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Achievement: Pull Shark

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avinashkarkada/README.md

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About Me

I am a Bioinformatics Engineer at the Johns Hopkins School of Medicine and an MS Bioinformatics candidate at Johns Hopkins University.

My work sits at the intersection of bioinformatics, computational biology, immunology, and structural biology. I build and improve workflow and analysis pipelines, work with large-scale sequencing data, and use computational methods to study antibodies, epitopes, proteins, and biological systems.

I currently work on

  • PhIP-Seq antibody-profiling investigating influence of microbial dysbiosis on humoral immunity in early-onset, late-onset colorectal cancer, and polyp/healthy control cohorts.
  • Developing and maintaining computational pipelines for InFlux, a highly multiplexed NGS-based influenza A neutralization assay, analyzing samples to profile humoral immunity across diverse patient cohorts.

Tech Stack

Programming and Platforms

Python R Bash SQL Java Git GitHub Linux HPC SLURM AWS Docker Singularity Conda Mamba Jupyter R Markdown Quarto Shiny VS Code RStudio

Bioinformatics, NGS, and Omics

PhIP-seq RNA-seq scRNA-seq ChIP-seq WGS Biopython Bioconductor SAMtools BCFtools BEDTools Bowtie Bowtie2 BWA Minimap2 Kallisto Salmon STAR HISAT2 Cutadapt Trimmomatic FastQC GATK IGV SRA Toolkit BLAST Clustal Omega MAFFT EMBOSS CD-HIT HMMER edgeR DESeq2 limma Seurat Scanpy MEGA IQ-TREE

Computational Biology and Data Science

pandas NumPy SciPy scikit-learn XGBoost matplotlib plotly ggplot2 dplyr tidyr randomForest SVM LASSO PCA UMAP t-SNE Clustering Differential Expression Enrichment Analysis Pathway Analysis Network Analysis

Structural Biology and Molecular Modeling

PyMOL ChimeraX Chimera VMD MODELLER AlphaFold ESMFold Rosetta HADDOCK AutoDock AutoDock Vina GROMACS AMBER gmx_MMPBSA FoldX Maestro Schrödinger CP2K Gaussian ORCA RDKit Open Babel Protein Structure Prediction Molecular Dynamics Protein-Protein Docking Protein-Ligand Docking Protein-DNA Docking Nucleic Acid Docking Binder Design

Visualization and Reporting

GraphPad Prism Excel PowerPoint BioRender LaTeX Dash Cytoscape UCSC Genome Browser Ensembl Genome Browser

GitHub Stats

Connect

Pinned Loading

  1. GROMACS-COLAB GROMACS-COLAB Public

    Contains gromacs notebooks for MD simulations.

    Jupyter Notebook 5 1

  2. MODELLER-GUI MODELLER-GUI Public

    This is a Tkinter based MODELLER GUI program

    Python 1

  3. MSA-Gap-Analyzer MSA-Gap-Analyzer Public

    Python

  4. Sequence_diversity_calculator Sequence_diversity_calculator Public

    Python

  5. PhIP-Seq-Pipeline-Installer PhIP-Seq-Pipeline-Installer Public

    These are the scripts developed for the Larman Lab which help new users install the PhIP-seq pipeline and its dependencies. This also installs Phipmake and ARscore dependencies.

    Shell

  6. ARscape-Groupwise ARscape-Groupwise Public

    Forked from jernbom/ARscape

    Extension of the ARScape package with modifications compatible to groupwise reactivity

    R