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VG转录组分析桌面软件
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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
Text Format Converts
dos2unix
unix2dos
Text Manipulation
Convert
Concatenate datasets
Cut
Paste
Select first
Join, Compare
Relational join
Compare two Datasets
NGS: Fastq/Fasta Tools
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
NGS: Ensembl Files Toolkit
Get GO and KEGG Annotation
Convert Ensembl BioMart GO annotation to VGsoft required format
Perform KEGG annotation
Preprocess for Quantification Analysis
Preprocess reference(fasta) and annatation(gtf) from Ensembl
Preprocess cDNA fasta file from Ensembl
Preprocess protein fasta file from Ensembl
NGS: I. Quantification by Transcript Alignment Based (deprecated)
Alignment against Transcripts
Contains:
Build Transcripts Index
RSEM and eXpress transcript index
Align and Estimate
RSEM: Align and Estimate Abundance
eXpress: Align and Estimate Abundance
Merge Estimates
merge RSEM estimates
merge eXpress estimates
NGS: II. Quantification by Transcript Alignment Free
Alignment Free
Contains:
Build Transcripts Index
Kallisto transcript index
Estimate
Kallisto quant
Merge Estimates
merge Kallisto estimates
NGS: III. Quantification by Genome Alignment
Alignment against Genome
Contains:
Build Genome Index
HISAT2 reference index
Spliced Aligner
HISAT2
Estimate
Cuffquant
Cuffnorm
DE By Cuffdiff
Cuffdiff
Parse Cuffdiff results
NGS: RNA-Seq Quality Control
Gene Body Coverage (BAM)
RPKM Saturation
Read Distribution
NGS: RNA Assembly & AS Analysis
Knowledge-based Assembly
Cufflinks
New Transcripts
Cuffcompare
Cuffmerge
Filter Cuffcompare output GTF
Alternative Splicing
ASprofile
NGS: Call SNPs & InDels
BWA -> GATK Pipeline
Contains
Build Reference Index
BWA reference index
BWA Mapping
Map with BWA
Map with BWA-MEM
SNPs/InDels Caller
GATK Unified Genotyper
VCF Filters
Filter VCF File
VCF Stat
Statistics Variation Information
NGS: BAM/SAM Tools
Converts
SAM-to-BAM
BAM-to-SAM
Utils
Filter BAM
Sort BAM
BAM Flagstat
BAM IdxStats
BAM RmDup
Merge sorted BAM Files
Region Depth Coverage
read depth per BED region
read coverage per BED region
NGS: FPKM/TPM Normalization
Gene/Transcript Length
Get gene and isoform length from gtf file
Get gene and isoform length from transcripts fasta file
Normalization: TPM recommended
FPKM normalization
TPM normalization
TMM scaling and FPKM normalization
NGS: Matrix Operations
Utils
Fetch all genes(row names) list from matrix
Retrieve Rows from matrix/tabular file
Transformation
FPKM/TPM matrix log2 transform
Replicates to Sample averages
Matrix Transpose
Merge and Reorder
Merge Matrices
Reorder Matrix columns
Sub-Matrix
Get a sub-Matrix
NGS: RNA-Seq DE Analysis
Differential Expression Analysis
Differential Expression Analysis
Filter and Summary
Filter DE Analysis Result
Summary DE Analysis Result
Utils
Generate sample group file from file header
Retrieve All Diff Genes list
Batch Tools
Batch Mode: Filter DE Analysis Result
Batch Mode: Retrieve Diff Genes list
NGS: RNA-Seq Analysis Toolkits
PCA and PCOA
PCA analysis and plot PCA
PCOA analysis and plot PCOA
3D Scatterplot
Correlation and Distance
Create Sample Correlation Matrix
Generate distance matrix
Make Distance HeatMap
Make Distance Boxplots
Make Density Plot
Heatmap and Hclust Tree
Plot heatmap with tree
Plot hcluster tree
Plot Tree
Visualized Analysis
Plot FPKM/TPM distribution for all samples
FPKM/TPM Boxplot for all samples
FPKM/TPM Scatterplot for two samples
FPKM/TPM Scatterplot for all pair-wise samples
Matrix to gene plots
Plot Venn Diagram
NGS: GO Analysis
Utils
Add GO Annotation
GO level statistic about GO annotation file
Plot GO bar
Report all input Gene->GO Relations
Print the hierarchy below GO Term
Enrichment
GO Enrichment Analysis
Plot GO Enrichment
GO Enrichment Bar Plot
Summary GO Enrichment
Graph
Plot Enriched GO DAG Grapth
Plot GO lineage DAG Grapth
Plot GO lineage DAG Grapth with Pvalue
Batch Tools
Batch Mode: Add GO Annotation
Batch Mode: GO Enrichment Analysis
Batch Mode: Plot GO Enrichment
Batch Mode: GO Enrichment Bar Plot
Batch Mode: Plot Enriched GO DAG Grapth
NGS: KEGG Analysis
Utils
Add KEGG Annotation
KEGG statistic about KEGG annotation file
Enrichment
KEGG Enrichment Analysis
Plot KEGG Enrichment
Summary KEGG Enrichment
Batch Tools
Batch Mode: Add KEGG Annotation
Batch Mode: KEGG Enrichment Analysis
Batch Mode: Plot KEGG Enrichment
NGS: WGCNA Analysis
Preprocess
Filter samples and genes with too many missing entries
Plot sample hierarchical cluster tree
Analysis of scale free topology for multiple soft thresholding powers
Analysis
WGCNA Analysis - network construction and module detection
Visualization
Plot Genes Topological Overlap Matrix Heatmap
MDS Analysis and plot MDS
About Modules
Get Module Eigengenes
Plot module eigengene adjacency heatmap
Plot module cluster tree
Phenotype Association
Module eigengene correlation analysis with phenotype
NGS: Network Analysis
Expression Pattern
Subcluster Expression Analysis
Network
Plot Genes subClusters Network
Plot Gene Regulatory Network
For Cytoscape: Co-expression Network Analysis
For Cytoscape: retrieve pairs from Matrix
data_stat
univariate
Student T-test
Wilcoxon-test
Analysis of variance
Kruskal-Wallis rank sum test
multivariate
Support vector machine
Random forest
oths
logistic regression on two groups
Roc analysis
Blast Tools
Get Sequences from fasta file
Blast: pairwise alignment output
NCBI BLAST+ blastn
NCBI BLAST+ blastp
NCBI BLAST+ blastx
NCBI BLAST+ tblastn
NCBI BLAST+ tblastx
Blast: tabular output
NCBI BLAST+ blastn(tabular)
NCBI BLAST+ blastp(tabular)
NCBI BLAST+ blastx(tabular)
NCBI BLAST+ tblastn(tabular)
NCBI BLAST+ tblastx(tabular)
Image File Converters
Convert PDF-to-PNG
Convert PDF-to-TIFF
Convert PDF-to-JPG