OUM (OmicsBox User Manual)

Space Details:

Key	OUM
Name	OmicsBox User Manual
Description
Created by	557058:bb255439-d0e0-406b-a09b-e26518cad97e (24.04.2024)

Available Pages:

• OmicsBox User Manual
• Welcome
• Software Installation and Activation
  • Technical Requirements and Support Services
  • Uninstalling OmicsBox
• OmicsBox Application
  • Preferences
  • Cloud Computation and Storage
  • User Interface
  • File Menu
  • View Menu
  • Help Menu
  • General Tools
  • FASTA Tools
  • FASTQ Tools
    • 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
  • 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 Completeness Assessment
  • Genome Assembly Quality Assessment
  • Repeat Masking
  • Gene Finding
    • Eukaryotic Gene Finding by AUGUSTUS
    • Prokaryotic Gene Finding by Glimmer
  • Multi-Locus Sequence Typing (MLST)
  • Module Genetic Variation
  • VCF Tools
    • Merge VCFs
    • Extract VCFs
  • Variant Calling
    • Variant Calling using BCFtools
    • Variant Calling using Freebayes
  • Variant Filtering
    • General Variant Filtering
    • dDocent Variant Filtering Pipeline
  • Phasing and Imputation
  • Variant Annotation
  • Population Structure Analysis
  • Genome Wide Association Study
    • Gene Set Analysis with MAGMA
  • Module Transcriptomics
  • Load
  • 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 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 Trajectory Inference
    • Single Cell RNA-Seq Monocle3 Autocorrelation
    • Single Cell RNA-Seq Differential Expression Analysis
  • Long Read Data Analysis Tools
    • 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
  • Load Data
  • BLAST
    • Create Blast Database
  • InterProScan
  • Gene Ontology Mapping
  • Gene Ontology Annotation
  • Functional Annotation with EggNOG Mapper
  • Functional Analysis (Side Panel)
    • GO-Slim
    • Enrichment Analysis
    • Fisher Exact Test
    • Gene Set Enrichment Analysis (GSEA)
    • Combined Pathway Analysis
    • Comined Graph
  • Gene Ontology Graphs
  • Selection
  • Tools
  • Subcellular Localization Prediction with PSORTb
  • Rfam RNA Family Search
  • Export
  • Quick Start
  • Module Metagenomics
  • Taxonomic Classification
  • Contaminant Removal
  • Metagenome Assembly
  • MetaGenome Gene Prediction
  • Functional Annotation with EggNOG
  • Comparative Analysis
  • rRNA Removal with SortMeRNA
• How to cite OmicsBox