Bioinfomatics: Difference between revisions
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== Overview == | == Overview == | ||
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* 왜 필요한가? - HPC 및 서버 환경에서 필수 개념 | * 왜 필요한가? - HPC 및 서버 환경에서 필수 개념 | ||
* 언제 사용하는가? - 서버 구성, 성능 튜닝, 문제 해결 시 | * 언제 사용하는가? - 서버 구성, 성능 튜닝, 문제 해결 시 | ||
== Purpose == | == Purpose == | ||
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* Scope: Bioinfomatics의 개념, 사용법, 설정 | * Scope: Bioinfomatics의 개념, 사용법, 설정 | ||
* Non-goals: 다른 주제로의 확장 | * Non-goals: 다른 주제로의 확장 | ||
== Key Concepts == | == Key Concepts == | ||
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| [[Linux]], [[Server]] | | [[Linux]], [[Server]] | ||
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== Detailed Explanation == | == Detailed Explanation == | ||
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* Tools for Cancer Genomics | * Tools for Cancer Genomics | ||
** [https://www.genepattern.org/modules/docs/MutPanning#gsc.tab=0 MutPanning] is designed to detect rare cancer driver genes from aggregated | ** [https://www.genepattern.org/modules/docs/MutPanning#gsc.tab=0 MutPanning] is designed to detect rare cancer driver genes from aggregated | ||
== Best Practices == | == Best Practices == | ||
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* 공식 문서 참고 | * 공식 문서 참고 | ||
* 테스트 환경에서 먼저 검증 | * 테스트 환경에서 먼저 검증 | ||
== References == | == References == | ||
* [https://wiki.hpcmate.com Bioinfomatics] | * [https://wiki.hpcmate.com Bioinfomatics] | ||
== Related Pages == | == Related Pages == | ||
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* [[Hardware]] | * [[Hardware]] | ||
* [[Network]] | * [[Network]] | ||
[[Category:AI]] | [[Category:AI]] | ||
Revision as of 13:22, 2 October 2026
Overview
Bioinfomatics에 대한 기술 문서입니다.
Summary
- 무엇인가? - Bioinfomatics
- 왜 필요한가? - HPC 및 서버 환경에서 필수 개념
- 언제 사용하는가? - 서버 구성, 성능 튜닝, 문제 해결 시
Purpose
이 문서가 존재하는 이유
- Goal: Bioinfomatics에 대한 기술 정보 제공
- Scope: Bioinfomatics의 개념, 사용법, 설정
- Non-goals: 다른 주제로의 확장
Key Concepts
| Concept | Description | Related |
|---|---|---|
| Bioinfomatics | HPC/서버 환경에서 중요한 기술 개념 | Linux, Server |
Detailed Explanation
Bioinfomatics
A combined technologies with biology, computer science, mathmatics and statistics. [1]
Bioinfomatics workflow steps
- quality control assessmemt steps
- sequence alignment
- data summarization into genes/regions
- data annotation to genomics features
- statistical comparisons
- mutltiomic ingetration
Bioinfomatics curated software list[2]
- Package suites
- Data Tools
- Downloading
- Compressing
- Data Processing
- Command Line Utilities
- Next Generation Sequencing
- Workflow Managers
- Pipelines
- Sequence Processing
- Data Analysis
- Sequence Alignment
- Pairwise
- Multiple Sequence Alignment
- Clustering
- Quantification
- Variant Calling
- Structural variant callers
- BAM File Utilities
- VCF File Utilities
- GFF BED File Utilities
- Variant Simulation
- Variant Prediction/Annotation
- Tools for Assessment of Variants
- PolyPhen-2 is a tool for predicting the effect of an amino acid substitution on protein structure and function, based on comparative genomics and experimentally determined protein structures. It is available as a web service, and can also be downloaded as a standalone application.
- SNPtrack is a simple interface for mutation mapping and identifying causal mutations from whole-genome sequencing studies. It is available as a web service.
- Tools for Mass Spectrometry and Proteomics
- MS-BLAST is a tool for searching protein sequences identified with tandem mass spectrometry against databases of protein sequences. It is available as a web service and as a standalone software.
- Tools for Statistical Genetics
- Joint Likelihood Mapping (JLIM) is a tool to test for shared genetic effect between two genetic association data, for example, a disease GWAS study and gene expression QTL (eQTL) study.
- Joint Likelihood Mapping 2 (JLIM_2.0) is a version of JLIM which supports meta-analysis across more than one cohort of matching ancestry.
- Joint Likelihood Mapping (JLIM) 2.5 is a new version of JLIM based on summary statistics.
- NPS is a tool for polygenic risk scoring based on partitioning-based non-parametric shrinkage algorithm.
- RVTT is a novel statistical test of trend that assesses the relationship of the frequency of qualifying rare variants in a pathway with dichotomous disease phenotypes leveraging the Cochran-Armitage test statistic.
- Tools for Cancer Genomics
- MutPanning is designed to detect rare cancer driver genes from aggregated
Best Practices
- 최신 버전 사용 권장
- 공식 문서 참고
- 테스트 환경에서 먼저 검증
References
Related Pages
Knowledge Graph
Related