# HG changeset patch # User padge # Date 1661951853 0 # Node ID d5832ac370e3db756c1534b393585266f3f57ae7 # Parent 4a5c94d1d8bb9a146bb9fa8815e60b582dcd8719 planemo upload for repository https://github.com/kirstvh/MultiplexCrisprDOE commit a920127294bcfcb708881e28144a77a5c10d46d2-dirty diff -r 4a5c94d1d8bb -r d5832ac370e3 main.jl --- a/main.jl Wed Aug 31 12:13:10 2022 +0000 +++ b/main.jl Wed Aug 31 13:17:33 2022 +0000 @@ -1,15 +1,15 @@ using Pkg -Pkg.add("Plots"); -Pkg.add("Distributions"); +Pkg.add(Pkg.PackageSpec(name="Plots", version="1.31.7")); +Pkg.add(Pkg.PackageSpec(name="Distributions", version="0.25.68")); Pkg.add("LinearAlgebra"); -Pkg.add("Combinatorics"); -Pkg.add("BioCCP"); -Pkg.add("ArgParse"); -Pkg.add("XLSX"); -Pkg.add("DataFrames"); -Pkg.add("Weave"); -Pkg.add("DataStructures"); -Pkg.add("PrettyTables"); +Pkg.add(Pkg.PackageSpec(name="Combinatorics", version="1.0.2")); +Pkg.add(Pkg.PackageSpec(name="BioCCP", version="0.1.1")); +Pkg.add(Pkg.PackageSpec(name="ArgParse", version="1.1.4")); +Pkg.add(Pkg.PackageSpec(name="XLSX", version="0.8.2")); +Pkg.add(Pkg.PackageSpec(name="DataFrames", version="1.3.4")); +Pkg.add(Pkg.PackageSpec(name="Weave", version="0.10.10")); +Pkg.add(Pkg.PackageSpec(name="DataStructures", version="0.18.13")); +Pkg.add(Pkg.PackageSpec(name="PrettyTables", version="1.3.1")); using Random using Plots diff -r 4a5c94d1d8bb -r d5832ac370e3 report.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/report.html Wed Aug 31 13:17:33 2022 +0000 @@ -0,0 +1,707 @@ + + + + + + MultiplexCrisprDOE + + + + + + + + + + + + + + + +

+

+

+

+

MultiplexCrisprDOE

+ + +

+ + + + + + +

Tool

+

Method: BioCCP
+
Description: BioCCP-based approaches for computing the minimal plant library size that guarantees full combinatorial coverage (and other relevant statistics)
+
Mode: BioCCP_γx2
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Mode description: Computes the expected coverage of all pairwise combinations of gene knockouts (E[γx,2]) for an experiment with given plant library size using BioCCP
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+

Variables

+ + +

10 rows × 2 columns

	Argument	Value
	Any	Any
1	# of target genes in the experiment	20
2	# of gRNAs designed per target gene	6
3	# of gRNAs / combi gRNA/Cas construct	2
4	Total number of gRNAs	120
5	Relative frequencies for all gRNAs	./test-data/example_data.xlsx
6	Genome editing efficiencies for all gRNAs	./test-data/example_data.xlsx
7	Global knockout efficiency	0.8
8	Step size	5
9	Maximum Plant library size	6000
10	Plant library size	0

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+ +

+ +

+At a given number of plants, what is the expected coverage of pairwise gene
+ knockout combinations?
+N_95: 1315
+

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