Musketeer_D's repositories
Methylation_notes
Notes on DNA methylation analysis
broad-prod-wgs-germline-snps-indels
Workflows for germline short variant discovery in WGS data. PairedEndSingleSampleWf has been superseded in Broad production by https://github.com/gatk-workflows/five-dollar-genome-analysis-pipeline
encode_dna_dynamics
Custom scripts used in "Spatiotemporal DNA Methylome Dynamics of the Developing Mammalian Fetus"
EndNote_Tutorial_Hand_by_Hand
手把手教你使用 EndNote X9/NoteExpress
ensembl-vep
The Ensembl Variant Effect Predictor predicts the functional effects of genomic variants
gatk
Official code repository for GATK versions 4 and up
GENIE3
Machine learning-based approach for the inference of gene regulatory networks from expression data.
haplotyped-methylome
Reproducibility workflow for Gigante et al., 2018: Using long-read sequencing to detect imprinted DNA methylation
iterativeWGCNA
Extension of the WGCNA program to improve the eigengene similarity of modules and increase the overall number of genes in modules.
medaka
Sequence correction provided by ONT Research
methplotlib
Plotting tools for nanopore methylation data
MultiQC
Aggregate results from bioinformatics analyses across many samples into a single report.
nanopolish
Signal-level algorithms for MinION data
nCovMemory
2020新冠肺炎记忆：报道、非虚构与个人叙述（持续更新） Memory of 2020 nCov: Media Coverage, Non-fiction Writings, and Individual Narratives (Continuously updating)
oneliners
Useful bash one-liners for bioinformatics.
pyda-2e-zh
:book: [译] 利用 Python 进行数据分析 · 第 2 版
Sniffles
Structural variation caller using third generation sequencing
SNPsplit
Allele-specific alignment sorting
tombo
Tombo is a suite of tools primarily for the identification of modified nucleotides from raw nanopore sequencing data.
ViewBS
ViewBS - a powerful toolkit for visualization of high-throughput bisulfite sequencing data