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100_days_of_python

This repository chronicles my 100-day Python learning journey, where I'll start from the very basics and work my way up to more advanced concepts. Each day, I'll upload my progress, including Jupyter Notebook files (.ipynb) that contain code, explanations, and exercises.

1brc

1️⃣🐝🏎️ The One Billion Row Challenge -- A fun exploration of how quickly 1B rows from a text file can be aggregated with Java

2018-03-06-ibioic

Teaching materials for 6-7th March 2018 delivery of introductory bioinformatics training course for IBioIC.

2019-07-01-bioinformatics_for_biologists

2019fa-pset-final-dchen71

Final project using Airflow to orchestrate metagenomics processing pipeline

2023-manuscript-materials

Example script and input for positioning of helices to make protein bricks, as described in manuscript

2brad_denovo

Genome-wide de novo genotyping with 2bRAD

2brad_gatk

Genome-wide reference-based genotyping with 2bRAD

3d-cell-model

3d project that allows users to learn the anatomy of an animal cell.

3dmol.js

WebGL accelerated JavaScript molecular graphics library

abdiv

Alpha and beta diversity measures for community ecology

abricate

:mag_right: :pill: Mass screening of contigs for antimicrobial and virulence genes

abyss

:microscope: Assemble large genomes using short reads

acmg-guideline-in-chinese

中文版ACMG官方基因组解读指南《Standards and guidelines for the interpretation of sequence variants》

acmg_2015_mindchart

ACMG

adam

ADAM is a genomics analysis platform with specialized file formats built using Apache Avro, Apache Spark, and Apache Parquet. Apache 2 licensed.

addmodulescore

Exploring the inner workings of the `AddModuleScore` function from the Seurat R package.

admixture-map

The Admixture Map for the 1001 genomes project

admixturepipeline

A pipeline that accepts a VCF file to run through Admixture

adna-analysis

A beginner's guide to aDNA analysis, including scripts to streamline the process.

adna-tools

This project is a collection of tools for bioinformatic processing of ancient DNA data at the Harvard Medical School Reich Lab.

adna-workflow

Workflow for processing Illumina sequencing runs for ancient human DNA

adobo

functions and algorithms for single cell RNA-seq analyses

aegis

Source code and documentation for AEGIS - GO analysis software

aftermerge

aftermerge: A script for merging paired reads after mapping, based on the locations on the reference genome

ag2pi_gwas_workshop_june2021

agepy

Bioinformatics tools for Python

ai-act-requirements-graph

ai-artifacts

Hackable open-source version of Anthropic's AI Artifacts chat

aios

AIOS: LLM Agent Operating System