Softwares/Tools Development

2023 - 2024

  • methNext A NextFlow pipeline to analyse DNA methylation data from different sequencing platforms, Illumina, Twist, Nanopore, PacBio

Languages: Nextflow, R, python, Singularity/Apptainer, Docker, Conda, Rmarkdown, Quarto

Developer: Jyotirmoy Das

 Github repo

  • TranscriptR - a shiny‐based transcriptome analysis and visualisation

Languages: Shiny, R, Snakemake, Docker, Bioconductor, Rmarkdown, Quarto

Developer: Jyotirmoy Das
Co-developers: Massimiliano Volpe, Marco Miralto

 Github repo

  • MethylRv2 - a single shiny solution from sequencer data to pathway analysis

Languages: Shiny, R, Docker, Singularity/Apptainer, Bioconductor, Rmarkdown, Quarto

Developer: Jyotirmoy Das
Co-developers: Massimiliano Volpe, Marco Miralto

https://zenodo.org/badge/DOI/10.5281/zenodo.11105017.svg  Github repo  Add to Mendeley

2022 - 2023

  • MethylR - a single shiny solution from sequencer data to pathway analysis

Languages: Shiny, R, Docker, Singularity/Apptainer, Bioconductor, Quarto, Jupyter

Developer: Jyotirmoy Das
Co-developers: Massimiliano Volpe

https://zenodo.org/badge/DOI/10.5281/zenodo.11105017.svg  Github repo  Add to Mendeley

2020 -2021

  • ComplexPCA - a ggplot PCA with complex annotation

Languages: R, ggplot2, Bioconductor

Developer: Jyotirmoy Das

https://zenodo.org/badge/DOI/10.5281/zenodo.11104257.svg  Github repo  Add to Mendeley

2019 -2020

  • Alveolar‐Cell‐Type‐Deconvolution - DNA methylome‐based validation of induced sputum as an effective protocol to study lung immunity: construction of a classifier of pulmonary cell types

Languages: R, Bioconductor

Developer: Jyotirmoy Das

https://zenodo.org/badge/DOI/10.5281/zenodo.11103984.svg  Github repo  Add to Mendeley

  • Image‐Processing‐MATLAB - Acquired time lapse images from the IncuCyte® and processed with MATLAB to create a time‐lapse video of one particular aggregate of bacteria

Languages: MATLAB

Developer: Jyotirmoy Das

https://zenodo.org/badge/DOI/10.5281/zenodo.11104952.svg  Github repo  Add to Mendeley

Community works

2020 - 2024

  • gms‐artic - A Nextflow pipeline for running the ARTIC network’s fieldbioinformatics tools.

Languages: Nextflow, python, Conda, Docker, Singularity/Apptainer, Bash, R

Co-developer: Jyotirmoy Das

 Github repo

  • JASEN - Epitypification pipeline for clinical NGS data. Written in NextFlow, Python & Bash.

Languages: Nextflow, python, Conda, Docker, Singularity/Apptainer, Bash, R

Co-developer: Jyotirmoy Das

 Github repo