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软件介绍
VG多样性分析桌面软件
多样性数据管理和分析系统
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OTU聚类和分类学注释流程操作说明
生成分组信息文件操作说明
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模块帮助文档
Basic Tools
Copy File to project
Link File to project
Convert One of XLS Sheet to tabular txt file ( !!rather slow, big data not recommended )
Text Format Converts
dos2unix
unix2dos
Text Manipulation
Convert
Concatenate datasets
Cut
Paste
Select first
Join, Compare
Relational join
Compare two Datasets
NGS: Amplicon Sequences Process
Automation Analysis
One Step Automate Analysis: 1.QC 2.Assembly 3.OTU Cluster
x32. Make OTU Table by Usearch Pipline
Fastq Summary
FASTQ Summary Statistics
Draw nucleotides distribution chart
Draw quality score boxplot
Fastq Quality Control
Trimmomatic SE(single-end)
Trimmomatic PE(paired-end)
Fasta Tools
Convert FASTQ to FASTA
Compute sequence length
Filter sequences by length
Fasta Statistics
Merge Fastq Pairs
Using FLASH to merge paired-end reads
OTU Cluster and Taxonomy (x64 full set)
Open Source Tool: Vsearch
Vsearch: otu cluster and mapping
Vsearch-sintax
Others (x32 training set)
Usearch otu cluster and mapping
16S reference-based chimera detection using the UCHIME algorithm
RDP classifier assign taxonomy
Usearch utax command assign taxonomy
NGS: Amplicon Standard Analysis
Utils
Generate sample group file
Generate sample group file from file header
Biom-To-Table
Table-To-Biom
Convert table to biom with taxonomy assignment information
Summary the representation of taxonomic groups
Merge Samples Abundance in same Group
Normalize the OTU Table
Alaph Diversity
Alpha Diversity Index calculator
Calculate Faith's Phylogenetic Diversity
Plot samples rarefaction curves
Plot Shannon-Wiener rarefaction curves
Plot groups rarefaction curves
Plot Rank Abundance curves
Plot Species Accumulation curves
Community Bar Plot
Community Pie Plots
Beta Diversity
PCA analysis and plot PCA
3D Scatterplot
Plot heatmap with tree
Generate distance matrix
PCOA analysis and plot PCOA
NMDS analysis and plot NMDS
Plot hcluster tree
H Cluster Bar Plot
Plot Venn Diagram
NGS: Amplicon Advanced Analysis
Utils
Creates a subsampled OTU table
Summary OTU Table
Merge Samples Abundance in one Group
Get a sub-OTU Table
Select top N highest abundance rows in OTU/Taxon Table
Filter OTU/Taxon Table
Differential Abundance Analysis
Mothur-metastats command
Filter Mothur-metastats Analysis Result
Metastats Analysis ( !!rather slow, not recommended )
Wilcoxon Test
Anova Test
LEfSe Analysis
LEfSe formatting
LDA Effect Size (LEfSe) Analysis
Filter LEFSe result
Plot LEfSe Results
Plot Cladogram
Plot Differential Features
UniFrac Analysis
Select representative seqs
Construt phylogenetic tree by OTU represent seqs
Get Unifrac Distance Matrix
Plot Tree
Make Distance HeatMap
Make Distance Boxplots
Category Comparison Techniques
Runs the ANOSIM statistical method
Runs the adonis statistical method
Beta Diversity
PLS-DA and plot Plsda
Plot Venn Diagram
Taxonomy Tree
Single sample Taxonomy analysis tree
Multi samples Taxonomy analysis tree
Plot Krona Pie Chart
NGS: Amplicon Function Analysis
misc
Filter illegall characters in OTU/Taxon/Function Table
16S GG13.5 PICRUSt
1. Get Greengenes13.5 closed reference OTU Table
2. Get Greengenes13.5 closed reference OTU Table
PICRUSt: Normalize the relative abundance of each OTU
PICRUSt: Predict Metagenome
PICRUSt: Categorize KEEG Pathways/COG Category
16S Others
Tax4Fun
FAPROTAX
BugBase
Fungi
FUNGulid
NGS: ENV Correlation Analysis
Generate distance matrix
Correlation coefficient analysis
Mantel-Test
VPA(Variation Partition Analysis)
RDA/CCA Analysis
DCA Analysis
RDA Analysis
CCA Analysis
src2sink
SourceTracker
For Cytoscape: Network Analysis
Utils
Merge Matrices
Matrix Transpose
Network
Subcluster Analysis
For Cytoscape: Co-occurrence Network Analysis
Create Correlation Matrix
For Cytoscape: retrieve pairs from Matrix
Statistical Analysis
Univariate Statistical Analysis
Student T-test
Wilcoxon-test
Analysis of variance
Kruskal-Wallis rank sum test
Multivariate Statistical Analysis
Support vector machine
Random forest
Other Tools
logistic regression on two groups
Roc analysis
MISC Tools
Process Tax Assign file
Get Sequences from fasta file
Combine FASTA and QUAL
Image File Converters
Convert PDF-to-PNG
Convert PDF-to-TIFF
Convert PDF-to-JPG
Convert SVG-to-PDF