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/AdvancedPythonForBio
Work from the book 'Advanced Python for Biologists'
SunbyMoon/An-Introduction-To-Applied-Bioinformatics
Interactive lessons in bioinformatics.
SunbyMoon/AutoCAT
SunbyMoon/awesome-bioinformatics-formats
Curated list of bioinformatics formats and publications
SunbyMoon/awesome-cancer-variant-databases
A community-maintained repository of cancer clinical knowledge bases and databases focused on cancer variants.
SunbyMoon/awesome-multi-omics
List of software packages for multi-omics analysis
SunbyMoon/bamsurgeon
tools for adding mutations to existing .bam files, used for testing mutation callers
SunbyMoon/BayesTyper
A method for variant graph genotyping based on exact alignment of k-mers
SunbyMoon/biofx_python
Code for Mastering Python for Bioinformatics (O'Reilly, 2021, ISBN 9781098100889)
SunbyMoon/bioinformatics-workbook
SunbyMoon/catch
A package for designing compact and comprehensive capture probe sets.
SunbyMoon/cfdna-wgs-manuscript-code
Code used to generate the results in "Somatic chronology of treatment-resistant prostate cancer via deep whole-genome ctDNA sequencing"
SunbyMoon/ctdna
Python package for cancer early detection based on a model of cancer evolution and circulating tumor DNA (ctDNA) shedding
SunbyMoon/ctDNA-dynamic-prediction-lung-cancer
SunbyMoon/ctDNAtools
R package to work with ctDNA sequencing data
SunbyMoon/dash
Analytical Apps for Python. Dash Is Productive™
SunbyMoon/freebayes
Bayesian haplotype-based genetic polymorphism discovery and genotyping.
SunbyMoon/htslib
C library for high-throughput sequencing data formats
SunbyMoon/LFS-early-detection-ctdna
Multi-modal analysis of cell-free DNA for the early detection of cancer in Li-Fraumeni syndrome.
SunbyMoon/methylclock
DNA methylation-based clocks
SunbyMoon/mixcr
MiXCR is a universal software for fast and accurate extraction of T- and B- cell receptor repertoires from any type of sequencing data. Free for academic use only.
SunbyMoon/pyensembl
Python interface to access reference genome features (such as genes, transcripts, and exons) from Ensembl
SunbyMoon/rnaseq
RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
SunbyMoon/RTCR
A pipeline for complete and accurate recovery of TCR repertoires from high throughput sequencing data.
SunbyMoon/samplot
Plot structural variant signals from many BAMs and CRAMs
SunbyMoon/seekr
A library for counting small kmer frequencies in nucleotide sequences.
SunbyMoon/seqcap_processor
Bioinformatic pipeline for processing Sequence Capture data for Phylogenetics
SunbyMoon/somaticseq
An ensemble approach to accurately detect somatic mutations using SomaticSeq
SunbyMoon/TCRsequencing
Bulk TCR sequencing and analysis with MiXCR and Immunarch
SunbyMoon/UNI
Towards a general-purpose foundation model for computational pathology - Nature Medicine