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  • User Manual
    • System Requirements
    • Software Installation and Activation
    • OmicsBox Modules
      • Module Functional Analysis
        • Quick Start
        • Load Data
        • BLAST
          • Create Blast Database
        • 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
        • 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 RNAseq Clustering
          • Single Cell RNA-Seq Differential Expression Analysis
          • Single Cell RNA-Seq Trajectory Inference Analysis
        • Long Read Data Analysis Tools
          • IsoSeq
          • 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
      • 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 Menus
      • File Menu
      • View Menu
      • Help Menu
    • User Interface
      • Cloud Storage
    • Uninstalling OmicsBox
    • Troubleshooting
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