Workflows

Transcriptomics

Bulk RNAseq Data Processing

Bulk RNA sequencing data processing with the nf-core rnaseq pipeline on Mantle

Differential Gene Expression from Bulk RNAseq

Differential gene expression from bulk RNAseq using Scanpy on Mantle

Visium Data Processing

10x Genomics Visium spatial transcriptomics data processing with the spaceranger count pipeline on Mantle

Visium Spatial Transcriptomics Visualizations

Visualizing results from Visium spatial transcriptomics with Scanpy on Mantle

Element Bases2Fastq Demultiplexing

Demultiplexing Element AVITI base calls with the Bases2Fastq pipeline on Mantle

Cellular Segmentation Using Cellpose

Cellular segmentation from fluorescence microscopy images using Cellpose on Mantle

Cell Tracking Using SC-Track

Tracking single cells in time-lapse microscopy image sequences using SC-Track

Image Analysis Using CellProfiler

Running CellProfiler pipelines on Mantle

Fluorescence Quantification After Segmentation

Fluorescence quantification after image segmentation using Cellpose

Flow Cytometry File Parsing

Parsing a flow cytometry FCS file using FCSparser

Declarative Plotting

Beyond Matplotlib -- Declarative plotting in Python

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