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Trogenix's Projects

bamtofastq icon bamtofastq

Converts bam or cram files to fastq format and does quality control.

cageseq icon cageseq

CAGE-sequencing analysis pipeline with trimming, alignment and counting of CAGE tags.

configs icon configs

Config files used to define parameters specific to compute environments at different Institutions

cutandrun icon cutandrun

Analysis pipeline for CUT&RUN and CUT&TAG experiments that includes QC, support for spike-ins, IgG controls, peak calling and downstream analysis.

differentialabundance icon differentialabundance

Differential abundance analysis for feature/ observation matrices from platforms such as RNA-seq

ena-metadata-templates icon ena-metadata-templates

TSV and XLSX templates for submitting ENA objects (study, experiment, sample and run) using the ENA-upload-tool

scdownstream icon scdownstream

A single cell transcriptomics pipeline for QC, integration and making the data presentable

scrnaseq icon scrnaseq

A single-cell RNAseq and Multiome pipeline for 10X genomics data

spatialvi icon spatialvi

Pipeline for processing spatially-resolved gene counts with spatial coordinates and image data. Designed for 10x Genomics Visium transcriptomics.

test-datasets icon test-datasets

Test data to be used for automated testing with the nf-core pipelines

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