Forum:Handbooks for Bioinformatics Ninjas
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8.2 years ago
Shicheng Guo ★ 9.5k

Some interesting poster which is useful for our scientific career and basic skills:

Writing reviews of academic papers: https://github.com/jtleek/reviews

A guide to reading scientific papers: https://github.com/jtleek/readingpapers

Good Habit for Bioinformatics Analyst: Good Habit for Bioinformatics Analyst or Scientist

Lab notebook for data analysis work: recommendation on lab notebook for bioinformatics/data analysis work

Most Common Stupid Mistakes: What Are The Most Common Stupid Mistakes In Bioinformatics?

9 Common metrics to measure tissue specificity: http://www.ncbi.nlm.nih.gov/pubmed/26891983

Bayesian tool for methylation analysis: https://en.wikipedia.org/wiki/Bayesian_tool_for_methylation_analysis

Cluster analysis to methylation data: http://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-9-365

How to share your data as public hub at UCSC: http://genomewiki.ucsc.edu/index.php/Public_Hub_Guidelines

List of open-source bioinformatics software: https://en.wikipedia.org/wiki/List_of_open-source_bioinformatics_software

Software you need to prepare better figure: Illustrator, Photoshop, Cytoscape, Mega, heatmap.2, String 9.0, Venn, smoothScatter

Performance of 30 different pipelines to make variation and Indel callling: http://www.hindawi.com/journals/bmri/2015/456479/

Windows user? Strawberry Perl is better than active perl in the usage of bioperl (lastest active perl not support bioperl).

Install BioPerl Without Root Privilege in Linux: How To Install BioPerl Without Root Privileges in Ubuntu/Linxu

Deconvolution Methods on RNA-Seq Data: Deconvolution Methods on RNA-Seq Data (Mixed cell types)

PCR primer batch design: http://batchprimer3.bioinformatics.ucdavis.edu/cgi-bin/batchprimer3/batchprimer3.cgi

Use Ensembl annotation, rather than UCSC or other annotation and be sure to note the version of Ensembl annotation

Circular RNAs (circRNAs) database: http://circnet.mbc.nctu.edu.tw/

Pathway, GO and Enrichment Analysis: Enrichr : http://amp.pharm.mssm.edu/Enrichr/

How to get MSI (Microsatellite Instabilty) status in TCGA Project: TCGA MSI status

A program for reliable multiplex PCR primer design: http://biocompute.bmi.ac.cn/MPprimer/

Prepare all the script in github (Version Control System) and prepare the Rmd for records.

Multiple data cluster (mRNA, Methylation, CNV, Mutation): iCluster

Mutation calling: MutSig

BBSplit: Read Binning Tool for Metagenomes and Contaminated Libraries

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categorical different domain tools - - http://molbiol-tools.ca/

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How about:

The Art of Unix Programming: http://www.catb.org/esr/writings/taoup/html/

Grymoire: http://www.grymoire.com/

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Software you need to prepare better figure:

Why not GIMP and Inkscape ? These are very useful free softwares for Linux users (Inkscape is available for Windows users too,FREE). And in R 'pheatmap' and 'ggplot2'.

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It is not free but I have used Adobe Acrobat Pro to great effect. If your institution has access to it, check it out as well. Very useful to touching up the text on PDF figures.

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Inkscape is an awesome free-source alternative to Adobe Illustrator whereas GIMP is a free-source alternative to Adobe Photoshop. Both are good tools depending on what your ultimate aim is. GIMP/Photoshop are raster/bitmap graphics and are often used to edit photographs by adding effects and making them stylish. Inkscape/Illustrator, on the other hand, are vector-based graphic editor software which are used for more precise and mathematical graphics designing. Vector-based files allow you to size your figures properly without losing resolution, as they can be altered in size while maintaining high print-quality resolution which is what you're going to need if your submitting for publication in Science, Nature, PNAS etc.

ggplot2 is awesome! Here's two links I would strongly suggest checking out 1) Getting started with ggplot2 2) Top 50 ggplots (with code)

I agree pheatmap is a nice package (the "p" stands for pretty-heatmap) and it's intuitive to use; however, sometimes you may want/need to arrange multiple heatmaps or add multiple layers of annotation so I would suggest learning ComplexHeatmap. If you're doing EDA, sharing heatmaps with collaborators, or something special for the supplements, try out Interactive Heat Maps for R Using plotly>.

I like this Shiny App for Venn Diagrams.

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It is a nice paper for whole exome pipelines comparison:

Systematic comparison of variant calling pipelines using gold standard personal exome variants

http://www.nature.com/articles/srep17875

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