README.md

Knowledge: collection of cheat Sheets / overviews / summaries

Table of Contents

• Programming
  • Bash
  • Perl
  • Python
• Format
  • BAM and SAM
  • CIGAR
  • GFF and GTF
  • MD tag in bam format
  • Markdown syntax
  • SUGAR
  • VULGAR
  • Wiki syntax
  • External ressource about many different formats
• Convertion
  • gff to gtf
  • gff to bed
• Others
  • Git
  • MinHash
  • Annotation tools
    • Genome (protein coding genes)
    • Mitochondrion
    • Chloroplast
    • Plasmid
  • Overview of RNA-seq library types
  • Rackham
  • Screen
  • Schedulers: LSF,Torque,SGE,Slurm,etc
  • Taxonomic classification
• Blogs
• Knowledge bank
• Statistics
• Data visualisation

Programming

BASH

• Cheat Sheets:
  • Cheat Sheet Level1
  • Cheat Sheet Level2
  • Cheat Sheet Level3
• course
• others
• one-liners:
  • Stephen is Turner
  • Bonnie I-Man Ng

Perl

• Perl code profiler

Python

• Create a package on PyPI

Format

BAM and SAM

CIGAR

GFF and GTF

MD tag in bam format

• MD Tags in BAM Files

• The history the MD tag and the CIGAR X operator

Markdown syntax

• Git Markdown
• Anchors in Git Markdown

SUGAR

VULGAR

Wiki syntax

• textile - Used by Redmine

External ressource about many different formats

• UCONN - University of Connecticut

• lastz README

• UCSC - University of California, Santa Cruz

Conversion

gff to gtf

gff to bed

Others

Git

MinHash

• sourmash
• Kmer-db
• Applying MinHash to cluster RNAseq samples
• [http://ivory.idyll.org/blog/2016-sourmash-sbt.html] (http://ivory.idyll.org/blog/2016-sourmash-sbt.html)

Annotation tools

• Genome (Protein coding genes)

• Mitochondrion

• Chloroplast

• Plasmid

Overview of RNA-seq library types

Rackham

Screen

Schedulers: LSF,Torque,SGE,Slurm,etc

Taxonomic classification

Blogs

• Bioinformatics I/O
• Living in an Ivory Basement
  From C. Titus Brown
• The Genome Factory
  From Torsten Seemann
• avrilomics
  From Avril Coghlan
• OPINIOMICS
  From Mick Watson
• Omics! Omics!
  From Keith Robison
• DNA Zoo
  From Aiden lab
• NBIS
• List from biostars
• Bioinformatics Workbook

Knowledge bank

• ecSeq Bioinformatics

Statistics

• seeing-theory
• Modern Statistics for Modern Biology
• Scientists rise up against statistical significance
• methodologie - fr
• bioinfo-fr - fr
• Introduction aux Statistiques - fr

Data visualisation

• Orange: Data Mining Fruitful and Fun

• Data Visualization Type Catalogs (from Yuri Engelhardt)

  • Classic
  • Thorough
  • R
  • Python
  • FT Vocab
  • Searched
  • Tools
  • Weird

• Some blog posts on specific data types (from James Scott-Brown):

  • Distributions (16 ways)
  • Graphs (6 ways)
  • Two numbers (45 ways)
  • Proportions (9 ways)
  • Change over time (11 ways)

• Circular plots

  • circlize: circular visualization in R
  • circos plots

• ClustVis a web tool for visualizing clustering of multivariate data