Charlie smartgamer

Essential Cibersort links:

Cibersort webpage: https://cibersort.stanford.edu/

Cibersortx webpage: https://cibersortx.stanford.edu/

Biomart web link: https://m.ensembl.org/info/data/biomart/index.html

Biomart R package: https://bioconductor.org/packages/release/bioc/html/biomaRt.html

A complete list of books, articles, blog posts, videos and neat pages that support Data Fundamentals (H), organised by Unit.

Formatting

If the resource is available online (legally) I have included a link to it. Each entry has symbols following it.

⨕⨕⨕ indicates difficulty/depth, from ⨕ (easy to pick up intro, no background required) through ⨕⨕⨕⨕⨕ (graduate level textbook, maths heavy, expect equations)
⭐ indicates a particularly recommended resource; 🌟 is a very strongly recommended resource and you should look at it.

Hello  (<-- two spaces)
World

Hello
World

MongoDB Cheat Sheet

Show All Databases

show dbs

Show Current Database

Hi:

perl -e 'print "hello world!\n"'

A simple filter:

perl -ne 'print if /REGEX/'

Filter out blank lines (in place):

A little experiment using restarts.

(And while we’re at it, let’s torture R’s syntax a little.)

![screenshot][]

In the following we will be using R’s “restarts” feature to implement the state machine that drives generators in languages such as Python. Generators allow lazily generating values on demand: a consumer invokes a generator, and consumes values as they are produced. A new value is only produced once the previous one has been consumed.

	RUNS, = glob_wildcards("/pine/scr/m/i/milove/{run}_1.fastq.gz")

	SALMON = "/proj/milovelab/bin/salmon-1.3.0_linux_x86_64/bin/salmon"

	ANNO = "/proj/milovelab/anno"

	rule all:
	input: expand("quants/{run}/quant.sf", run=RUNS)

	rule salmon_index:

	# The difference between the `sep` and `collapse` arguments
	# in paste can be thought of like this:
	#
	# paste can accept multiple vectors as input, and will
	# concatenate the ith entries of each vector pairwise
	# (or tuplewise), if it can.
	#
	# When you pass paste multiple vectors, sep defines what
	# separates the entries in those tuple-wise concatenations.
	#