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OmicsBox User Manual

Single Cell Data Analysis Tools

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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
- 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
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Single Cell Data Analysis Tools

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