yueyang0907

python-100-day

学习 Python 100 天系列文章代码

SCALE

A tissue-specific single-cell biological age model

cs-self-learning

计算机自学指南

HistoBistro

Weakly-supervised learning pipeline for histopathology images. Publications: Biomarker prediction in colorectal cancer (CRC)

biostat_final_exam

biostat final exam data and code

hgvs

Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`

ICGC-TCGA-DREAM-Mutation-Calling-challenge-tools

Tools for participants in the ICGC-TCGA DREAM Mutation Calling challenge

NGS-pipe

NGS-pipe: next-generation sequencing pipelines for precision oncology

snakemake-workflow-template

A template for standard compliant snakemake-workflows

giab-asm-benchmarking

GIAB pipeline for benchmarking genome assemblies

OMCL--KIRC--oxidative

Using genomic and transcriptome analyses to identify the role of the oxidative stress pathway in renal clear cell carcinoma and its potential therapeutic significance

R-ChIP-data-analysis

scRNAseq-analysis-notes

scRNAseq analysis notes from Ming Tang

ML-NLP

此项目是机器学习(Machine Learning)、深度学习(Deep Learning)、NLP面试中常考到的知识点和代码实现，也是作为一个算法工程师必会的理论基础知识。

igv-reports

Python application to generate self-contained pages embedding IGV visualizations, with no dependency on original input files.

PyVCF

A Variant Call Format reader for Python.

Bioinformatics-with-Python-Cookbook-Second-Edition

Bioinformatics with Python Cookbook Second Edition, published by Packt

Workshop

课题组每周研讨会

fastp

An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)

bamdst

a lightweight bam file depth statistical tool

awesome-single-cell

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

benchmarking-tools

Repository for the GA4GH Benchmarking Team work developing standardized benchmarking methods for germline small variant calls

vgraph

vgraph is a command line application and Python library to compare genetic variants using variant graphs. ``vgraph`` utilizes a graph representation of genomic variants in to precisely compare complex variants that are refractory to comparison by conventional comparison methods.

hap.py

Haplotype VCF comparison tools

training-material

A collection of Galaxy-related training material

giab_data_indexes

This repository contains data indexes from NIST's Genome in a Bottle project.

readthedocs

Documentation for the Google Genomics cookbook.

scikit-learn

scikit-learn: machine learning in Python

dna-seq-gatk-variant-calling

This Snakemake pipeline implements the GATK best-practices workflow

single-cell-tutorial

Single cell current best practices tutorial case study for the paper:Luecken and Theis, "Current best practices in single-cell RNA-seq analysis: a tutorial"