Transposase-accessible chromatin workflow for ATAC-Seq data. The workflow incorporates steps for quality control assessment, alignment, peak-calling, annotation and epigenetic variability inference between conditions. Elaborates a final interactive report to explore the results.
Identification of gene fusions and other structural events in RNA sequencing data. Integrates all the steps for quality control assessment, alignment, identification of aberrant transcripts and interactive visualization of results.
Evaluation of microbial diversity and differential abundance analysis. An end-to-end pipeline to perform quality controls, rarefactions, abundance estimation, alpha and beta diversity as well as visualization and statistical tests for these components.
Create beta diversity ordination plots using Phyloseq.
Create scatter-plots using Plotly.
RNA-Seq gene fusion detection using Arriba.
Report RNA-Seq quality control metrics and bias estimations using Qualimap2.
QIIME Method to visualize taxonomy with an interactive bar plot.
Fast preranked gene set enrichment analysis (GSEA) using fgsea.
Annotate ChIP-seq peaks using ChIPseeker
Create an interactive abundance visualization using Krona.
Annotate gene features, CpG islands or regulatory sequences using annotatr.