sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
2048802e44b29e194b4004c48cfd0a1b51a704073acd6f65a1106cd08de30be8 | R | 2,407 | 118 | # ==========================
# 1. Input
# ==========================
file_chromosome <- file.path(
data_processed_dir,
"chromosome_methylation_summary.tsv"
)
df <- read_tsv(file_chromosome)
# rename
df <- df %>%
rename(
Chromosome = Chromoso
)
# fix age group
df$Age_group <- factor(
df$Age_grou... |
282c1d7d44aff86e2908dd1215a849d402b846b3155657fe5ff861c2b0b8f69d | R | 2,410 | 91 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
clustering_table_parcoord_ui <- function(
id,
label = "",
title,
info.text,
caption,
height,
width
) {
ns <- shiny::NS(id)
TableModuleUI(
ns("datasets"),
info.t... |
70e4c951a72242fbd4765ca618461650e124eff18c47e4dcd76f66d3f853e519 | R | 2,411 | 89 | #!/usr/bin/env Rscript
if (commandArgs()[1] != "RStudio") {
ARGS <- c(
"tlxfiles", "character", "comma-separated list of files or dir and will grab all *.tlx",
"bedfile","character","",
"outdir","character", "file path to plot to"
)
OPTS <- c(
"tlxlabels","character","",""
)
... |
ed31b1b63e2f854f0b74f7e76bf872fb7e14240e137f8efa31b83caad6b29452 | R | 2,424 | 50 | .onAttach <- function(libname, pkgname) {
options(future.globals.maxSize = Inf)
env <- FALSE
if (isTRUE(getOption("SCP_env_init", default = TRUE))) {
conda <- find_conda()
if (!is.null(conda)) {
envs_dir <- reticulate:::conda_info(conda = conda)$envs_dirs[1]
env <- env_exist(conda = conda, env... |
a21a4a7956458fedb3bbe8b2b1b19547a8a7aa76b42756dd8955e3f3606787f7 | R | 2,451 | 62 | suppressMessages(library(dplyr))
suppressMessages(library(data.table))
suppressMessages(library(ggplot2))
plotNBdist <- function(probs, alpha = 0.05) {
assert_that(is.data.table(probs),
"sample" %in% colnames(probs),
"cell" %in% colnames(probs),
"chrom" %in% colnames(p... |
40691315775a20436ad0da9ad0adc0663279fe4ab06710813ca3f1cb85e287d1 | R | 2,466 | 89 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
wgcna_plot_s_independence_ui <- function(
id,
label = "",
title = "",
info.text = "",
caption = info.text,
height,
width,
...
) {
ns <- shiny::NS(id)
PlotModuleUI(
... |
35fa0f7ef1e0553f58fbf8b5be71c87344a55af478f57bf7ed50f7d1b655b483 | R | 2,472 | 83 | rm(list = ls())
library(Seurat)
library(BASS)
set.seed(1234)
# The data with format required by BASS are available at:
# https://drive.google.com/drive/folders/1NVROB3oyBgBEzCt1yH_AJe6uSIjspDLf?usp=sharing, and
# https://drive.google.com/drive/folders/1qJiZUYhTCVlpYXwFa6xE9JsCnZn8qrMP?usp=sharing
cluster_df <- re... |
2f137448413c62a749989d9d34653301b20bed8fb49d8754383fa34547f17bf1 | R | 2,494 | 105 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
drugconnectivity_table_dsea_ui <- function(
id,
title,
info.text,
caption,
width,
height
) {
ns <- shiny::NS(id)
TableModuleUI(
ns("datasets"),
title = title,
... |
e96cb3e8cf4cefa5a6065f5f1fcc36f767bcb32f1d581593799516746f611414 | R | 2,494 | 60 | rm(list=ls())
library(ggplot2)
library(gridExtra)
library(ggrepel)
setwd("D://work//skoltech//lipid//writing//GitHub//data")
info.milk <- read.csv("brain_milk_FA.info.milk.csv", row.names = 1)
info.PFC <- read.csv("brain_milk_FA.info.PFC.csv", row.names = 1)
info.CB <- read.csv("brain_milk_FA.info.CB.csv",... |
647e4763b1359872354b2ae8cf63649ea6ac4fff5894712d0110547c43df3905 | R | 2,499 | 102 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
mofa_plot_moduleheatmap_ui <- function(
id,
title = "",
info.text = "",
caption = "",
label = "",
height = 400,
width = 400
) {
ns <- shiny::NS(id)
options <- shiny::tag... |
8ea1f0e2b4d33427e77442241378ef3346bf695dc8223d7a7a2d1f605b16f710 | R | 2,514 | 69 | ---
title: "Figure 1E: All-Subclass DotPlot with Collapsed 'IT' Subclass"
output:
---
```{r setup, include=FALSE}
# This sets the project root based on the repo structure.
# If you move this file, you may need to set the root manually to find config.R
knitr::opts_knit$set(root.dir = dirname(dirname(rstudioapi::getSou... |
13a0790ff04c1d497dc080cd77262efe953be04f60d48f64f8477350688c0713 | R | 2,520 | 82 | # This program will eliminate ambient RNA via SoupX
####################
## Load Libraries ##
####################
library(Seurat)
library(SoupX)
library(dplyr)
###########################
## Set working directory ##
###########################
setwd('/share/lasallelab/Osman/2021_PEBBLES_Cortex/2021_mouse_PCB_raw_rea... |
2699502338128ef027003c194f56ac42b6650b95f5154ed4bb7b07eb70ed5694 | R | 2,522 | 84 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
wgcna_plot_heatmap_membership_ui <- function(
id,
label = "",
title = "",
info.text = "",
caption = "",
height,
width
) {
ns <- shiny::NS(id)
intraHeatmap_opts <- shiny:... |
97e48848c78a3fc041b40929c59449d3f24652a331dcc423585d5a09566a7722 | R | 2,523 | 88 |
#' @docType package
#'
#' @keywords internal package
#'
#' @aliases pbmc3k-package NULL
#'
'_PACKAGE'
#' PBMC 3k
#'
#' 2,700 peripheral blood mononuclear cells (PBMC) from 10X genomics; this is
#' effectively what one would get with
#' \code{\link[Seurat:Read10X]{Seurat::Read10X}()}
#'
#' @format A \code{\link[Matrix... |
2c2267a5f1af9e717f44ae16cbe19c8231a6f0665f79e8015457c5797039a8e7 | R | 2,537 | 80 | burden<-list()
burden$id <- "burden"
burden$title <- "Burden Evidence"
burden$loadData<- function(){
#read the minimum p values for allburden tests for all the genes
burdenData <<- fread("www/burden/BurdenPValueData.csv")
}
burden$generateUI<- function(){
div(id = "burdenSection",
fluidRow(
... |
7ffbe7d98b62a09ae47eb0fcf193875773b9e62e33e22aa8ed1342b1baa49435 | R | 2,539 | 94 | lasagna_multipartite_edges_table_ui <- function(id,
label = "",
title = "",
info.text = "",
caption = "",
... |
659f3a2a6d6ae1915aaba8a6de5d03789e7f7dd707c850d4a5c234d26773ee5d | R | 2,556 | 91 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
signature_table_genes_in_signature_ui <- function(
id,
title,
info.text,
caption,
width,
height
) {
ns <- shiny::NS(id)
TableModuleUI(
ns("datasets"),
info.text = ... |
3a38324026fc182927bf894f90be53d8a23efcc31ff945dfe6654812257f5a72 | R | 2,559 | 62 | #################
### Load data ###
#################
rm(list=setdiff(ls(),c('params','grp')))
basedir <- params$basedir
setwd(basedir)
savedir <- paste(params$opdir,'diffmodel/traintest/',sep='')
dir.create(savedir,recursive=T)
source('code/fitfxns.R')
load(paste(params$opdir,'processed/pathdata.RData',sep='')) # lo... |
dabe96a091b604603fbfeb8a8619fad54d905f98973d1a5ffa5d30ff2d49e8aa | R | 2,559 | 97 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
RDIR = "../R"
FILES = "../lib"
FILESX = "../libx"
PGX.DIR = "../data"
FILES
source(file.path(RDIR,"pgx-include.R"))
pgx.files <- dir(".", pattern=".pgx$")
##pgx.files <- grep("X.pgx$",pgx... |
6df74ecfc328bd6dd6597cc652e1f5f5bcd1e0f7110b8cac04e3689104a2d0c9 | R | 2,574 | 105 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
wgcna_plot_geneset_heatmap_ui <- function(
id,
label,
title,
info.text,
caption,
height,
width
) {
ns <- shiny::NS(id)
options <- shiny::tagList(
shiny::checkboxGrou... |
e276262f0f3a584672b221528d9840f5995e0e73b1cd40210d3af96fa41a5a09 | R | 2,581 | 98 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
wgcna_plot_module_membership_ui <- function(
id,
label = "",
title = "",
info.text = "",
caption = "",
height,
width
) {
ns <- shiny::NS(id)
opts <- shiny::tagList(
... |
3c5b44122f6fcc8bfbfd59f85baae81e3249bf5a515fee077db079043153a969 | R | 2,598 | 76 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
## Create global "source_all" file
##path='R';hdr.file="R/00Headers.R";excl.files=NULL
create_SourceAll <- function(path='R',
add.comments=TRUE,
... |
8c524dc0734f58ff076b768cdcb60a46a0535b9fd3425ff27e89eec67ff21dbe | R | 2,600 | 107 | #' returns the hapotyoe name
#'
#' @param hap.code The haplotype coding
#' @author Maryam Ghareghani
#' @export
#'
get_hap_name <- function(hap.code)
{
hap.codes <- c("1010", "0010", "1000", "0000", "0110", "1001", "0101", "2010", "1020", "2020", "1110", "1011")
hap.names <- c("ref_hom", "del_h1", "del_h2", "del... |
54b34334b1e2de3ae94f49b6c48b981e21ee499b04c22245d333df7542715ab8 | R | 2,601 | 69 | library(data.table)
meta<-read.csv("cell-annotation.n424.csv.gz",header=T)
meta$cell.type<-gsub(" ","_",meta$cell.type)
library(Seurat)
library(SeuratDisk)
library(SeuratData)
returndata<-function(celltype,filename){
cell.in<-as.character(meta[meta$cell.type==celltype,]$barcode)
meta2<-meta[meta$cell.type==celltyp... |
f1d0c068524b93fd4f7448d8fb19854af4f5ba2df4d68954a6d21f7b0a9f64a1 | R | 2,603 | 103 | #' ============================================================================
#' Logging Utilities for PCB snRNA-seq Analysis
#' ============================================================================
#' Log Message with Timestamp
log_message <- function(message, level = "INFO", verbose = TRUE) {
if (!verb... |
9d54f86506b2f26aa53992d793585fdffc05cb4c7dd120123190d5a26e024285 | R | 2,622 | 58 | v2_2 <- read.delim("raw/cognition/V2.csv", sep = ",")
v2_3 <- read.delim("raw/cognition/V2 vs V3.csv", sep = ",")
v2_4 <- read.delim("raw/cognition/V2 vs V4.csv", sep = ",")
inter <- read.delim("raw/cognition/intervention.csv", sep = ",")
wash <- read.delim("raw/cognition/washout.csv", sep = ",")
colnames(v2_... |
fb33cd101227c3351e2836a3909e766c4fe8bcb3b9eaecfbbe6554877ccb94a0 | R | 2,622 | 101 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
mofa_plot_modulegraph_ui <- function(
id,
title = "",
info.text = "",
caption = "",
label = "",
height = 400,
width = 400
) {
ns <- shiny::NS(id)
options <- tagList(
... |
e420d1a90ed6b57a2b669815aa09ea48f39a578680eb932f0d756cb1bb12a5fe | R | 2,634 | 107 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
mofa_plot_snf_ui <- function(
id,
title = "",
info.text = "",
info.references,
info.methods,
caption = "",
label = "",
height = 400,
width = 400
) {
ns <- shiny::NS(id)... |
80bb3833038539db88ed2c5b720a6cfa7b21882a44cfcbd896bdc32016a68437 | R | 2,641 | 151 | library(dampack)
strategies <- c(
"AUG",
"COM",
"PSY alone",
"PSY+AD",
"ESK+AD",
"rTMS+AD",
"ECT+AD"
)
costs <- c(
16185,
16163,
19538,
21555,
29061,
30607,
46471
)
qalys <- c(
2.895,
2.903,
2.879,
2.926,
2.950,
2.936,
3.004
)
icer_my <- calculate_icers(
cost = costs,
e... |
2ec2ef12b8cd47da616fcb9437fa2842bd71e12feb5b131d39046c7406d6d7e3 | R | 2,646 | 96 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
signature_table_overlap_ui <- function(
id,
title,
info.text,
caption,
width,
height
) {
ns <- shiny::NS(id)
TableModuleUI(
ns("datasets"),
info.text = info.text,
... |
6f9e3680387c0dfa6c792afc624a5b43952894bcce65ceb7ccbac83af51d1826 | R | 2,650 | 60 | ##############################
## Upset plot of KEGG terms ##
##############################
# Author : Osman Sharifi
# Load libraries
library(UpSetR)
library(dplyr)
library(ggplot2)
library(glue)
#load data
file_paths <- list(
Glut_human = "/Users/osman/Documents/GitHub/PEBBLES_mouse_snRNAseq/09_human_DEG_analysis... |
3af2be3cb547309129f376bf143e42a913e58cd1e48b72d28c6fe04eecbc09ae | R | 2,652 | 98 | #### config.R
## 1. Read YAML config
## 2. Install/load comparatome
## 3. Build dir.list with absolute paths
## 4. Create directories if needed
## 5. (Optional) Download processed GEO data
if (!requireNamespace("yaml", quietly = TRUE)) {
install.packages("yaml")
}
library(yaml)
# Read YAML
cfg <- yaml::read_yaml("c... |
f2c75e775cf5568d8dcc7d0d898768b69a00ff257d7f4ab2feffebea9b6e83e1 | R | 2,659 | 68 | # Read in data from directory where you have it stored using read.csv in R
file_path <- file.choose()
file_directory <- dirname(file_path)
CHL <- read.csv(paste0(file_directory, "/step7_CL.out"))
A570 <- read.csv(paste0(file_directory, "/step7_570A.out"))
B570 <- read.csv(paste0(file_directory, "/step7_570B.out"... |
9ed0978e785217efeda03542828da5a3dfc2c31f46f9fc15feb66c97d90b1f11 | R | 2,663 | 57 | # plot fLME models
## Figure 4
plot.freg <- function(fit_dat, r, align, Hz, var_name = NULL, title = NULL){
library(gridExtra)
name = NULL
# var_name <- c("Intercept", "Case", "Scan Date (yr)", "Sex", "Age at Baseline (yr)")
if(is.null(var_name)) var_name <- paste0("Variable", r)
# if(nrow(fit_dat$beta.ha... |
566edba60a4d09b24807caf3a5ad06a05a260591a8323dae579bec3866e897d3 | R | 2,665 | 68 | # Read in data from directory where you have it stored using read.csv in R
file_path <- file.choose()
file_directory <- dirname(file_path)
SOD <- read.csv(paste0(file_directory, "/step7_NA.out"))
A570 <- read.csv(paste0(file_directory, "/step7_570A.out"))
B570 <- read.csv(paste0(file_directory, "/step7_570B.out"... |
d445c8a45e496d7c2b595494d2fdc3178158a72c843893e169221257d62d0fee | R | 2,666 | 87 |
shinyServer(function(input, output,session) {
drive_deauth()
tutorialLogic(session,input,output)
source("about.R", local = T)
shinyjs::show("splashLogo")
startAnim(session,
id = "splashLogo",
type = "flipInX")
output$logoImage <- renderImage({
list(src = "IDPGC-locusbr... |
b0f330d9647931ae358a480f2056d09e74628ef7b7084c0b98726b4cdfbed009 | R | 2,675 | 79 | get.L.out <- function(W){
# stepwise prediction, i.e. from one month to the next
# Where i is row element and j is column element
# Wij is a connection from region i to region j
# convention is the opposite, so without transposing W
# I am capturing "retrograde" connectivity
in.deg <- colSums(W)
out.de... |
b880eedcaff20d8817c428f31355135e3b61b9b11de2fd01d4e494464ce53bfb | R | 2,679 | 90 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
#' AdminPanel module UI Input function
#'
#' @description A shiny Module. Renders the input parts (sidebar contents) for the module.
#'
#' @param id Internal parameters for {shiny}.
#'
#'... |
58d678da701a1fe41dd6a8bac9c5519f7db055dfa5af3ef10dd02b15d52206f0 | R | 2,704 | 94 | # This is a copy of the original code from the standard version of the
# sva package that can be found at
# https://bioconductor.org/packages/release/bioc/html/sva.html
# The original and present code is under the Artistic License 2.0.
# If using this code, make sure you agree and accept this license.
# Following f... |
bc8fec907352d1b9e3db3188e7b3db74ecb484643953b4c4b95d046aee618b68 | R | 2,706 | 105 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
mofa_plot_boxplots_ui <- function(
id,
title = "",
info.text = "",
caption = "",
label = "",
height = 400,
width = 400
) {
ns <- shiny::NS(id)
options <- shiny::tagList(... |
f981e08f9ed4073feb06032dfa4e549132a8d102b397c65adaaeec117ff4c840 | R | 2,717 | 93 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
# PlotModuleUI for pcaplot
upload_plot_pcaplot_ui <- function(id,
title,
info.text,
... |
a66067bec0909811caab04907e6a141a7313db94e159ea1405107f1581f72e3f | R | 2,725 | 99 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
plot_deepnet_gradients_ui <- function(
id,
title = "",
info.text = "",
info.methods,
info.references,
caption = "",
label = "",
height = c("100%", TABLE_HEIGHT_MODAL),
wi... |
94f8de4ae3903256feeed9c6c9b2a79d6ae3e7d5e284652af18ccc371fa5fe5d | R | 2,728 | 93 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
preservationWGCNA_plot_eigenNetwork_ui <- function(
id,
title = "",
info.text = "",
caption = "",
label = "",
height = 400,
width = 400
) {
ns <- shiny::NS(id)
options <... |
8d493f39d4b39fd1f914a50878e7338ba92b011c7f311675a4ed5e7ffb74fedf | R | 2,733 | 105 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
mofa_plot_lasagna_partite_ui <- function(
id,
title = "",
info.text = "",
info.methods = "",
info.references = NULL,
info.extra_link = NULL,
caption = info.text,
label = ""... |
7a41293804c24956a49d37c1dd6633b2c585a7e6d0da3d2200e335171beda626 | R | 2,761 | 102 | suppressMessages(library(dplyr))
suppressMessages(library(data.table))
suppressMessages(library(assertthat))
addPositions <- function(segs, counts) {
assert_that(
is.data.table(counts),
"chrom" %in% colnames(counts),
"start" %in% colnames(counts),
"end" %in% colnames(counts),
"sample" %in% colnam... |
de6710531930ffecf739ddfe6d55d8ff9998d4b1b0d4b3052ad36b27d976d5e7 | R | 2,761 | 92 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
wordcloud_plot_enrichment_ui <- function(
id,
title,
info.text,
info.methods,
info.references,
info.extra_link,
caption,
height
) {
ns <- shiny::NS(id)
PlotModuleUI(
... |
d820732b6dc9e521746cd4eac550d038133db9db122e1147d856a95315701ce6 | R | 2,765 | 85 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
## ---------------------------------------------------------------
## Color Theme Defaults
## ---------------------------------------------------------------
COLOR_THEME_DEFAULTS <- list(... |
4acbc4ebb2cd1f6d8dc72df01ad66f2ffdfee1a300a4915e8544d42d564a5edb | R | 2,771 | 102 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
mofa_table_mgsea_ui <- function(
id,
label = "",
title = "",
info.text = "",
caption = "",
height = 400,
width = 400
) {
ns <- shiny::NS(id)
TableModuleUI(
ns("table... |
66692cce6bad7dfe4623aac37c8e44a71533ee2fe9f5c8727b71c2e65f6d3cb1 | R | 2,798 | 84 | library(coloc)
options(stringsAsFactors=F)
library(stringr)
library(dplyr)
library(data.table)
chunk<-commandArgs(trailingOnly = T)[1]
# prep chunk file
chunkfile<-read.table(paste0("/path/to/chunkfile.txt"))
colnames(chunkfile)<-c("chr","gene")
# prep sample size
nuc_n<-sample_n_in_nucseq
bulk_n<-1092
data="ROSMA... |
25a7c1c7f63d13fc6633be246f5ae7636ef6d31284022b67fe32460b8d633b39 | R | 2,801 | 74 | rm(list=ls())
library(ggplot2)
library(reshape2)
library(stringr)
library(gridExtra)
library(ggrepel)
library(plyr)
setwd("D://work//skoltech//lipid//writing//GitHub//data")
DATA.milk <- read.csv("milk_FA.normalized.csv", row.names = 1)
info.milk <- read.csv("milk_FA.info.csv", row.names = 1)
info.shg... |
9d9f7c812eaddb9361560ec27836b78acd60f3be8907c0e4c352e5107767be84 | R | 2,813 | 103 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
#' Importance plot UI input function
#' @description A shiny Module for plotting (UI code).
#' @param id
#' @param label
#' @param height
#' @export
biomarker_plot_importance_ui <- functio... |
74498b8468d29683dadf29d25e9497a88153ecbb421ff6bbdc1557176afb9e8f | R | 2,819 | 87 | suppressMessages(library(mc2d))
suppressMessages(library(dplyr))
suppressMessages(library(data.table))
suppressMessages(library(assertthat))
source("workflow/scripts/mosaiclassifier_scripts/mosaiClassifier/getDispParAndSegType.R")
# defining multinomial parameters based on haplosegType and alpha
getMultinomialParams <... |
c4a5cd5d1dbd2e157930e6a9368b5675fa2d9ee53a74c8e268c900e21953b9ec | R | 2,820 | 73 | file_path <- file.choose()
file_directory <- dirname(file_path)
CHL <- read.csv(paste0(file_directory, "/ZFA_CLA.out"))
A570 <- read.csv(paste0(file_directory, "/ZFA_570A.out"))
B570 <- read.csv(paste0(file_directory, "/ZFA_570B.out"))
A551 <- read.csv(paste0(file_directory, "/ZFA_551A.out"))
B551 <- read.csv(pas... |
7d92d2d298e5504480d2431464b0de90770bb6b5b65f90936f21ef79e5a07bcd | R | 2,826 | 73 | file_path <- file.choose()
file_directory <- dirname(file_path)
POT <- read.csv(paste0(file_directory, "/ZFA_POT.out"))
A570 <- read.csv(paste0(file_directory, "/ZFA_570A.out"))
B570 <- read.csv(paste0(file_directory, "/ZFA_570B.out"))
A551 <- read.csv(paste0(file_directory, "/ZFA_551A.out"))
B551 <- read.csv(pas... |
cab7a289cd7a2910fe976b8496bbf735998c36d096ac001d95fee0317a1b34fd | R | 2,831 | 61 | #################
### Load data ###
#################
rm(list=setdiff(ls(),c('params')))
basedir <- params$basedir
setwd(basedir)
savedir <- paste(params$opdir,'G20vsNTG/',sep='')
dir.create(savedir,recursive=T)
source('code/fitfxns.R')
load(paste(params$opdir,'processed/pathdata.RData',sep='')) # load path data and ... |
8822fd67503cc0cf9b44aa18a20a221faef3c71722e0bb53f40a35a25926fcba | R | 2,834 | 93 | #==========
# GEE analysis
# used to test phenotypic associations
#
# author: Giorgia Bussu
# project: BT missing data
# version: June 2024
#==========
rm(list=ls())
data <- read.csv(file='C:/Users/myfolder/long_wcontinuous_data.csv',header=T,
sep=',')
names(data);dim(data)
quest<-rea... |
99dfe380a08796b4820d672b897fe362fb012301b2070ea1299324cc8c17f57a | R | 2,841 | 122 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
wordcloud_plot_wordtsne_ui <- function(
id,
height,
title,
info.text,
info.methods,
info.references,
info.extra_link,
caption
) {
ns <- shiny::NS(id)
wordtsne_options ... |
5e069009c107ef3bc6e881b76ac53e1674b2f5b4223183153d44436e41080e4e | R | 2,853 | 105 | # =========================================================
# Plot Figure 1 from PCA results
# =========================================================
library(data.table)
library(ggplot2)
library(patchwork)
# -----------------------------
# 1. Paths
# -----------------------------
data_processed_dir <- "... |
6c7bbb287d3b980fbaa445fb0e92e4a5d95091890094bfd69ad8fb62c6f6d257 | R | 2,854 | 84 | library(data.table)
library(dplyr)
library(assertthat)
f_segments <- "/g/korbel2/weber/MosaiCatcher_output/POOLING/POOLING2_190822_200KB/segmentation/HGSVCxpool2/Selection_jointseg.txt"
f_counts = "/g/korbel2/weber/MosaiCatcher_output/POOLING/POOLING2_190822_200KB/counts/HGSVCxpool2/HGSVCxpool2.txt.gz"
f_segments = "/g... |
629c0ecd7740c65d3285952a14fd322530ca03cc76eeeb6444d5dea2f97b9a43 | R | 2,868 | 107 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
mofa_plot_enrichment_ui <- function(
id,
title = "",
info.text = "",
caption = "",
label = "",
height = 400,
width = 400
) {
ns <- shiny::NS(id)
options <- tagList(
... |
66a2821c8ef3a8ec64b9b0e347c0b48535ebb8e53debbf4075da684293bc3d87 | R | 2,874 | 97 | lasagna_multipartite_pheno_table_ui <- function(id,
label = "",
title = "",
info.text = "",
caption = "",
... |
31e0f534487f8cdc103fe4c43dc6f133f4891e989760578d49e6b31219ea2401 | R | 2,878 | 140 | # ==========================
# Figure 2: Feature methylation (NO statistics)
# ==========================
library(tidyverse)
library(patchwork)
# ==========================
# 1. Input
# ==========================
file_feature <- file.path(
data_processed_dir,
"feature_methylation_matrix.tsv"
)
df ... |
2d5e98cffd657cb0434d013af4d00ce3323e331daaf5c19d6ec6236bee92bca0 | R | 2,885 | 77 | suppressMessages(library(dplyr))
suppressMessages(library(data.table))
suppressMessages(library(assertthat))
addPositions <- function(segs, counts) {
assert_that(is.data.table(counts),
"chrom" %in% colnames(counts),
"start" %in% colnames(counts),
"end" %in% colnames(counts... |
75b9a7e5d671f70d5f58917bda25fc7e5d9495a9a23038bc6da600c625ff5d06 | R | 2,890 | 66 | locusZoom<-list()
locusZoom$id <- "locuszoom"
locusZoom$title <- "Locus Zoom"
locusZoom$loadData<- function(){
}
locusZoom$generateUI<- function(){
fluidRow(
column(tabsetPanel(type="pills",
tabPanel("Interactive",
fluidRow(
... |
59afb9e9200b247e71ade280b873e1b2a42c0b9f70e8383e5c1eefb7023fe841 | R | 2,894 | 76 | # log <- file(snakemake@log[[1]], open = "wt")
# sink(file = log, type = "message")
# sink(file = log, type = "output")
options(show.error.locations = TRUE)
options(warn = 1)
library(data.table)
library(assertthat)
source("/g/korbel2/weber/workspace/mosaicatcher-update/workflow/scripts/arbigent_utils/mosaiclassifier_... |
4a43c6137c4c057131e532285145c82a6fd117083cf387abf8098cbfd5cbd753 | R | 2,895 | 122 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
#' Expression plot UI input function
#' @description A shiny Module for plotting (UI code).
#' @param id
#' @param label
#' @param height
#' @param width
#' @export
expression_plot_fc_fc_u... |
be858c648dd01115d0ab5f4264e12692c4601c9b68cd8feae0764a892adfe300 | R | 2,899 | 94 | library(ggplot2)
library(data.table)
library(dplyr)
#gwases we want to make plots for
gwases <- c("Asian","Progression")# c("META5","Progression", "Asian")
genes_by_locus <- fread("genes_by_locus.csv")
gwas_genes_df <- unique(genes_by_locus %>% filter(GWAS%in% gwases) %>% select(GENE))
gwas_genes_list <- genes_by_l... |
2a5f3dfe801ab079a54e8dad6f74094345819c1f70a6b1359a230d12e9d3fd90 | R | 2,901 | 111 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
preservationWGCNA_table_enrichment_ui <- function(
id,
label = "a",
title = "Title",
info.text = "Info",
caption = "Caption",
height = 400,
width = 400
) {
ns <- shiny::NS(... |
fdafb9760d460b10cd46a85c3e39e25f8fcd516cde8155e1220ffce1b9e78553 | R | 2,916 | 116 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
#' UI code for table code: expression board
#'
#' @param id
#' @param label
#' @param height
#' @param width
#'
#' @export
clustering_table_clustannot_ui <- function(
id,
title,
info... |
fc82939faf42f544a8ce82cbab8d2341b8bfdb0e85fa4b7bc79028d075ce400c | R | 2,919 | 109 | library(platetools)
library(ggplot2)
library(viridis)
library(dplyr)
library(stringr)
# df <- data.frame(vals = rnorm(384),
# well = num_to_well(1:384, plate = 384))
# print(df)
# stop()
args <- commandArgs(trailingOnly = T)
prefix = args[1]
## collect ASHLEYS prediction and count files
ashleys_d... |
ff118b7ae43ac25f8a5c00bde5fac72049f008a1a35d308ea6f406e0716505c1 | R | 2,935 | 103 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
mofa_table_genetable_ui <- function(
id,
label = "",
title = "",
info.text = "",
caption = "",
height = 400,
width = 400
) {
ns <- shiny::NS(id)
TableModuleUI(
ns("t... |
22b7c51f95028aa46a00733802529454cd7c8630fa8779b4c80ff42754a3aff5 | R | 2,938 | 89 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
upload_plot_countstats_ui <- function(id,
label = "",
height,
width,
... |
3b32c27ba0ded4eba2d4b69cb07f19776de7d408467388c0bf5377208a60f82c | R | 2,944 | 112 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
dataview_plot_phenoheatmap_ui <- function(
id,
label = "",
height,
width,
title,
info.text,
info.methods,
caption
) {
ns <- shiny::NS(id)
opts <- shiny::tagList(
w... |
01de3ed5dc786a7a37446975f1a565a45fa6e32a950520ca24e532767e91074c | R | 2,949 | 107 | # Whoeps, 07th Jan 2021
# Making a large overview over the results from the arbigent folder.
# I'm giving myself 2h to make this nice today.
# Input: callmatrix from clean_genotype.R
# Input: a csv from david from which to extract samplenames
# Output: a matrix with added entries:
# Filter - Pass, NoReadsPass, Mende... |
e9e7b67b9e62c8669ca09fefc1a7126e48f09b3d23d93c95f4889b2e6e08386e | R | 2,950 | 98 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
## DEAN ATTALI code recommendation:
## example of how a board module should be written (TcgaBoard)
##
## https://github.com/bigomics/omicsplayground/pull/20/commits/bd943d84d316d76dca9140f... |
d21093dfb6ab674384a52638f0a3ff22b035d3641425e8f93cfadf2a2cfe2f34 | R | 2,964 | 116 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
multiwgcna_table_enrichment_ui <- function(
id,
label = "a",
title = "Title",
info.text = "Info",
caption = "Caption",
height = 400,
width = 400
) {
ns <- shiny::NS(id)
... |
35dfb22e03d72d5e377bc3432a8ec9780c77c376f449be6e1f0e4879be956d7b | R | 2,968 | 93 | ---
title: "Getting Started with rddm"
output: rmarkdown::html_vignette
vignette: >
%\VignetteIndexEntry{Getting started with rdmm}
%\VignetteEngine{knitr::rmarkdown}
%\VignetteEncoding{UTF-8}
---
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>"
)
```
*****
## Drift Diffusio... |
a62e746568d1709309355889f9aa59ef0a3a996c6335b3959a9f5cb274b727b9 | R | 2,985 | 80 | constraint<-list()
constraint$id <- "constraint"
constraint$title <- "Constraint Values"
constraint$loadData<- function(){
#read the constraint values for all the genes
constraintData <<- fread("www/constraint/ConstraintData.csv")
}
constraint$generateUI<- function(){
div(id="constraintSection",
fluidRow(... |
da24e7d520b8e10db1dcc668dd93ce558c81616ac35b4853a42b92662e5a2c95 | R | 2,991 | 79 | # Whoeps 5th Dec 2020
# Horizontal GT concordance plot for both.vcf
library(ggplot2)
library(optparse)
# Read input
#INPUT INSTRUCTIONS
option_list = list(
make_option(c("-f", "--file"), type="character", default=NULL,
help="vcf file to be checked", metavar="character"),
make_option(c("-s", "--sname... |
f7aa3c01d017344164b72363a38ce96ccd502818dd873de2087a4f5f2822a58c | R | 3,001 | 71 | # package <- snakemake@params[["selected_package"]]
args <- commandArgs(TRUE)
package <- args[1]
# Check if the package is already available.
# `package` may be a tarball PATH (e.g. ".../BSgenome.T2T.CHM13.V2_1.0.0.tar.gz") or a plain
# package name. Using the tarball path directly with require() never matches an inst... |
477e1f0cf5c879ed8554ac543ab2174c99770bcec9fa5c675add2d0765f3eed9 | R | 3,005 | 80 | diseaseGene<-list()
diseaseGene$id <- "diseasegene"
diseaseGene$title <- "Disease Genes"
diseaseGene$loadData<- function(){
#read in disease gene data
diseaseData <<- fread("www/diseasegene/DiseaseGeneData.txt")
}
diseaseGene$generateUI<- function(){
div(
fluidRow(
column(div(uiOutput('diseaseSelec... |
59bb9baa76e1b089d044812249cad57325ccce00180d3ee637f87caca81bcead | R | 3,009 | 113 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
consensusWGCNA_table_enrichment_ui <- function(
id,
label = "a",
title = "Title",
info.text = "Info",
caption = "Caption",
height = 400,
width = 400
) {
ns <- shiny::NS(id)... |
67a0a56b849d97b07f048031e853f36ace3f833caadc19ecbdc0a3e246fa97be | R | 3,012 | 123 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
multiwgcna_plot_modulecorr_ui <- function(
id,
title = "",
info.text = "",
caption = "",
label = "",
height = 400,
width = 400
) {
ns <- shiny::NS(id)
options <- shiny::... |
6f303cbcc146764ac7055cfbd84792e90f6aa9ed83a23663c9cf93d6302ea4b5 | R | 3,024 | 89 | rm(list=ls())
library(dplyr)
library(stringr)
library(car)
setwd("D://work//skoltech//lipid//writing//GitHub//data")
data <- read.csv("brain_FA.normalized.csv", row.names = 1)
info <- read.csv("brain_FA.info.csv", row.names = 1)
info <- info[info$species != "QC", ]
level.s <- c("HS", "PT", "MM", "CA"... |
00a9af0d651e42e49efe4cb3d6fd0d2362febdb7c6f17345864a56668d6c2232 | R | 3,031 | 102 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
mofa_table_enrichmentgenes_ui <- function(
id,
label = "a",
title = "Title",
info.text = "Info",
caption = "Caption",
height = 400,
width = 400
) {
ns <- shiny::NS(id)
T... |
ceb16cf641fe4ab7c7d11253034ea7a4626a6b7fb2a912fdc0694dd403a9be5a | R | 3,060 | 79 |
coexpression<-list()
coexpression$id <- "coexpression"
coexpression$title <- "Co-Expression Data"
coexpression$loadData<- function(){
coexpressionData <<- fread("www/coexpression/coExpressionData.csv")
}
coexpression$generateUI<- function(){
div(
fluidRow(
column(div(uiOutput('coExpSelectUI'),class="... |
53f7996dab9014128f1643bc4ed930c451b8f05cae2cc263f511b4f9426326ed | R | 3,069 | 131 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
#
#
#
TimerModuleUI <- function(id) {
ns <- shiny::NS(id)
## empty
}
TimerModule <- function(id,
condition,
timeout,
... |
e4dfeea860b91ddb75cf5e0cfdce3db0751fc4fa3f146eddfe5d2e2b78696e54 | R | 3,079 | 109 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
upload_plot_phenostats_ui <- function(id,
label = "",
height,
width,
... |
43f1bfe455a209119435161ff5a84b2b7db9f39d3f0b979efdf0a7ff1e87c716 | R | 3,086 | 111 | ---
title: "scRNA-seq_Mecp2e1_genotype_diffExp_01_filtering"
author: "Kari Neier"
date: "12/6/2021"
output: html_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
knitr::opts_knit$set(root.dir="/Users/karineier/Documents/scRNA-seq/Females")
```
## Setting up
Loading libraries, setting worki... |
0754b1643b0a082e7345e724aa4ab5695d7277a66617e511867c56e5a5250ecd | R | 3,089 | 69 | fileInputArea <- function(inputId, label, multiple = FALSE, accept = NULL,
width = NULL,
buttonLabel = "Drag your file here or click to browse",
placeholder = "No file selected") {
restoredValue <- restoreInput(id = inputId, default = NULL)... |
ea8da1215161b7225cc88b5d0445610a7d03edfd1c333369b7711b8ed94e8f4b | R | 3,091 | 112 | #' ============================================================================
#' ggplot2 Themes and Color Palettes for PCB snRNA-seq Analysis
#' ============================================================================
library(ggplot2)
#' PCB Analysis ggplot2 Theme
theme_pcb <- function() {
theme_minimal() +
... |
a011274d015408df6e5adbde28cba1f79bae907bbeb7e48bde2623801dd7eb41 | R | 3,097 | 118 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
mgsea_plot_enrichment_ui <- function(
id,
title = "",
info.text = "",
info.methods,
caption = "",
label = "",
height = 400,
width = 400
) {
ns <- shiny::NS(id)
options... |
45633dca9f7471bf3e27a8fb463e260823fba2415af131059866608f3c7f9123 | R | 3,123 | 114 | ---
title: "HUDECA — Extended Data Figure 1: Concordance with bulk genotypes"
author: "Mbouamboua Yvon <yvon.mbouamboua@inserm.fr>"
output:
html_document:
toc: true
toc_float: true
number_sections: true
date: '`r format(Sys.Date())`'
---
## Goal
Final figures
## Setup
```{r setup, include=TRUE, message=... |
b1322ef6a166b43a019a5bf1f61181e220a129f5613415b0bc0d64fbc2b99709 | R | 3,127 | 128 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
multiwgcna_plot_moduletrait_ui <- function(
id,
title = "",
info.text = "",
caption = "",
label = "",
height = 400,
width = 400
) {
ns <- shiny::NS(id)
options <- shiny:... |
6b73d771471ff4ac9baab92ce3ebcadcd3927cd9a01bdd4f88950fde8d0e6eaf | R | 3,128 | 94 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
plot_deepnet_confusionmatrix_ui <- function(
id,
title = "",
info.text = "",
info.methods,
info.references,
caption = "",
label = "",
height = c("100%", TABLE_HEIGHT_MODAL)... |
069434813293ef64bd45bbee019f48186e5079a411ce6de050bde216030557b1 | R | 3,140 | 110 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
#' Expression plot UI input function
#'
#' @description A shiny Module for plotting (UI code).
#'
#' @param id
#' @param label
#' @param height
#'
#' @export
tcga_plot_survival_ui <- funct... |
485b29a426a5dee89a55678b911438f408dc85c7f4a7ac992065be558aa9f04b | R | 3,144 | 88 | #!/usr/bin/env R
#
# This file is part of the AlignmentAndQCWorkflow plugin.
#
# This script is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 or 3 of the License.
#
# This script is distributed... |
12681c26a3f204f2eb9d6930af517b372471270b7d2487d8efb3ad82a7d7162d | R | 3,152 | 91 | ---
title: "Figure 1C-D: All-Cell UMAPs with Collapsed 'IT' Subclass"
output:
---
```{r setup, include=FALSE}
# This sets the project root based on the repo structure.
# If you move this file, you may need to set the root manually to find config.R
knitr::opts_knit$set(root.dir = dirname(dirname(rstudioapi::getSourceE... |
c8a7ff35bd5275250fa978d3654f0b13b869c840a2f77eed22db3dcc6660824d | R | 3,152 | 113 | ---
title: "000-HUDECA — 001-integration"
output: html_document
date: '`r Sys.Date()`'
---
## Goal
Batch correction & integration
## Setup
```{r setup, message=FALSE, warning=FALSE}
knitr::opts_chunk$set(message = FALSE, warning = FALSE)
root <- '/Users/yvon.mbouamboua/projects/singlecell/000-hudeca'
outdir <- file.p... |
10ad99cbc2fc4b21c727a7562c107db9251ef700d2a0e2cce10888c5fa1b4f76 | R | 3,164 | 108 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
upload_plot_contraststats_ui <- function(id,
label = "",
height,
... |
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