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OmicsBox User Manual

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OmicsBox User Manual

Welcome
Setup
Setup
OmicsBox Application
OmicsBox Application
- Application Overview
- Preferences
- Cloud Computation and Storage
- User Interface
  User Interface
- General Tools
  General Tools
  - Overview
  - FASTA Tools
  - FASTQ Tools
    FASTQ Tools
    
    Overview
    
    FastQC Quality Check
    
    Fastq Preprocessing with Trimmomatic
    
    Long Read Quality Assessment with LongQC
    
    Merge FastQ and FastA Files
    
    Barcode Splitter
    
    Demultiplexing with Cutadapt
  - BAM Tools
  - Genome Browser
  - Venn Diagram
- Workflows
OmicsBox Modules
OmicsBox Modules
- Modules Overview Modules Overview
  Table of contents
  - Five modules to easily process large and complex data sets
- Module Genome Analysis
  Module Genome Analysis
  - Genome Analysis Overview
  - DNA-Seq de Novo Assembly
    DNA-Seq de Novo Assembly
    
    Overview
    
    ABySS
    
    SPAdes
    
    Flye
  - DNA-Seq Alignment
    DNA-Seq Alignment
    
    Overview
    
    DNA-Seq BWA
    
    DNA-Seq Bowtie 2
  - DNA-Seq Polishing
  - Genome Completeness Assessment
  - Genome Assembly Quality Assessment
  - Repeat Masking
  - Gene Finding
    Gene Finding
    
    Overview
    
    Eukaryotic Gene Finding by AUGUSTUS
    
    Prokaryotic Gene Finding by Glimmer
  - Multi-Locus Sequence Typing (MLST)
- Module Genetic Variation
  Module Genetic Variation
  - Genetic Variation Overview
  - VCF Tools
    VCF Tools
    
    Overview
    
    Merge VCFs
    
    Extract VCFs
  - Variant Calling
    Variant Calling
    
    Overview
    
    Variant Calling using BCFtools
    
    Variant Calling using Freebayes
  - Variant Filtering
    Variant Filtering
    
    Overview
    
    General Variant Filtering
    
    dDocent Variant Filtering Pipeline
  - Phasing and Imputation
  - Variant Annotation
  - Population Structure Analysis
  - Genome Wide Association Study
    Genome Wide Association Study
    
    Overview
    
    Gene Set Analysis with MAGMA
- Module Transcriptomics
  Module Transcriptomics
  - Transcriptomics Overview
  - Load
  - RNA-Seq de novo Assembly
  - Completeness Assessment
  - Predict Coding Regions
  - Clustering
  - RNA-Seq Alignment
    RNA-Seq Alignment
    
    Overview
    
    RNA-Seq STAR
    
    RNA-Seq BWA
  - BAM File Quality Control
  - Create Count Table
    Create Count Table
    
    Overview
    
    Gene-level Quantification
    
    Transcript-level Quantification
  - Differential Expression Analysis
    Differential Expression Analysis
    
    Overview
    
    Pairwise Differential Expression Analysis
    
    Time Course Expression Analysis
    
    Pairwise Differential Expression Analysis (Without Replicates)
  - Coding Potential
  - Single Cell Data Analysis Tools
    Single Cell Data Analysis Tools
    
    Overview
    
    Single Cell RNA-Seq Quantification
    Single Cell RNA-Seq Quantification
    
    Overview
    
    Single-cell RNA-Seq Count Matrix
    
    Single-cell RNA-Seq Filtering
    
    Merge Single Cell Counts
    
    Single Cell RNA-Seq Clustering
    
    Single Cell UMAP/tSNE Viewer
    
    Single Cell RNA-Seq Cell Type Prediction
    Single Cell RNA-Seq Cell Type Prediction
    
    Overview
    
    Single Cell RNA-Seq Cell Type Prediction with SingleR
    
    Single Cell RNA-Seq Cell Type Prediction with CellKB
    
    Single Cell RNA-Seq Trajectory Inference
    Single Cell RNA-Seq Trajectory Inference
    
    Overview
    
    Single Cell RNA-Seq Monocle3 Autocorrelation
    
    Single Cell RNA-Seq Differential Expression Analysis
  - Long Read Data Analysis Tools
    Long Read Data Analysis Tools
    
    Long Read Data Analysis Overview
    
    Long-Read Alignment
    
    PacBio-Based Identification with IsoSeq
    
    Identification and Quantification with FLAIR
    
    Identification and Quantification with IsoQuant
    
    Reference-free Isoform Reconstruction
    
    Curation of Long-Read Transcriptomes with SQANTI3
    
    Combining Transcriptomes with TAMA Merge
- Module Functional Analysis
  Module Functional Analysis
  - Functional Analysis Overview
  - Load Data
  - BLAST
    BLAST
    
    Overview
    
    Create Blast Database
  - InterProScan
  - Gene Ontology Mapping
  - Gene Ontology Annotation
  - Functional Annotation with EggNOG Mapper
  - Functional Analysis (Side Panel)
    Functional Analysis (Side Panel)
    
    Overview
    
    GO-Slim
    
    Enrichment Analysis
    Enrichment Analysis
    
    Overview
    
    Fisher Exact Test
    
    Gene Set Enrichment Analysis (GSEA)
    
    Combined Pathway Analysis
    
    Comined Graph
  - Gene Ontology Graphs
  - Pathway Browser
  - Selection
  - Tools
  - Subcellular Localization Prediction with PSORTb
  - Rfam RNA Family Search
  - Export
  - Quick Start
- Module Metagenomics
  Module Metagenomics
How to cite OmicsBox

Table of contents

Five modules to easily process large and complex data sets

OmicsBox Modules

Five modules to easily process large and complex data sets

From raw reads to functional insights fast and easy

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