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wortjohn's Projects

bcbio-nextgen icon bcbio-nextgen

Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis

bioinformatic_kit icon bioinformatic_kit

The python version is 2.7. This repository includes some script programs by myself.

bwa icon bwa

Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)

chatgpt icon chatgpt

🔮 ChatGPT Desktop Application (Mac, Windows and Linux)

cnvkit icon cnvkit

Copy number variant detection from targeted DNA sequencing

d2l-zh icon d2l-zh

《动手学深度学习》：面向中文读者、能运行、可讨论。中英文版被70多个国家的500多所大学用于教学。

deepcpg icon deepcpg

Deep neural networks for predicting CpG methylation

facets icon facets

Algorithm to implement Fraction and Copy number Estimate from Tumor/normal Sequencing.

hmmcopy_utils icon hmmcopy_utils

Tools for extracting read counts and gc and mappability statistics in preparation for running HMMCopy.

htslib icon htslib

C library for high-throughput sequencing data formats

learn_django icon learn_django

This repository is used for learning the web frame "Django"

minimap2 icon minimap2

A versatile pairwise aligner for genomic and spliced nucleotide sequences

ml-nlp icon 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。

openms icon openms

The codebase of the OpenMS project

pindel icon pindel

Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data. It uses a pattern growth approach to identify the breakpoints of these variants from paired-end short reads.

pysam icon pysam

Pysam is a Python module for reading and manipulating SAM/BAM/VCF/BCF files. It's a lightweight wrapper of the htslib C-API, the same one that powers samtools, bcftools, and tabix.

python-levenshtein icon python-levenshtein

The Levenshtein Python C extension module contains functions for fast computation of Levenshtein distance and string similarity

scrapy_project icon scrapy_project

The python version is 2.7 . This repository mainly includes scrapy projects that i have done.

tcr-dist icon tcr-dist

Software tools for the analysis of epitope-specific T cell receptor (TCR) repertoires (scroll down for the README)

vt icon vt

A tool set for short variant discovery in genetic sequence data.

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