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GammerdingerGammerdinger
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Polished ML lesson
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‎.Rhistory‎

Lines changed: 131 additions & 131 deletions
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as.data.frame() %>%
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sort() %>%
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View()
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ah$species %>%
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unique() %>%
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as.data.frame() %>%
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arrange() %>%
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View()
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# Query AnnotationHub
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Flathead <- query(ah, "Mugil cephalus")
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Flathead
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Flathead_annot <- ah[["AH118155"]]
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View(Flathead_annot)
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genes(Flathead_annot, return.type = "data.frame") %>% View()
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Flathead_annot
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genes(Flathead_annot)
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remove.packages("sccomp")
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remove.packages("cmdstanr")
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devtools::install_github("MangiolaLaboratory/sccomp")
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install.packages("cmdstanr", repos = c("https://stan-dev.r-universe.dev/", getOption("repos")))
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cmdstanr::check_cmdstan_toolchain(fix = TRUE) # Just checking system setting
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cmdstanr::install_cmdstan()
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cmdstanr::install_cmdstan(overwrite=TRUE)
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remove.packages("sccomp")
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remove.packages("cmdstanr")
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devtools::install_github("MangiolaLaboratory/sccomp")
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remove.packages("sccomp")
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install.packages("cmdstanr", repos = c("https://stan-dev.r-universe.dev/", getOption("repos")))
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cmdstanr::check_cmdstan_toolchain(fix = TRUE) # Just checking system setting
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cmdstanr::install_cmdstan()
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remove.packages("sccomp")
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remove.packages("cmdstanr")
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devtools::install_github("MangiolaLaboratory/sccomp")
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install.packages("cmdstanr", repos = c("https://stan-dev.r-universe.dev/", getOption("repos")))
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cmdstanr::check_cmdstan_toolchain(fix = TRUE) # Just checking system setting
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cmdstanr::install_cmdstan()
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seurat <- readRDS("~/Desktop/DGE_scRNA/data/BAT_GSE160585_final.rds")
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seurat_sub <- subset(seurat, subset = (condition %in% c("TN", "cold7")))
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library(sccomp)
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sccomp_result <- seurat_sub %>%
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sccomp_estimate(
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formula_composition = ~ condition,
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.sample = sample,
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.cell_group = celltype,
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bimodal_mean_variability_association = TRUE,
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cores = 1
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) %>%
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sccomp_remove_outliers(cores = 1, verbose = FALSE) %>% # Optional
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sccomp_test()
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library(tidyverse)
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sccomp_result <- seurat_sub %>%
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sccomp_estimate(
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formula_composition = ~ condition,
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.sample = sample,
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.cell_group = celltype,
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bimodal_mean_variability_association = TRUE,
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cores = 1
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) %>%
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sccomp_remove_outliers(cores = 1, verbose = FALSE) %>% # Optional
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sccomp_test()
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cmdstanr::check_cmdstan_toolchain(fix = TRUE)
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cmdstanr::install_cmdstan()
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cmdstanr::install_cmdstan(overwrite=TRUE)
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remove.packages(sccomp)
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remove.packages("sccomp")
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remove.packages("cmdstanr")
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devtools::install_github("MangiolaLaboratory/sccomp")
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install.packages("cmdstanr", repos = c("https://stan-dev.r-universe.dev/", getOption("repos")))
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cmdstanr::check_cmdstan_toolchain(fix = TRUE) # Just checking system setting
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cmdstanr::install_cmdstan()
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cmdstanr::install_cmdstan()
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cmdstanr::install_cmdstan(overwrite = TRUE)
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cmdstanr::check_cmdstan_toolchain(fix = TRUE)
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cmdstanr::install_cmdstan()
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cmdstanr::install_cmdstan(overwrite=TRUE)
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cmdstanr::remove_cmdstan()
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cmdstanr::install_cmdstan()
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cmdstanr::install_cmdstan(overwrite = TRUE)
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cmdstanr::install_cmdstan(overwrite = TRUE)
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install.packages("cmdstanr", repos = c("https://stan-dev.r-universe.dev/", getOption("repos")))
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cmdstanr::check_cmdstan_toolchain(fix = TRUE) # Just checking system setting
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cmdstanr::install_cmdstan()
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cmdstanr::install_cmdstan(overwrite = TRUE)
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system(quarto render schedule.qmd)
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getwd()
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setwd("Desktop/intro_r_rmd/lessons/")
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system(quarto render schedule.qmd)
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system("quarto render schedule.qmd")
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system("quarto render schedule.qmd")
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getwd()
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system("quarto render schedule.qmd")
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system("quarto render schedule.qmd")
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system("quarto render 01-introR-R-and-RStudio.qmd")
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system("quarto render 01_introR-R-and-RStudio.qmd")
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system("quarto render 01a_introR-R-and-RStudio.qmd")
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system("quarto render 01b_introR-R-and-RStudio.qmd")
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system("quarto render 01b_introR-R-and-RStudio.qmd")
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system("quarto render 01a_introR-R-and-RStudio.qmd")
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system("quarto render 01b_introR-R-and-RStudio.qmd")
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system("quarto render 01b_introR-R-and-RStudio.qmd")
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system("quarto render 01b_introR-R-and-RStudio.qmd")
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system("quarto render 01b_introR-R-and-RStudio.qmd")
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system("quarto render 01b_introR-R-and-RStudio.qmd")
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system("quarto render 01b_introR-R-and-RStudio.qmd")
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age <- c(10, 25, 60, NA)
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age > 26
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age [age > 26]
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which(age > 26)
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?which
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library(ggplot2)
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?read.table
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number-mean <- 2 +5
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pos_0 <- c(1,2,2,3,2,3,3,3,2,3,3)
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neg_0 <- c(0,0,0,0,0,0,0,0,0,0,1)
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cor(pos_0, neg_0, method = 'pearson')
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library(tidyverse)
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tib_0 <- tibble(pos_0, neg_0)
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cor(tib_0$pos_0, tib_0$neg_0, method = 'pearson')
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ggplot(tib_0) +
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geom_point(aes(x = pos_0, y = neg_0))
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ggplot(tib_0) +
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geom_point(aes(x = pos_0, y = neg_0)) +
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geom_jitter()
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ggplot(tib_0) +
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geom_jitter(aes(x = pos_0, y = neg_0))
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?geom_jitter
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load("~/Desktop/GOs_for_plotting.RData")
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# Subset data frame
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bp_plot <- bp_oe[1:30, ]
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ggplot(bp_plot) # what happens?
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library(tidyverse)
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devtools::install_github("immunogenomics/presto")
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install.packages("seurat")
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install.packages("Seurat")
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library(tidyverse)
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getwd()
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setwd("~/Documents/Intro-to-Python/")
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system("quarto render lessons/05_loops.qmd")
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system("quarto render lessons/05_loops.qmd")
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system("quarto render lessons/05_loops.qmd")
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system("quarto render lessons/05_loops.qmd")
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system("quarto render lessons/05_loops-Answer_key.qmd")
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system("quarto render lessons/05_loops.qmd")
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getwd()
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system("quarto render lessons/05_loops.qmd")
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system("quarto render lessons/05_loops.qmd")
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system("quarto render lessons/05_loops-Answer_key.qmd")
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system("quarto render lessons/06_functions-Answer_key.qmd")
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system("quarto render lessons/06_functions.qmd")
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system("quarto render lessons/07_libraries.qmd")
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system("quarto render lessons/08_numpy_arrays.qmd")
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python -m ipykernel install --user --name intro_python --display-name "intro_python"
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system("quarto render lessons/01_setting_up-Answer_key.qmd")
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