https://github.com/thejmazz/bcb

bioinformatics and computational biology links and notes
https://github.com/thejmazz/bcb

Last synced: 19 days ago
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bioinformatics and computational biology links and notes

• Host: GitHub
• URL: https://github.com/thejmazz/bcb
• Owner: thejmazz
• Created: 2016-05-14T23:20:00.000Z (over 8 years ago)
• Default Branch: master
• Last Pushed: 2016-05-21T22:40:47.000Z (over 8 years ago)
• Last Synced: 2024-11-07T08:51:36.321Z (2 months ago)
• Homepage:
• Size: 642 KB
• Stars: 0
• Watchers: 2
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

Awesome Lists containing this project

README

        
# Bioinformatics and Computational Biology

## Alignment

- [bwa](https://github.com/lh3/bwa)

- SRA toolkit

  * [ngs](http://github.com/ncbi/ngs)

  * [ncbi-vdb](http://github.com/ncbi/ncbi-vdb)

  * [sra-tools](http://github.com/ncbi/sra-tools)

- [samtools](https://github.com/samtools/samtools)

## Sequences

- [seqtk](https://github.com/lh3/seqtk)

## Databases

- [KEGG: Kyoto Encyclopedia of Genes and Genomes](http://www.genome.jp/kegg/)

- [dbSNP](http://www.ncbi.nlm.nih.gov/SNP/)

- [SGD](http://www.yeastgenome.org/)

- [PDB](http://www.rcsb.org/pdb/home/home.do)

## File Types

- [Biological data file formats](https://en.wikipedia.org/wiki/Biological_data#Data_File_Formats)

- [FASTA](https://en.wikipedia.org/wiki/FASTA)

- [FASTQ](https://en.wikipedia.org/wiki/FASTQ_format)

- [VCF](https://en.wikipedia.org/wiki/Variant_Call_Format) (variant call format)

- [SAM](https://en.wikipedia.org/wiki/SAM_(file_format)) (sequence alignment map) and BAM (binary alignment map)

## Ontologies

- [EFO](http://www.ebi.ac.uk/efo/)

- [GO](http://geneontology.org/) (Gene Ontology)

## Tutorials

- [Variant calling tutorial](https://wikis.utexas.edu/display/bioiteam/Variant+calling+tutorial)

- [griffithlab/rnaseq_tutorial](https://github.com/griffithlab/rnaseq_tutorial)

## RNASeq

- [Normalization of RNA-seq data using factor analysis of control genes or samples](http://www.nature.com/nbt/journal/v32/n9/full/nbt.2931.html)

## Pipeline Frameworks

- [nextflow](http://www.nextflow.io/)

## Algorithms

- [BWT](https://en.wikipedia.org/wiki/Burrows%E2%80%93Wheeler_transform) (Burrows-Wheeler transform)

## Other Things

- [nucleotides](http://nucleotid.es/)

- [repositive](https://repositive.io/)

## Graph Theory

- [Cluster and Visualize a Subset of Your Neo4j Database Using RNeo4j, igraph, and Alchemy.js.](http://nicolewhite.github.io/2014/07/24/visualize-subset-neo4j-alchemy.html)

## Containers

- [docker-bio-linux8](https://hub.docker.com/r/gawbul/docker-bio-linux8/)