gpcr

Drag a rectangle around an area of interest to zoom in.

If anyone is interested in a more general version (to take in custom data), or would like me to correct something, leave a comment on the gist.

dad	mom	kid	Inheritance description
HOM_REF	HOM_REF	HOM_REF	Expected
HOM_REF	HOM_REF	HET	Mendelian violation (plausible de novo)
HOM_REF	HOM_REF	HOM_ALT	Mendelian violation (implausible de novo)
HOM_REF	HOM_ALT	HOM_REF	Mendelian violation (uniparental disomy)
HOM_REF	HOM_ALT	HET	Expected
HOM_REF	HOM_ALT	HOM_ALT	Mendelian violation (uniparental disomy)
HOM_REF	HET	HOM_REF	Expected
HOM_REF	HET	HET	Expected

	========================================== ==========================================
	TMUX COMMAND WINDOW (TAB)
	========================================== ==========================================

	List tmux ls List ^b w
	New -s <session> Create ^b c
	Attach att -t <session> Rename ^b , <name>
	Rename rename-session -t <old> <new> Last ^b l (lower-L)
	Kill kill-session -t <session> Close ^b &

	## data input (number of reads mapped to each category)
	total=100
	rRNA=5 # mapped to nuclear rRNA regions
	mtRNA=7 # mapped to mitochondria genome
	# for the rest of above, then we divide into different category, like http://www.biomedcentral.com/1741-7007/8/149 did.
	intergenic=48
	introns=12
	exons=30
	upstream=3
	downstream=6

	"""
	Multiclass SVMs (Crammer-Singer formulation).

	A pure Python re-implementation of:

	Large-scale Multiclass Support Vector Machine Training via Euclidean Projection onto the Simplex.
	Mathieu Blondel, Akinori Fujino, and Naonori Ueda.
	ICPR 2014.
	http://www.mblondel.org/publications/mblondel-icpr2014.pdf
	"""

	#' When plotting multiple data series that share a common x axis but different y axes,
	#' we can just plot each graph separately. This suffers from the drawback that the shared axis will typically
	#' not align across graphs due to different plot margins.
	#' One easy solution is to reshape2::melt() the data and use ggplot2's facet_grid() mapping. However, there is
	#' no way to label individual y axes.
	#' facet_grid() and facet_wrap() were designed to plot small multiples, where both x- and y-axis ranges are
	#' shared acros all plots in the facetting. While the facet_ calls allow us to use different scales with
	#' the \code{scales = "free"} argument, they should not be used this way.
	#' A more robust approach is to the grid package grid.draw(), rbind() and ggplotGrob() to create a grid of
	#' individual plots where the plot axes are properly aligned within the grid.

	# slide 4
	curl https://s3.amazonaws.com/gemini-tutorials/trio.trim.vep.vcf.gz > trio.trim.vep.vcf.gz
	curl https://s3.amazonaws.com/gemini-tutorials/recessive.ped > dominant.ped
	gemini load --cores 4 \
	-v trio.trim.vep.vcf.gz \
	-t VEP \
	--skip-gene-tables \
	-p dominant.ped \
	trio.trim.vep.dominant.db

	#!/usr/bin/env python
	import sys
	import pprint

	def make_grantham_dict(grantham_mat_file):

	"""
	Citation: http://www.ncbi.nlm.nih.gov/pubmed/4843792
	Provenance: http://www.genome.jp/dbget-bin/www_bget?aaindex:GRAR740104