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awesome-bioinformatics

A curated list of awesome Bioinformatics libraries and software.

awesome-chatgpt-prompts

This repo includes ChatGPT prompt curation to use ChatGPT better.

bismark

A tool to map bisulfite converted sequence reads and determine cytosine methylation states

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 PairedEndSingleSampleWf has been superseded in Broad production by https://github.com/gatk-workflows/five-dollar-genome-analysis-pipeline

chip-seq-pipeline2

ENCODE ChIP-seq pipeline

chm13

The complete sequence of a human genome

cistransregulation

Project description and analytic scripts for cis/trans regulation of fiber development in G. hirsutum

cs-notes

:books: 技术面试必备基础知识、Leetcode、计算机操作系统、计算机网络、系统设计

daguguguji

《特师文集》——大咕咕咕鸡著

deeplearning-biology

A list of deep learning implementations in biology

deepsignal-plant

Detecting methylation using signal-level features from Nanopore sequencing reads of plants

deeptools

Tools to process and analyze deep sequencing data.

dragonstar2019

dss

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.

ggsci

🦄 Scientific journal and sci-fi themed color palettes for ggplot2

haplotyped-methylome

Reproducibility workflow for Gigante et al., 2018: Using long-read sequencing to detect imprinted DNA methylation

humansystemoptimization

健康学习到150岁 - 人体系统调优不完全指南

iterativewgcna

Extension of the WGCNA program to improve the eigengene similarity of modules and increase the overall number of genes in modules.

khmer

In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more

losslessswitcher

Automated Apple Music Lossless Sample Rate Switching for Audio Devices on Macs.

macs

MACS -- Model-based Analysis of ChIP-Seq

medaka

Sequence correction provided by ONT Research

methplotlib

Plotting tools for nanopore methylation data

methylation_notes

Notes on DNA methylation analysis

methylpy

WGBS/NOMe-seq Data Processing & Differential Methylation Analysis