to study the role of microbial dark matter (MDM)
liupfskygre/ontology-development-kit
Bootstrap an OBO Library ontology
liupfskygre/d3
Bring data to life with SVG, Canvas and HTML. :bar_chart::chart_with_upwards_trend::tada:
liupfskygre/kofam_scan
CLI tool to annotate genes with KOfam
liupfskygre/sunburstR
R htmlwidget for interactive sunburst plots
liupfskygre/PHISDector
liupfskygre/AcetoScan
AcetoScan - Automated pipeline for the unsupervised analysis of FTHFS amplicon sequencing
liupfskygre/epa-ng
Massively parallel phylogenetic placement of genetic sequences
liupfskygre/woltka
Web of Life Toolkit App
liupfskygre/make_SILVA_db
General procedure for making QIIME 2 compatible SILVA reference files
liupfskygre/sheng-xin-xiao-bai-yu
历史文档备份
liupfskygre/GRiD
Growth Rate Index (GRiD) measures bacterial growth rate from reference genomes (including draft quality genomes) and metagenomic bins at ultra-low sequencing coverage (> 0.2x).
liupfskygre/SMEG
Strain-level Metagenomic Estimation of Growth rate (SMEG) measures growth rates of microbial strains from complex metagenomic dataset
liupfskygre/QIIME2ChineseManual
QIIME 2中文文档(QIIME 2 Chinese Manual)
liupfskygre/raw
The missing link between spreadsheets and data visualization
liupfskygre/MetaPhlAn
MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data
liupfskygre/agricolae
Statistical Procedures for Agricultural Research
liupfskygre/TPMCalculator
TPMCalculator quantifies mRNA abundance directly from the alignments by parsing BAM files
liupfskygre/OrthoFinder
Phylogenetic orthology inference for comparative genomics
liupfskygre/ComplexHeatmap
Make Complex Heatmaps
liupfskygre/RDPTools
Collection of commonly used RDP Tools for easy building