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User Manual
System Requirements
Software Installation and Activation
Uninstalling OmicsBox
OmicsBox Modules
Module Functional Analysis
Quick Start
Load Data
InterProScan
Gene Ontology Mapping
Gene Ontology Annotation
Functional Analysis (Side Panel)
GO-Slim
Enrichment Analysis
Fisher Exact Test
Gene Set Enrichment Analysis (GSEA)
Comined Graph
Selection
Tools
Export
Functional Annotation with EggNOG Mapper
BLAST
Create Blast Database
Rfam RNA Family Search
Subcellular Localization Prediction with PSORTb
Gene Ontology Graphs
Combined Pathway Analysis
Module Genome Analysis
DNA-Seq de Novo Assembly
ABySS
SPAdes
Flye
DNA-Seq Alignment
DNA-Seq BWA
DNA-Seq Bowtie 2
DNA-Seq Polishing
Genome Assembly Quality Assessment
Repeat Masking
Gene Finding
Eukaryotic Gene Finding by AUGUSTUS
Prokaryotic Gene Finding by Glimmer
Genome Browser
Multi-Locus Sequence Typing (MLST)
Module Transcriptomics
RNA-Seq de novo Assembly
Completeness Assessment
Predict Coding Regions
Clustering
RNA-Seq Alignment
RNA-Seq STAR
RNA-Seq BWA
BAM File Quality Control
Create Count Table
Gene-level Quantification
Transcript-level Quantification
Differential Expression Analysis
Pairwise Differential Expression Analysis
Time Course Expression Analysis
Pairwise Differential Expression Analysis (Without Replicates)
Coding Potential
Single Cell Data Analysis Tools
Single Cell RNA-Seq Quantification
Single-cell RNA-Seq Filtering
Single-cell RNAseq Clustering
scRNA-Seq Trajectory Inference Analysis
Single Cell RNA-Seq Differential Expression Analysis
Long Read Data Analysis Tools
Long-Read Alignment with Minimap2
Transcripts Identification with IsoSeq3
Long-Read Isoform Definition with FLAIR
Long-Read Characterization with SQANTI3
Module Genetic Variation
Variant Calling
Variant Calling using BCFtools
Variant Calling using Freebayes
Variant Filtering
Variant Annotation using VEP
GWAS with GAPIT3
GWAS Gene Set Analysis with MAGMA
Module Metagenomics
Taxonomic Classification
Contaminant Removal
Metagenome Assembly
MetaGenome Gene Prediction
Functional Annotation with EggNOG
Comparative Analysis
rRNA Removal with SortMeRNA
General Tools
Tag Statistics
FASTQ Tools
FASTQ Quality Check
Long Read Quality Assessment with LongQC
FASTQ Preprocessing
Barcode Splitter
Venn Diagram
Fasta Tools
BAM Tools
Merge FastQ/A Files
Demultiplexing with Cutadapt
Workflows
OmicsBox Application
Preferences
Cloud Storage
User Interface
File Menu
View Menu
Help Menu
Troubleshooting
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Module Genetic Variation
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