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git
Python
Shell script
SSH
AWS (Linux)
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Kubernetes-related
Bioinformatics
Environment setup
Reference Genome Build
Misc
Manuscript-related
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Bioinformatics
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Bioinformatics
¶
Environment setup
¶
R
On MacOS, use
brew
cask
install
r-apps
rather than
brew
install
r
Reference Genome Build
¶
Reference genomes and Gene models: Impact on variant interpretation
Which human reference genome to use?
hs37d5 information
Misc
¶
Frequent File Formats
Installation of samtools
Human Reference Discrepancies
BAF
VCF files: Change Chromosome Notation
Generate vcf.gz file and its index file vcf.gz.tbi
Tools for coverage analysis:
1
,
2
WES and RNA-seq difference
BAM Tricks
How to check if duplicate reads are marked in bam file?
Manuscript-related
¶
Which Font Looks Best in a Figure?
How to write a manuscript by Springer Nature
Rainbow Color Map (Still) Considered Harmful
Related materials:
viridis
,
magma
,
plasma
, and
inferno
are colormaps recommended to be used in R.
for automatic alignment in R:
ggplot facet layout:
facet_wrap
Cowplot::plot_grid
gridExtra::arrange.grid
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