Bioinformatics-Resources

Bioinformatics-Resources是我创建的一个github项目,希望在我日常看文献、逛GitHub以及维护BioInstaller包时收集一些与生物信息学相关的一些软件和数据库。

一个人的力量是薄弱的,希望大家可以一起收集起来,如果你想对本列表进行贡献,可以STAR并fork我的仓库然后发起Pull Request,列表的最后将新增你的名字。

如果有可能,我想把omictools上的工具爬下来 :(

Abstract: A curated list of resources for learning bioinformatics. Some of this repo resources were collected by BioInstaller project. You can use BioInstaller to directly download the source code or database files, or fetch the meta information by BioInstaller::get.meta()$item.

Purpose:

  • Provide some of bioinformatics learning resources for beginners
  • Provide a profiling of bioinformatics

Field:

  • Next generation sequencing (NGS)
  • Bioinformatics Data Analysis

Table of content

Table of content


Resources

General

Journal

Sequencing Technology

This section mainly copied from enseqlopedia.

Thanks this work: Hadfield, J. & Retief, J. A profusion of confusion in NGS methods naming. Nat Methods 15, 7-8 (2018).

RNA Sequencing Methods

Low-Level RNA Detection
RNA Modifications
RNA Structure
RNA Transcription
RNA-Protein Interactions

DNA Sequencing Methods

Protein-Protein Interaction
Sequence Rearrangements
DNA Break Mapping
DNA Protein Interactions
Epigenetics
Low-Level DNA Detection

Tools

Package management

Web Application Developement Framework

Web-based Service

Clinical Annotation
  • CSCD
  • AtCircDB
  • CircNet
  • circBase
  • circRNADb
  • exoRBase
  • EVLncRNAs
  • NONCODE: an integrated knowledge database dedicated to non-coding RNAs (excluding tRNAs and rRNAs)
  • MiTranscriptome: a catalog of human long poly-adenylated RNA transcripts derived from computational analysis of high-throughput RNA sequencing (RNA-Seq) data from over 6,500 samples spanning diverse cancer and tissue types
  • FANTOM CAT: an atlas of human long non-coding RNAs with accurate 5’ ends

Sequencing Data Portal

Local tools

Quality Control
Alignment And Assembly
Variant Detection (SNVs, INDELs, SVs)
Variant Annotation
Variant Visualization (SNVs, INDELs, SVs)
Variant Screen
Alternative Splicing
Gene Expression Data Analysis
  • viral-ngs
  • qap
  • ROP: discovering the source of all RNA-seq reads, including those originating from repeat sequences, recombinant B and T cell receptors, and microbial communities
  • ViFi: Pipeline for identifying viral integration and fusion mRNA reads from NGS data
Single Cell
  • seurat
  • SCnorm
  • dropClust
  • scran: batch effect adjust
  • trendsceek: spatial expression trends in single-cell gene expression data
  • scRNA-tools: a database of software tools for the analysis of single-cell RNA-seq data.
  • awesome-single-cell: list of software packages (and the people developing these methods) for single-cell data analysis, including RNA-seq, ATAC-seq, etc.
  • SAVER: SAVER (Single-cell Analysis Via Expression Recovery) implements a regularized regression prediction and empirical Bayes method to recover the true gene expression profile in noisy and sparse single-cell RNA-seq data.
Expression Quantitative Trait Loci, eQTL
ChIP-seq analysis
Primer Design
Work flow
Unclassified
Statistical and Visualization
Text editor and IDE
Remote Connection (SSH)
Remote Connection (Desktop)
Other

Books&Tutorial

R

Linux&Shell

Python

C/C++

JAVA

Statistics and Deep learning

│  李航.统计学习方法.pdf
│  机器学习及其应用.pdf
│  All of Statistics - A Concise Course in Statistical Inference - Larry Wasserman - Springer.pdf
│  Machine Learning - Tom Mitchell.pdf
│  PRML.pdf
│  PRML读书会合集打印版.pdf
│  Programming Collective Intelligence.pdf
│  [奥莱理] Machine Learning for Hackers.pdf
│  [机器学习]Tom.Mitchell.pdf
│  《大数据:互联网大规模数据挖掘与分布式处理》迷你书.pdf
│  推荐系统实践.pdf
│  数据挖掘-实用机器学习技术(中文第二版).pdf
│  数据挖掘_概念与技术.pdf
│  机器学习-Mitchell-中文-清晰版.pdf
│  机器学习导论.pdf
│  模式分类第二版中文版Duda.pdf(全).pdf
│  深入搜索引擎--海量信息的压缩、索引和查询.pdf
│  矩阵分析.美国 Roger.A.Horn.扫描版.pdf
│  统计学习基础 数据挖掘、推理与预测.pdf
│  
├─机器学习实战
│      machinelearninginaction.zip
│      机器学习实战 单页.pdf
│      机器学习实战.pdf
│      
└─论文文集
    └─LDA
            LDA-wangyi.pdf
            LDA数学八卦.pdf
            text-est.pdf

Git

Cloud

Bioinfomatics

Skills

Programming language

Statistics

Code Management

Institute or business company

People

Blog

Contributors