Luke Zappia lazappi
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lazappi
/ graph-diffusion.R
Created
July 3, 2019 07:39
Toy implementation for propagating updates through a graph
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| library("igraph") | |
| set.seed(1) | |
| n_nodes <- 20000 | |
| raw_graph <- sample_forestfire(n_nodes, 0.1) | |
| graph_data <- get.data.frame(raw_graph) | |
| graph_data <- graph_data[, c("from", "to")] | |
| graph_data$weight <- rnorm(nrow(graph_data)) | |
| graph <- graph.data.frame(graph_data) |
lazappi
/ handy-pkgs.R
Created
September 3, 2018 01:38
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| # Handy packages! | |
| ## here | |
| # Provides a relative file path from your project directory | |
| # | |
| # https://here.r-lib.org/ | |
| # https://cran.r-project.org/web/packages/here/index.html | |
| # https://github.com/r-lib/here |
lazappi
/ splatSimulateFixedGenes.R
Created
April 9, 2018 06:04
Modified version of the splatSimulate function that allows the gene means to be fixed
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| #' Splat simulation (fixed genes) | |
| #' | |
| #' Modified version of the splatSimulate function that allows the gene means to | |
| #' be fixed | |
| #' | |
| #' @param params SplatParams object containing parameters for the simulation. | |
| #' See \code{\link{SplatParams}} for details. | |
| #' @param means vector of gene means, must be the same length as the number of | |
| #' genes to simulate | |
| #' @param method which simulation method to use. Options are "single" which |
lazappi
/ abacbs17_software.csv
Last active
November 27, 2017 22:56
Software tools mentioned at #COMBINE17 and #abacbs17 and #BiocAsia
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| url | name | user | type | |
|---|---|---|---|---|
| https://bioconductor.org/packages/splatter | splatter | NA | Bioconductor | |
| https://bioconductor.org/packages/Sushi | Sushi | NA | Bioconductor | |
| https://bioconductor.org/packages/diffHic | diffHic | NA | Bioconductor | |
| https://bioconductor.org/packages/miRBaseConverter | miRBaseConverter | NA | Bioconductor | |
| https://bioconductor.org/packages/miRLAB | miRLAB | NA | Bioconductor | |
| https://bioconductor.org/packages/miRsponge | miRsponge | NA | Bioconductor | |
| https://bioconductor.org/packages/scPipe | scPipe | NA | Bioconductor | |
| https://bioconductor.org/packages/ClassifyR | ClassifyR | NA | Bioconductor | |
| https://bioconductor.org/packages/monocle | monocle | NA | Bioconductor |
lazappi
/ clustering_tree.R
Created
October 19, 2017 01:48
Functions for plotting a clustering tree from a Seurat object that has been clustered at different resolutions, or a data.frame describing clusterings.
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| #' Get tree nodes | |
| #' | |
| #' Get the nodes required for a clustering tree | |
| #' | |
| #' @param clusterings data.frame describing clusterings at different | |
| #' resolutions. Columns must be named "res.X" where X is numeric and indicates | |
| #' the clustering resolution. | |
| #' @param tSNE data.frame giving the t-SNE positions of each cell | |
| #' | |
| #' @return data.frame contining the nodes of a clustering tree |