Description of available pipelines

  • Quality control and denoising (fastqc, multiqc, fastq-mcf, Dada2, Deblur). 
  • Taxonomic classification (QIIME2, DADA2, Mothur) 
  • Determination and graphical representation of alpha diversity (Shannon, Simpson, Cao1, Unifrac, etc.) 
  • Determination and graphical representation of beta diversity (PCoA, ANOSIN, PERMANOVA, etc.) 
  • Statistical comparisons between groups (DESeq2, ANCOM) 
  • Inference of functional profile (PICRUSt) 
  • Quality control (fastqc, multiqc, fastq-mcf) 
  • Taxonomic classification (Kraken2, MetaPhlAn4) 
  • Determination and graphical representation of alpha diversity (Shannon, Simpson, Cao1, Unifrac, etc.) 
  • Determination and graphical representation of beta diversity (PCoA, ANOSIN, PERMANOVA, etc.) 
  • Statistical comparisons between groups (DESeq2) 
  • Functional profiling (HUMAnN3) 
  • Quality control (fastqc, multiqc, fastq-mcf) 
  • Quantification (Kallisto, Salmon, HiSat2, HT-Seq, etc.) 
  • Exploratory analyses (correlation analysis, hierarchical clustering, PCA) 
  • Differential expression analysis (DESeq2, edgeR, Sleuth) 
  • Differential splicing (StringTie, tablemaker, DEXseq, Ballgown) 
  • Gene ontology and pathway analyses (clusterProfiler, topGO, GOseq) 
  • Postprocessing: volcano plots, UpSet plots, Chromosomal distribution of DE genes, boxplots, etc. 
  • Quality control (fastqc, multiqc, fastq-mcf) 
  • Quantification (CellRanger, Kallisto, Alevin, STAR-solo, etc.) 
  • Exploratory analysis (Voyager) 
  • Normalization, cell clustering (UMAP, tSNE) with Seurat, ScanPy, SquidPy, Giotto, etc.)  
  • Differential expression analysis (DESeq2, edgeR, Wilcoxon test). 
  • Trajectory analysis (TradeSeq, Monocle1, Scuba, éclair, etc.) 
  • Gene ontology and pathway analyses (clusterProfiler, topGO, GOseq) 
  • Postprocessing: volcano plots, UpSet plots, boxplots, etc.