Select Pipelines

ATAC-Seq - Chromatin Accessibility

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.

RNA-Seq - Gene Fusion and Alternative Splicing

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.

Metagenomics - Shotgun Sequencing

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.

Select Tools

Phyloseq - Ordination

Create beta diversity ordination plots using Phyloseq.

Plotly - Scatter-plot

Create scatter-plots using Plotly.

Arriba - Call-fusions

RNA-Seq gene fusion detection using Arriba.

Qualimap2 - RNA-Seq Quality Controls

Report RNA-Seq quality control metrics and bias estimations using Qualimap2.

QIIME2 - Taxa-barplot

QIIME Method to visualize taxonomy with an interactive bar plot.

FGSEA

Fast preranked gene set enrichment analysis (GSEA) using fgsea.

ChIPseeker - peak-annotation

Annotate ChIP-seq peaks using ChIPseeker

Krona - import-text

Create an interactive abundance visualization using Krona.

annotatr - Annotate regions

Annotate gene features, CpG islands or regulatory sequences using annotatr.

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