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Hello! πŸ‘‹ I’m Bulut Hamali, a dedicated computational biologist with over a decade of experience in molecular biology and a deep fascination with the complexities of genomics. Below is a snapshot of my professional toolkit and interests:

  • Programming Proficiency: Skilled in Python, R, and with a strong emphasis on applying these languages to solve complex biological problems.
  • Bioinformatics Tools: Proficient with essential tools such as BLAST, BEDTools, GATK, and SAMtools. Regular user of Bioconductor for genomic analysis.
  • NGS Expertise: Extensive experience in analyzing next-generation sequencing data, using pipelines such as BWA, Bowtie, and STAR for diverse studies including RNA-seq and ChIP-seq.
  • Visualization Skills: Adept in data visualization using ggplot in R and Matplotlib in Python, creating clear and impactful representations of complex data.
  • Cloud Computing: Utilize cloud platforms like AWS and Google Cloud for scalable bioinformatics workflows and data management.
  • Containerization Tools: Familiar with Docker and Singularity to maintain reproducible computing environments across various projects.
  • Workflow Automation: Use workflow management tools like Nextflow and Snakemake to streamline and automate bioinformatics processes.
  • Scientific Communication: Committed to clear and effective scientific communication, with experience in preparing publications and presenting at scientific conferences.

I am always excited to embark on new projects and collaborations that push the boundaries of what we can discover in computational biology. Feel free to reach out if you’re interested in collaborating or have questions about my work! πŸš€

Email: [email protected]


🧰 Languages and Tools

Python

Linux

Git

Vscode

R

Bash

JavaScript


Bulut Hamali's Projects

awesome-single-cell icon awesome-single-cell

Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.

aws-igenomes icon aws-igenomes

Documentation and description of AWS iGenomes S3 resource.

bioinformatics icon bioinformatics

:microscope: Path to a free self-taught education in Bioinformatics!

biojupies_hamali icon biojupies_hamali

Automated generation of tailored bioinformatics Jupyter Notebooks via a user interface.

cellbender icon cellbender

CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.

dust icon dust

A more intuitive version of du in rust

fastq-dl icon fastq-dl

Download FASTQ files from SRA or ENA repositories.

figeno icon figeno

Tool for plotting sequencing data along genomic coordinates.

flowcraft_bulut icon flowcraft_bulut

FlowCraft: a component-based pipeline composer for omics analysis using Nextflow. :whale::package:

generative-ai-for-beginners icon generative-ai-for-beginners

18 Lessons, Get Started Building with Generative AI πŸ”— https://microsoft.github.io/generative-ai-for-beginners/

gsea_r icon gsea_r

Updated implementation of the GSEA-P R application for modern R distributions

gwalkr icon gwalkr

Turn your data frame into a tableau style drag and drop UI interface to build visualization in R.

immunarch icon immunarch

🧬 Immunarch: an R Package for Fast and Painless Exploration of Single-cell and Bulk T-cell/Antibody Immune Repertoires

isobaric-prot-wf-r icon isobaric-prot-wf-r

Simple workflows for the isobaric-labeling proteomic data from Proteome Discoverer with ANOVA, t-testing, DEqMS/limma and annotation via fgsea

labs icon labs

Rmd source files for the HarvardX series PH525x

llm-course icon llm-course

Course to get into Large Language Models (LLMs) with roadmaps and Colab notebooks.

modern-unix icon modern-unix

A collection of modern/faster/saner alternatives to common unix commands.

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