Pinned Repositories
AdvancedPythonForBio
Work from the book 'Advanced Python for Biologists'
alignment-and-variant-calling-tutorial
basic walk-throughs for alignment and variant calling from NGS sequencing data
An-Introduction-To-Applied-Bioinformatics
Interactive lessons in bioinformatics.
beginning-python-for-bioinformatics
repository for the code featured in the blog
Bioinformatics-Programming-using-Python
Exercises from the 'Bioinformatics Programming using Python' book by Mitchell L Model
cutadapt
cutadapt removes adapter sequences from sequencing reads
fqc
Extensible quality control dashboard built around FASTQ assessment.
git_learn
PlasmaSeq
Analyze CNVs of ctDNA
the-first-month-practice-of-python
SunbyMoon's Repositories
SunbyMoon/beginning-python-for-bioinformatics
repository for the code featured in the blog
SunbyMoon/Bioinformatics-Programming-using-Python
Exercises from the 'Bioinformatics Programming using Python' book by Mitchell L Model
SunbyMoon/the-first-month-practice-of-python
SunbyMoon/bioinfo
Code from a bioinformatics course that dealt with basic statistical models as well as common bioinformatics algorithms using python.
SunbyMoon/cc2
SunbyMoon/copy-number-analysis
Explore, compare, and evaluate Bioconductor packages related to genomic copy number analysis
SunbyMoon/ctDNASomaticVariantCall.jl
Somatic Variant Call for ctDNA
SunbyMoon/denovoTargetCapturePopGen
Bioinformatics pipelines for processing transciptome-based exon capture data in population genomic analyses
SunbyMoon/GATK-pipeline
A shell script which implements GATK pipeline for variant calling.
SunbyMoon/jvarkit
Java utilities for Bioinformatics
SunbyMoon/ngs
PennSCAP-T Pipeline
SunbyMoon/NGS-pipeline
NGS pipeline based on the python module ruffus
SunbyMoon/ngsClean-1
Pipeline for NGS read (filtering, trimming, merging) and SNP (quality, depth, biases, ...) quality control
SunbyMoon/NGSTools
Next-Generation Sequencing(NGS) toolkits.
SunbyMoon/picard
A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
SunbyMoon/pybedtools
Python wrapper -- and more -- for Aaron Quinlan's BEDTools (bioinformatics tools)
SunbyMoon/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.
SunbyMoon/Python-Lectures
SunbyMoon/QC3
QC3, a quality control tool designed for DNA sequencing data for raw data, alignment, and variant calling.
SunbyMoon/samtools
Tools (written in C using htslib) for manipulating next-generation sequencing data
SunbyMoon/Sitedossier-Crawler
Crawler for sitedossier.com
SunbyMoon/tcr-analysis
Scripts and files that I use to analyse T cell receptor repertoire data, produced by deep-sequencing
SunbyMoon/umich-eecs545-lectures
This repository contains the lecture materials for EECS 545, a graduate course in Machine Learning, at the University of Michigan, Ann Arbor.
SunbyMoon/umicount
umicount is a collection of Python scripts which allows to remove and count PCR duplicates from paired-end libraries prepared with unique molecular identifiers