Welcome to genexplain-platform’s documentation!
Guide
- Introduction
- How it works
- Load data
- Workflows
- Common
- Analyze multiple BAM files to detect DEGs
- ChIP-Seq - Identify and classify target genes
- Compute differentially expressed genes (Affymetrix probes)
- Compute differentially expressed genes (Agilent Tox probes)
- Compute differentially expressed genes (Agilent probes)
- Compute differentially expressed genes (Illumina probes)
- Compute differentially expressed genes using EBarrays
- Compute differentially expressed genes using Hypergeometric test (Affymetrix probes)
- Compute differentially expressed genes using Hypergeometric test (Agilent probes)
- Compute differentially expressed genes using Hypergeometric test (Illumina probes)
- Compute differentially expressed genes using Limma
- Compute differentially expressed genes using Limma and Metadata
- Estimate DEGs with guided linear model analysis
- Find genome variants and indels from RNA-seq_hg19 (single-end)
- Find genome variants and indels from RNA-seq_hg38 (single-end)
- Find genome variants and indels from full-genome NGS_hg19
- Find genome variants and indels from full-genome NGS_hg38
- From multiple BAM files to gene counts
- Full RNAseq analysis with HISAT2, featureCounts and limma (paired-end)
- Full RNAseq analysis with HISAT2, featureCounts and limma (single-end)
- Full RNAseq analysis with HISAT2, htseq-counts and limma (paired-end)
- Full RNAseq analysis with HISAT2, htseq-counts and limma (single-end)
- Full RNAseq analysis with subread, featureCounts and limma (paired-end)
- Full RNAseq analysis with subread, featureCounts and limma (single-end)
- Mapping to GO ontologies and comparison for two gene sets
- Mapping to ontologies (Gene table)
- Mapping to ontologies for multiple gene sets
- Mapping to ontology - select a classification (2 Gene tables)
- Mapping to ontology - select a classification (Gene table)
- Mapping to ontology - select a classification (Multiple Gene tables)
- RNAseq analysis with HISAT2 (paired-end)
- RNAseq analysis with HISAT2 (single-end)
- RNAseq analysis with Subread (paired-end)
- RNAseq analysis with Subread (single-end)
- HumanPSD
- ChIP-Seq - Identify and classify target genes (HumanPSD(TM))
- Get gene list for selected tissue (HumanPSD(TM))
- Get gene list for selected tissue with specified protein classification (HumanPSD(TM))
- Mapping to ontologies (HumanPSD(TM))
- Mapping to ontologies and comparison for two gene sets (HumanPSD(TM))
- Mapping to ontologies for multiple gene sets (HumanPSD(TM))
- Prediction of miRNA binding sites in tissue-specific genes (HumanPSD(TM))
- TRANSFAC(R)
- Analyze SNP list (TRANSFAC(R))_hg19
- Analyze SNP list (TRANSFAC(R))_hg38
- Analyze any DNA sequence (TRANSFAC(R))
- Analyze any DNA sequence for site enrichment (TRANSFAC(R))
- Analyze promoters (TRANSFAC(R))
- ChIP-Seq - Identify TF binding sites on peaks (TRANSFAC(R))
- ChIP-Seq - Identify composite modules on peaks (TRANSFAC(R))
- Combinatorial regulation analysis of genomic or custom sequences
- Identify enriched motifs in cell line specific miRNA promoters (TRANSFAC(R))
- Identify enriched motifs in cell specific promoters (TRANSFAC(R))
- Identify enriched motifs in promoters (TRANSFAC(R))
- Identify enriched motifs in tissue specific miRNA promoters (TRANSFAC(R))
- Identify enriched motifs in tissue specific promoters (TRANSFAC(R))
- Identify enriched motifs in tracks (TRANSFAC(R))
- Identify enriched motifs in tracks with MATCH (TRANSFAC(R))
- Upstream analysis (TRANSFAC(R) and GeneWays)
- TRANSFAC(R) and TRANSPATH(R)
- Common
- RNA-seq
- RNA-seq preprocessing
- Detect differentially expressed gene (DEG)
- Proteomics
- Epigenomics
- MEALR combinatorial regulation analysis
- ChIP-seq
- Sequence analysis
- miRNA
- Microarrays
- Normalize data
- Detect differentially expressed genes
- Discover functional enrichment
- Analyze regulatory regions
- Drug targets
- Genomic variants
- Metabolism
- Popular functions
- Working with the different databases
- Description of analysis methods
- Sequence analysis methods
- SNP matching
- Molecular networks
- Site search on gene set
- Creation of customized profiles
- Construct composite modules
- About the GSEA analysis and the interpretation of the results
- Operations field
- Editing and creating workflows
- Editing and creating diagrams
- Editing and creating JS scripts