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BilalsGituation/README.md

Bilal Asser - BilalsGituation

💬 Ask me about arranging a project or personalised training and support in programming, NGS Bioinformatics, or Machine Learning.

I enjoy working on 💻 and teaching 👨‍🏫:

  • Single-cell 🦠 and spatial 🔬 transcriptomics in Seurat, Bioconductor and Python.
    • This includes integrative, multimodal and tumour microenvironment-related analysis
  • Short and long read Bulk RNASeq analysis from mammalian 🐭 and pathogenic 😷 samples
    • This includes Differential expression analysis 📊 and Variant analysis 🧬
  • Academic and technical reading and writing 📑
  • Computational and biological contexts of the above material

Image in profile picture depicting plot from omics analysis is from Seurat vignettes and used under MIT License. Copyright (c) 2021 Seurat authors. Not affiliated with or endorsed by the Seurat project or Satija lab.

Pinned Loading

  1. nf-core/pathogenepidemiology nf-core/pathogenepidemiology Public

    [UNDER DEVELOPMENT] A profile-based pipeline for genomic epidemiological analysis of predefined pathogens.

    Nextflow 1 1

  2. Seurat_vs_OSTA_TME Seurat_vs_OSTA_TME Public

    Model Project for teaching Tumour Microenvironment (TME) analysis using Seurat-based Spatial Transcriptomics, at an accessible scale for first-timers without high-end computers.

    R

  3. artic_batches_SARS-CoV2 artic_batches_SARS-CoV2 Public

    Set of scripts to download and process batches of patient SARS-CoV2 MinION (ONT) sequencing data from the ENA produced using Artic amplicons

    Shell

  4. RnAnalySeq_example RnAnalySeq_example Public

    THIS SOFTWARE HAS BEEN UPDATED LOCALLY. Updates and fixes can be released once I get permanent work. Example use of work-in-progress software that analyses samples from RNA-Seq experiments. The rea…

    R

  5. wrappedtools wrappedtools Public

    Forked from abusjahn/wrappedtools

    Forked from @abusjahn: wrappedtools R package. I have worked on compare_n_numvars(), as well as to optimise the help documentation for newer users. Currently we, the authors, are designing and impl…

    R

  6. MLexam MLexam Public

    An exam I did in Machine-Learning. I do not have the result other than the module result of German 1.5, but I have uploaded a version with comments from assessor @thomasmanke

    Jupyter Notebook