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atac-seq-pipeline

ENCODE ATAC-seq pipeline

atom

:atom: The hackable text editor

auto_barcode

Extracts fastq reads for specified barcode(s) from one or multiple FASTQ files

awesome-pipeline

A curated list of awesome pipeline toolkits inspired by Awesome Sysadmin

bamtools

C++ API & command-line toolkit for working with BAM data

cardiac-progenitors

Coming soon: scRNA-seq analysis of cardiac progenitor cells

cerebellumdev

Code for processing data

chipseeker

:dart:ChIP peak Annotation, Comparison and Visualization

clusterprofiler

:bar_chart:statistical analysis and visualization of functional profiles for genes and gene clusters

cookbook-for-r-chinese

:books:Cookbook for R 中文翻译

crassphage_project

Source code for the crAssphage project

datanote-code

devnetwork

ebook

galaxy

modENCODE Galaxy on Amazon Cloud

git-hankbook

Git使用手册

handbook_of_biostatistic_r

:green_book:handbook of biostatistic and R

in-depth-ngs-data-analysis-course

Materials for 12-day course on analyzing RNA-Seq, ChIP-Seq and variant calling data.

kentutils

UCSC command line bioinformatic utilities

knn

机器学习实战

linux-command

Linux命令大全搜索工具，内容包含Linux命令手册、详解、学习、搜集。

liuyang0681.github.io

macs

MACS -- Model-based Analysis of ChIP-Seq

maier_et_al_nature_2020

This repository contains scripts used for analysis and figure generation in Maier, B., Leader, A.M., Chen, S.T. et al. A conserved dendritic-cell regulatory program limits antitumour immunity. Nature 580, 257–262 (2020). https://doi.org/10.1038/s41586-020-2134-y

ngs

Scripts for next generation sequencing

ngs-pipeline

By study this, it won't be costly or time-consuming to customize a NGS data analysis pipeline

pagoda2

R package for analyzing and interactively exploring large single-cell RNA-seq datasets

paired-seq

Paired-seq

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.

plate_scatac-seq

A rapid and robust plate-based single cell ATAC-seq (scATAC-seq) method