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Achievement: Pull Sharkx2Achievement: Arctic Code Vault Contributor

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@frattalab

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SamBryce-Smith/README.md

Hi there 👋

I'm a final year bioinformatics PhD student studying amyotrophic lateral sclerosis (ALS) in the labs of Prof Pietro Fratta & Dr Maria Secrier at UCL. I mainly focus on bioinformatic analysis of alternative polyadenylation with RNA-seq data, especially bulk short-read RNA-seq and Nanopore long-read sequencing. Generally very interested in using sequencing approaches to understand how RNA-binding proteins influence the transcriptome and taking any opportunity to build Snakemake pipelines!

Due to submit PhD thesis in July 2024 - open to job opportunities in Belgium (from October 2024)!

Currently working on:

  • PhD thesis (!)
  • Novel methods for identifying, quantifying and assessing differential usage of polyA sites from bulk RNA-seq data (watch this space!).
  • APAeval - a community project to develop a framework for reproducible benchmarking of bioinformatic algorithms and assess the performance of tools that identify and/or quantify polyA sites from bulk RNA-seq data.

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  1. iRNA-COSI/APAeval iRNA-COSI/APAeval Public

    Community effort to evaluate computational methods for the detection and quantification of poly(A) sites and estimating their differential usage across RNA-seq samples

    Python 13 14

  2. frattalab/PAPA frattalab/PAPA Public

    PAPA (Pipeline-Alternative Polyadenylation) - Snakemake pipeline for analysis of APA from short-read RNA-seq data

    Python 1

  3. frattalab/QAPA_snakemake frattalab/QAPA_snakemake Public

    Snakemake pipeline to run QAPA and perform differential polyA site usage analysis

    Python 1

  4. frattalab/rna_seq_single_steps frattalab/rna_seq_single_steps Public

    Snakemake pipelines for common bioinformatics tasks

    Python 1

  5. frattalab/rna_seq_snakemake frattalab/rna_seq_snakemake Public

    Snakemake Pipeline For RNA-Seq in UCL Cluster

    Python 9 4

  6. frattalab/paqr_annotations frattalab/paqr_annotations Public

    Snakemake workflow to generate annotation files for PAQR

    Python 2