sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
2d5973a871ecfc3faf76f14793d8203e9727b0f57633112f34890938e0a0d6da | R | 8,614 | 234 | #######################################################################################################
# ===================================================================================================
# Function for pathway analysis
# ===============================================================================... |
54488f7a8b33f277ea0071bd1041fa30913d6d42d5b4d590c563f368cbe96d18 | R | 8,640 | 173 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
BiomarkerInputs <- function(id) {
ns <- shiny::NS(id) ## namespace
bigdash::tabSettings(
class = "p-1",
shiny::tagList(
withTooltip(
shiny::selectInput(ns("pdx_ta... |
61459f43bfc37a7e6b34cdcda1beb2269bd31f3545c4b8a32d36d549b0244877 | R | 8,741 | 250 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
##===================================================================
##================ Script to build PGX object =======================
##==============================================... |
d26e84fcbaf595f1b11efd31f3ad9ca4bda4b178ad967c507aab20b4464caf75 | R | 8,790 | 211 | ---
title: "Figure 2G-K, O, P: IT Neuron Archetype Analysis and Cross-Species Projection"
output:
---
```{r setup, include=FALSE}
# This sets the project root based on the repo structure.
# If you move this file, you may to set the root manually to find config.R
knitr::opts_knit$set(root.dir = dirname(dirname(rstudioa... |
57c850906acafa000dfd43601faf5ada9cc93523cf718de71c4fd3f1c59049e6 | R | 8,818 | 300 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
enrichment_plot_volcanoall_ui <- function(
id,
title,
info.text,
info.methods,
info.references,
info.extra_link,
caption,
height,
width
) {
ns <- shiny::NS(id)
plot_... |
e6c3596aac6883099ec49705f27c31f6945be946e3c1a2a97dd15b2d03e8ff7d | R | 8,861 | 304 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
compare_plot_genecorr_ui <- function(
id,
title,
info.text,
label = "",
height = c(600, 800)
) {
ns <- shiny::NS(id)
genecorr.opts <- shiny::tagList(
withTooltip(
... |
e8f59a743b524bb401c0b3205ffb38d6e6d1a28d69b86ab6679e91686d6c0b22 | R | 8,868 | 334 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
#' Mechanism-of-action plot UI input function
#'
#' @description A shiny Module for plotting (UI code).
#'
#' @param id
#' @param label
#' @param height
#'
#' @export
mofa_report_summary_u... |
c6ef13893ee4be14f70299d3759a2bb41dd2e8271bc0c44284ce5d975b0f1a95 | R | 8,887 | 312 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
dataview_plot_tsne_ui <- function(
id,
label = "",
title,
height,
width,
caption,
info.text,
info.methods,
info.references,
info.extra_link
) {
ns <- shiny::NS(id)
... |
069ecd46152366e0cd48fbf8d12815c68f59d43ed8c16876b3adaef77e4c85d3 | R | 8,904 | 290 | ---
title: "2c. Opossum, Label Nonneuronal"
output:
---
```{r setup, include=FALSE}
# This sets the project root based on the repo structure.
# If you move this file, you may need to set the root manually to find config.R
knitr::opts_knit$set(root.dir = dirname(dirname(rstudioapi::getSourceEditorContext()$path)))
kni... |
6e733989ce1dd1257ee6701caf8051218cc17b8b36f9aa876a7dfddaa5c92b8d | R | 8,909 | 300 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
#' Expression plot UI input function
#' @description A shiny Module for plotting (UI code).
#' @param id
#' @param label
#' @param height
#' @param width
#' @export
expression_plot_volcano... |
ce9abd7b56b1f931d437196d959588a7f8c7689353a9f9771f1ceca01a827adf | R | 8,950 | 310 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
#' Expression plot UI input function
#'
#' @description A shiny Module for plotting (UI code).
#'
#' @param id
#' @param label
#' @param height
#' @param width
#'
#' @export
expression_plo... |
147d3265cb6b97b4fdbc1054dc3dc3cd892c7e8f2725b1027bafa32ec1c45f04 | R | 8,959 | 199 | #######################################################################################################
# =================================================================================================== #
# Auxillar function for coMethDMR
# ============================================================================... |
47ca366d9abff82065a6ead2f52f15aecb17a803151edc886d164c780a709c68 | R | 8,966 | 185 | args=commandArgs(trailingOnly=TRUE)
#--------------------------------------------------------------------------------------------------------------------------------------
# Extract single-cell copy-number variation based on MosaiCatcher result for normalization purpose (lenient call from mosaicatcher)
#-------------... |
347e56b8fc6ff3d62b612c21486c322c1f9399b5d51ae394dfdee1d0b9cd8179 | R | 9,005 | 175 | #################
### Load data ###
#################
rm(list=setdiff(ls(),c('params','grp')))
basedir <- params$basedir
setwd(basedir)
savedir <- paste(params$opdir,'sncamodel/',sep='')
dir.create(savedir,recursive=T)
dir.create(paste(savedir,'roilevel',sep=''),recursive = T)
source('code/fitfxns.R')
load(paste(para... |
7e8e93889b8b980b132ae73cb89175856997fdff059232ffe4653dc2b15aeeaa | R | 9,014 | 301 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
#' Expression plot UI input function
#'
#' @description A shiny Module for plotting (UI code).
#'
#' @param id
#' @param label
#' @param height
#'
#' @export
expression_plot_volcanoAll_ui ... |
b029f1a7ec409fdf2b0eeab9ba28b2149b138aae2aabd269f51e0e447abd5215 | R | 9,039 | 146 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
LasagnaInputs <- function(id) {
ns <- shiny::NS(id) ## namespace
bigdash::tabSettings(
shiny::selectInput(ns("contrast"), "Select comparison", choices = NULL),
shiny::selectInp... |
13b9c9daaf7b37ea645a235b000efb250c1ed0c3c2881d1abee67de036642e30 | R | 9,070 | 294 | ---
title: "2b. Opossum, Label GABAergic"
output:
---
```{r setup, include=FALSE}
# This sets the project root based on the repo structure.
# If you move this file, you may need to set the root manually to find config.R
knitr::opts_knit$set(root.dir = dirname(dirname(rstudioapi::getSourceEditorContext()$path)))
knitr... |
2e02bbab5c5afde48f932426040887eec61860c059e3d8a8ae46f57a606979e3 | R | 9,095 | 267 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
LasagnaBoard <- function(id, pgx) {
moduleServer(id, function(input, output, session) {
ns <- session$ns ## NAMESPACE
fullH <- 700 ## full height of page
rowH1 <- 250 ## row ... |
35c403bfd2271d56134d31952fee6d8e0b0b166b1a5faa1200052d88554624f4 | R | 9,156 | 339 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
#' Mechanism-of-action plot UI input function
#'
#' @description A shiny Module for plotting (UI code).
#'
#' @param id
#' @param label
#' @param height
#'
#' @export
drugconnectivity_repo... |
71b065135e09d5013ede3c5e651f64c5617d10ffb4bf9d22773409cc15d05e85 | R | 9,164 | 322 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
#' Create UI for top enriched gene set plots
#'
#' @description
#' Generates the Shiny UI for plotting the top enriched gene sets.
#'
#' @param id Widget id to use for the output.
#' @par... |
bfbd7ac200ca71ca832c8145860fd1a80a799ce553a4bc7599a5a1c0b8836fb2 | R | 9,169 | 205 | library(ggplot2)
library(dplyr)
library(showtext)
library(hrbrthemes)
library(stats)
# Add Google fonts
font_add_google("Outfit", "title_font")
font_add_google("Cabin", "body_font")
showtext_auto()
title_font <- "title_font"
body_font <- "body_font"
# Create the directory if it doesn't exist
if (!dir.exists("demogra... |
b2e61faa6fb44ff1d73994ea7968ab14dc0ed02b3e7550e308942d9318e18351 | R | 9,224 | 332 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
#' Single cell plot UI input function
#'
#' @description A shiny Module for plotting (UI code).
#'
#' @param id
#' @param label
#' @param height
#' @param width
#'
#' @export
singlecell_pl... |
3af8189bf54808ca84c636d3de02165603fedfb5b2c0f3b39f7cdf445db1444b | R | 9,248 | 222 | # Genotype
library(ggplot2)
library(reshape)
library(dplyr)
library(tibble)
source('workflow/scripts/arbigent/clean_genotype_defs.R')
source('workflow/scripts/arbigent/vcf_defs.R')
# but first explore
runname = 'review_david323'
debug_file = paste0('~/PhD/projects/huminvs/mosaicatcher/analysis/results/', runname, '/ms... |
1415f39a7d029b0b7372df099559fc45558c16ed076ecb74cfdf343fe9ee481c | R | 9,251 | 230 | # ============================================================
# Script 04: Spearman Rank Correlation Analysis
# Candrea et al. - Gut Microbiota Comparative Analysis
# Biomedicines 2025
# ============================================================
# Description:
# Spearman rank correlation analysis between microbial t... |
67789e95e8f0cb9217d398c800f1ead4768071fce28c1547e933bf67ba21f638 | R | 9,254 | 257 | sideBarLoadData <- function(){
#Load basic gwas data for sidebar
gwas_risk_variants <<- fread("www/summarystats/gwas_risk_variants.csv")
#gwas_id_string <- "META5"
gwas_info <<- fread("www/summarystats/gwasInfo.csv")
#build the gwas_list that will hold names and values for the "Choose a GWAS" drop... |
8d988fc712da8acf01af927a18c52f0c8051fc5bb1d93636c2c082533ae17fb6 | R | 9,304 | 243 | ###############################################################################
# Renamed Functions (same behavior/IO as originals)
###############################################################################
# ---------- small helpers ----------
.melt_mat <- function(mat) {
mat <- as.matrix(mat)
data.frame(
... |
fd05b6cb090cdec491a933af2e339251d9cd14c23f9876d2e24cbd722192d419 | R | 9,306 | 331 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
featuremap_plot_gene_map_ui <- function(
id,
title,
info.text,
info.methods,
info.references,
info.extra_link,
caption,
label = "",
height,
width
) {
ns <- shiny::NS(... |
a9015fca1d274ae1e2861540950bed6a4f12b351c3739e26d9d84f7395415337 | R | 9,307 | 259 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
upload_module_received_ui <- function(id, height = 720) {
ns <- shiny::NS(id)
}
upload_module_received_server <- function(id,
auth,
... |
8ce1d0064b45fd204357da6bd43d273b65ef749e7ffdbb1463a979cad5a663d4 | R | 9,314 | 256 | #!/usr/bin/env Rscript
# RNA-seq Pipeline Step 6: Functional Enrichment Analysis (GO and KEGG)
# This script performs Gene Ontology and KEGG pathway enrichment analysis
suppressPackageStartupMessages({
library(clusterProfiler)
library(org.Hs.eg.db)
library(enrichplot)
library(ggplot2)
library(tidy... |
0e15a7efba449ee5de35054749da7d0fa7884747dff406a1a62a99a0faa14b54 | R | 9,317 | 329 | ---
title: "Mouse Spatial Preprocessing: Subset and Combine Columns"
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$set(root.dir = dirname(dirname(rstudioapi::getSourceEdi... |
2db7b423a745c18fd8b4c76faf1aba159ebf8a9c881b13556510034af6486c54 | R | 9,330 | 283 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
##===================================================================
##================ Script to build PGX object =======================
##==============================================... |
8b8f2935b886a72cf29eb96bef942e58e66d7f561c95e9ce29272ae006c04844 | R | 9,337 | 253 | #!/usr/bin/env Rscript
suppressPackageStartupMessages(library(argparser))
suppressPackageStartupMessages(library(magrittr))
parser <- arg_parser("detect translocation hotspots using scan statistics",
name="TranslocHotSpots.R") %>%
add_argument("tlxfile",
"input tlx file of t... |
bfefd9847eab1e59297c1aea890ae457cb7de0fca3b8bd29e3f02941f0fc7a0f | R | 9,353 | 170 | ## Complete Pipeline for Driver Estimation and Master Table Creation ##
############### Step 0: Preparation ###############
# Load NetBID2 package
library(NetBID2)
# Get the demo's constructed network data
network.dir <- sprintf('%s/demo1/network/',system.file(package = "NetBID2")) # use demo network in the ... |
d977a286d5ea13ed6aa8e119d230d03bf06769afaa7bb81c8aa05b638c19d263 | R | 9,384 | 329 | ---
title: "Opossum Spatial Preprocessing: Subset and Combine Columns"
output:
---
```{r setup, include=FALSE}
# This sets the project root based on the repo structure.
# If you move this file, you may need to set the root manually to find config.R
knitr::opts_knit$set(root.dir = dirname(dirname(rstudioapi::getSourceE... |
4a650e3c6c768d0fe021134c39d49db55a102bb5b15996b05d0307953c6b656b | R | 9,436 | 187 |
title: "Female_PCB_Cortex"
author: "Osman Sharifi"
library(Seurat)
library(biomaRt)
library(scCustomize)
library(ggplot2)
### The percentage of reads that map to the mitochondrial genome
# We use the set of all genes, in mouse these genes can be identified as those that begin with 'mt'.
#load data
load("/Users/osm... |
43fb7c32e2232eaea4fae5cf169a4c0c297b56f14d4902cbd245201b91deaae7 | R | 9,485 | 194 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
FeatureMapInputs <- function(id) {
ns <- shiny::NS(id) ## namespace
bigdash::tabSettings(
## data set parameters
withTooltip(
shiny::radioButtons(
ns("showvar"), ... |
696c6ab4f2fac64c9d5f9b14efdd7ddea1e1b114e2a3ae298ab131b2b05d908f | R | 9,499 | 337 | ---
title: "HUDECA — Extended Data Figure 2: Quality control of human olfactory epithelium snRNA-seq data"
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 ... |
0f73a930bf71d06106db86773e8c4c30710759ea29e7c160b2c70f078da19920 | R | 9,514 | 151 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
CorrelationInputs <- function(id) {
ns <- shiny::NS(id) ## namespace
bigdash::tabSettings(
withTooltip(shiny::selectInput(ns("gene"), tspan("Gene:"), choices = NULL),
"Choose... |
40a3d0bf1b65a83721a206313763d5186c95abb030a0f837b633d1428a500200 | R | 9,579 | 191 | # Load packages
library(readxl)
library(dplyr)
library(ggplot2)
# Get a list of all directories
all_directories <- list.dirs(path = "/Users/osman/Documents/GitHub/PEBBLES_mouse_snRNAseq/soupx", full.names = TRUE)
# Create an empty data frame to store the combined data
combined_data <- data.frame()
# Loop through eac... |
2faeba2f31ea2f915ae66c7fc33a634974af2bf9e2b78dfc4829d16bc93d89be | R | 9,595 | 320 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
MofaBoard <- function(id, pgx) {
moduleServer(id, function(input, output, session) {
ns <- session$ns ## NAMESPACE
fullH <- 700 ## full height of page
rowH1 <- 250 ## row 1 ... |
c271a2b2d5b513e7b5c15c6c092748db780a7b1a0ae9f47c496c26072bd29482 | R | 9,600 | 232 | library(data.table)
library(coloc)
Ferr <- fread("Ferritin_AF0p005.mr_ready.tsv.gz")
# Opening primary panel
primary <- fread("2019-12-11-cis-eQTLsFDR-ProbeLevel-CohortInfoRemoved-BonferroniAdded.txt.gz")
# Opening the proxy panel
proxy1 <- fread("GTEx_Analysis_v8_eQTL/Whole_Blood.v8.signif_variant_gene... |
cd75d8a6e9e6fb8ab231c7cfe69c68259a2cac5cd83c5bf6736771bc932c9c06 | R | 9,633 | 297 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
#' Drug Connectivity plot UI input function
#'
#' @description A shiny Module for plotting (UI code).
#'
#' @param id
#' @param label
#' @param height
#'
#' @export
drugconnectivity_plot_c... |
172de394f15eff3b0e7755c7495b24d71d2b753c49849ac9dcabc6693b9e7ecb | R | 9,636 | 272 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
##===================================================================
##================ Script to build PGX object =======================
##==============================================... |
682d1aaa9469c5e0ed0be4d064f864a3c8a11056465ea8a80f2b26adc274e90e | R | 9,649 | 302 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
clustering_plot_clusterannot_ui <- function(
id,
label = "",
title,
info.text,
info.methods,
info.references,
info.extra_link,
caption,
height,
width
) {
ns <- shiny:... |
0ac2502a51723335d77ced2be57aa1775a2f52eaf999bb3972006651faa977fe | R | 9,686 | 284 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
##===================================================================
##================ Script to build PGX object =======================
##==============================================... |
83c80137ccc8586aacff5677859c1abc4cb68a767138c8f12ba8aa735153b81f | R | 9,689 | 240 | ## load required libraries
library(GenomicAlignments)
library(ggplot2)
library(cowplot)
library(BiocParallel)
#' Print haplotagged read counts
#'
#' This function will take \code{list} of haplotagged bams files and will return \link{data.frame}
#' counts of reads per haplotype.
#'
#' @param sv.table A path to a table ... |
6155c2e6d4fef9273effffa563b6719de4904908f80e7a503887001f3118d9c4 | R | 9,696 | 317 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
## --------------------------------------------------------------------------
## convert list of checks to html tags for display in the data preview modal
## -----------------------------... |
c9d3eb27240269d7ffca481a209a7a16ba0a23fe78deeeb37baeb7f998b99efc | R | 9,752 | 249 | #!/usr/bin/env Rscript
# Generate Complete Differential Expression Table
# This script creates a comprehensive publication-ready table with all detected genes
# and explicit fold change direction annotations
# Using base R - no packages needed
cat("==========================================\n")
cat("Generating Compl... |
1f325b30c84fc3864a1ef6a486ba707e87d214b2f9059486fe7d29758ccb8666 | R | 9,823 | 283 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
ConsensusWGCNA_Board <- function(id, pgx) {
moduleServer(id, function(input, output, session) {
ns <- session$ns ## NAMESPACE
fullH <- 700 ## full height of page
rowH1 <- 250... |
abf144699469be5c6d51da9c634aebae320942e05d8da0c0e67ec4a13dd760af | R | 9,864 | 283 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
PathwayBoard <- function(id,
pgx,
selected_gsetmethods = reactive(colnames(pgx$gset.meta$meta[[1]]$fc))) {
moduleServer(id, function(inp... |
c5dde7e480b866814a41aea9821bb597397e2cd5e861702869379731e49837d0 | R | 9,868 | 207 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
ConnectivityInputs <- function(id) {
ns <- shiny::NS(id) ## namespace
bigdash::tabSettings(
withTooltip(
shiny::selectInput(ns("contrast"), "Contrast:",
choices = NUL... |
aab07490e866f3db29488c0e8f9cb85b0621160898685a59badf29d31089a11a | R | 9,880 | 352 | ##
## 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
signature_plot_volcano_ui <- f... |
78fe99903333bd396604d23779a37e81c0b239877c8deded3fff8bb83e8438bf | R | 9,932 | 251 | #
# Copyright (c) 2018 German Cancer Research Center (DKFZ).
#
# Distributed under the MIT License (license terms are at https://github.com/DKFZ-ODCF/AlignmentAndQCWorkflows).
#
##################
## start Daniel ##
##################
extractFWHM <- function(ratio_density){
half_max_ratio_density <- max(ratio_densi... |
c4b15e411f47891d905688b932914d31e06e5b52b9c9e62ae3f4d81918b64e05 | R | 9,941 | 299 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
#' Single cell plot UI input function
#'
#' @description A shiny Module for plotting (UI code).
#'
#' @param id
#' @param label
#' @param height
#' @param width
#'
#' @export
singlecell_pl... |
df3eecf006b6b36ac5f4b9af096b1dd504b9bba9bb3310135249ee0539d2c5b1 | R | 9,952 | 180 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
DrugConnectivityInputs <- function(id) {
ns <- shiny::NS(id) ## namespace
bigdash::tabSettings(
withTooltip(shiny::selectInput(ns("contrast"), "Contrast:", choices = NULL),
"... |
9c2448f3a7090376751c3e30b907af0373797efccaf584d58eb7daeaf7ddba6c | R | 10,020 | 301 | #######################################################################################################
# =================================================================================================== #
# Function for plot
# =========================================================================================... |
05cf5945471e0821e333b028d930e2fc8f9b7c12f2cd07db6fd171a6057e0caa | R | 10,055 | 294 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
InviteFriendUI <- function(id) {
ns <- shiny::NS(id)
shiny::actionButton(
ns("action"), "Invite!",
width = "auto", class = "quick-button"
)
}
InviteFriendModule <- function(... |
0d1099cf0a6286268fc60de07088dd5d18500d829760a0ee3c03c64a425b2623 | R | 10,087 | 336 | #==========
# Univariate twin model: trial-level missing
#
# author: Giorgia Bussu
# project: BT missing data
# version: June 2024
#=================================================
rm(list=ls())
### set a working directory (otherwise create a new R project):
setwd('C:/Users/myfolder/missingdata_BATSS... |
bf622133e424189dda7fd97bac520446baff2884425552061f1371ccda4a62fc | R | 10,143 | 241 | ####################
## Load libraries ##
####################
library(magrittr)
library(VennDiagram)
library(grDevices)
library(dplyr)
library(Seurat)
library(glue)
library(scCustomize)
library(edgeR)
library(ggplot2)
library(ggrepel)
library(GeneOverlap)
library(enrichR)
##################
## Load samples ##
########... |
195a8f51e875c1bf8d0d0a50ee9a2c9e7cdd1938ada3664dc76cae2ed70d2d60 | R | 10,150 | 199 | ---
title: "QC plot for network generated by SJAracne"
output:
html_document
---
```{r include=FALSE}
library(NetBID2)
library(kableExtra)
```
```{r echo=FALSE}
deg <- igraph::degree(net,mode='out')
source_list <- names(deg)[which(deg>0)]
full_info <- FALSE
if(html_info_limit==FALSE) full_info<-TRUE
c1 <- componen... |
880c8da7256689392ac4c8415f2fc95b5cbc41eff4e53a01c7db4542cd5c0148 | R | 10,171 | 241 | ####################
## Load libraries ##
####################
library(magrittr)
library(VennDiagram)
library(grDevices)
library(dplyr)
library(Seurat)
library(glue)
library(scCustomize)
library(edgeR)
library(ggplot2)
library(ggrepel)
library(GeneOverlap)
library(enrichR)
##################
## Load samples ##
########... |
6128183a65d65cfbc97f5c027a064244b2a6f921c04e5b11b2532602a4c933aa | R | 10,175 | 241 | ####################
## Load libraries ##
####################
library(magrittr)
library(VennDiagram)
library(grDevices)
library(dplyr)
library(Seurat)
library(glue)
library(scCustomize)
library(edgeR)
library(ggplot2)
library(ggrepel)
library(GeneOverlap)
library(enrichR)
##################
## Load samples ##
########... |
d6488eef56f8481da216a7a541250d64426231a823f67bd966ebccba25f79875 | R | 10,175 | 279 | ##
## 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
TimeSeriesBoard.feature... |
60f2997a2c2580acaaadc0b65332dd4586c2532546c0d24cf0f0722c9df060ec | R | 10,178 | 241 | ####################
## Load libraries ##
####################
library(magrittr)
library(VennDiagram)
library(grDevices)
library(dplyr)
library(Seurat)
library(glue)
library(scCustomize)
library(edgeR)
library(ggplot2)
library(ggrepel)
library(GeneOverlap)
library(enrichR)
##################
## Load samples ##
########... |
79a30bf9d9dea983accdb800af98345b5732f36827cf4a4dc29ec052847e7c26 | R | 10,184 | 241 | ####################
## Load libraries ##
####################
library(magrittr)
library(VennDiagram)
library(grDevices)
library(dplyr)
library(Seurat)
library(glue)
library(scCustomize)
library(edgeR)
library(ggplot2)
library(ggrepel)
library(GeneOverlap)
library(enrichR)
##################
## Load samples ##
########... |
7b85facfa1fd7ecda3173a09dafd5704c204c7918db53de50f600d83a6cdee2a | R | 10,199 | 310 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
##===================================================================
##================ Script to build PGX object =======================
##==============================================... |
8b09c8a10ddc0b7c5d9fa6e3f226af9eb58c02b5d4d48b2e91016aed76969f6b | R | 10,207 | 297 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
#' Single cell plot UI input function
#'
#' @description A shiny Module for plotting (UI code).
#'
#' @param id
#' @param label
#' @param height
#' @param width
#'
#' @export
singlecell_pl... |
c19052c48db1cb91a284dfe94e18f398f3d1dd3cc2dcde1be7f773bf4926845a | R | 10,220 | 242 | ####################
## Load libraries ##
####################
library(magrittr)
library(VennDiagram)
library(grDevices)
library(dplyr)
library(Seurat)
library(glue)
library(scCustomize)
library(edgeR)
library(ggplot2)
library(ggrepel)
library(GeneOverlap)
library(enrichR)
##################
## Load samples ##
########... |
b326560e0980042643227773e67c0778706af774f4f8f907cbadce3bbebf0a7a | R | 10,224 | 242 | ####################
## Load libraries ##
####################
library(magrittr)
library(VennDiagram)
library(grDevices)
library(dplyr)
library(Seurat)
library(glue)
library(scCustomize)
library(edgeR)
library(ggplot2)
library(ggrepel)
library(GeneOverlap)
library(enrichR)
##################
## Load samples ##
########... |
0e4d7f2aab4462ec2b9a30238cd3ed6a59b6bc39a418c893008015d3d43134da | R | 10,249 | 242 | ####################
## Load libraries ##
####################
library(magrittr)
library(VennDiagram)
library(grDevices)
library(dplyr)
library(Seurat)
library(glue)
library(scCustomize)
library(edgeR)
library(ggplot2)
library(ggrepel)
library(GeneOverlap)
library(enrichR)
##################
## Load samples ##
########... |
9e5d8ec1d3059a8ed9835c18a0c813c864f9d110bd9a77bf1474a4d8aebf3e2f | R | 10,250 | 242 | ####################
## Load libraries ##
####################
library(magrittr)
library(VennDiagram)
library(grDevices)
library(dplyr)
library(Seurat)
library(glue)
library(scCustomize)
library(edgeR)
library(ggplot2)
library(ggrepel)
library(GeneOverlap)
library(enrichR)
##################
## Load samples ##
########... |
e56816b4f8476ef1159a64e9844b0964756a08161bffeba5eeb51af2b1446553 | R | 10,292 | 285 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
##===================================================================
##================ Script to build PGX object =======================
##==============================================... |
e114860ca6ee3465969a472e97afd233dc0b63fa15980b65b6e01d8f2f1ce924 | R | 10,299 | 242 | ####################
## Load libraries ##
####################
library(magrittr)
library(VennDiagram)
library(grDevices)
library(dplyr)
library(Seurat)
library(glue)
library(scCustomize)
library(edgeR)
library(ggplot2)
library(ggrepel)
library(GeneOverlap)
library(enrichR)
##################
## Load samples ##
########... |
7e3d71e8fdc785992c896534684c4fafe72dcf4af272f082764104c7bdc86dd9 | R | 10,319 | 364 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
featuremap_plot_geneset_map_ui <- function(
id,
label = "",
title,
info.text,
info.methods,
info.references,
info.extra_link,
caption,
height,
width
) {
ns <- shiny::... |
d10ee4a84cc7ae5914be065f0c54370601a4584ac648c9dacb2a7ab7e25e9b13 | R | 10,322 | 217 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
CompareInputs <- function(id) {
ns <- shiny::NS(id) ## namespace
bigdash::tabSettings(
withTooltip(
shiny::selectInput(ns("contrast1"), "Dataset1:",
choices = NULL, m... |
70d0fc2b7e975067baa51024869771a13b95475808390df493c2e202dc2211d1 | R | 10,334 | 245 | ####################
## Load libraries ##
####################
library(magrittr)
library(VennDiagram)
library(grDevices)
library(dplyr)
library(Seurat)
library(glue)
library(scCustomize)
library(edgeR)
library(ggplot2)
library(ggrepel)
library(GeneOverlap)
library(enrichR)
##################
## Load samples ##
########... |
c98f039cf430d91caf51a8dbbcda03cfa0b17407ee60684aa5708be9fd33b3ed | R | 10,358 | 166 |
#########################################
### Taylor-Bateman et al., 2025 - Repurposing drugs for the prevention of vascular dementia: Evidence from drug target Mendelian randomization
### Cis&Trans_DTMR.R requires 2 input files
### An Exposure protein GWAS -
### An Outcome GWAS
Exposure_GWAS <-
Outcome_GWAS <-... |
3584ef77dc53746233ec7bd2930b1aa2fdf86f0ba14dd95faada56d3ee5706ca | R | 10,381 | 295 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
CorrelationBoard <- function(id, pgx, labeltype = shiny::reactive("feature")) {
moduleServer(id, function(input, output, session) {
ns <- session$ns ## NAMESPACE
fullH <- 800 ##... |
bfa0c00a9822819d953a1e48aafd599dcaf0f33ab0778cd8039cc12864e6fb27 | R | 10,382 | 241 | ########################################################
## Create broad categories and run mosiacism analysis ##
########################################################
library(magrittr)
library(VennDiagram)
library(grDevices)
library(dplyr)
library(Seurat)
library(glue)
library(scCustomize)
library(edgeR)
library(gg... |
a85daef96e96755551235626a916e90d91b6620e70843eb6db5a89e708e15d7b | R | 10,397 | 241 | ########################################################
## Create broad categories and run mosiacism analysis ##
########################################################
library(magrittr)
library(VennDiagram)
library(grDevices)
library(dplyr)
library(Seurat)
library(glue)
library(scCustomize)
library(edgeR)
library(gg... |
f1d893f86bfafc8fc79678054e41a3ce8c47ceb89357b49a8388be7635c85ea6 | R | 10,451 | 242 | ########################################################
## Create broad categories and run mosiacism analysis ##
########################################################
library(magrittr)
library(VennDiagram)
library(grDevices)
library(dplyr)
library(Seurat)
library(glue)
library(scCustomize)
library(edgeR)
library(gg... |
9f24247571ad356f264c4a4f689e151bce206e920672fdfa1e8bc2fbd86f7a5f | R | 10,457 | 303 | # 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... |
3f28d7739d61bc8bc57482f8f6666cf81af46f59b96d09059ecf677b66cef910 | R | 10,480 | 387 | ---
title: "Integration of in vitro hGPCs and Fetal scRNA-seq"
author: "John Mariani"
date: "07/30/2025"
output: github_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
knitr::opts_knit$set(root.dir = rprojroot::find_rstudio_root_file())
```
```{r, echo = TRUE, message=FALSE, warning=FALSE... |
8c83bdf169a4c57314a51f1f1a76b0cf3b78ba681be2cd8a349409fb3a4432b7 | R | 10,482 | 308 | library(GenomicRanges)
library(rtracklayer)
library(tidyverse)
library(ChIPseeker)
library(TxDb.Mmusculus.UCSC.mm10.knownGene)
library(org.Mm.eg.db)
library(clusterProfiler)
library(ggplot2)
library(gridExtra)
# Initialize txdb object
txdb <- TxDb.Mmusculus.UCSC.mm10.knownGene
# Parse command line arguments
library(o... |
4426aa6264d0422a6b568a74e63412374a8ef51a4eac17ec7a742499a773f5b7 | R | 10,510 | 326 | ## library(dotenv)
## library(shiny)
## library(shinychat)
## library(bslib)
CopilotUI <- function(id, layout = c("sidebar", "fixed")[1]) {
ns <- shiny::NS(id)
sections <- c(
"description", "dataset_info", "compute_settings",
"differential_expression", "geneset_enrichment",
"drug_similarity", "pcsf_re... |
07051556ac259daf1ce23a0f530645e3f7a73bcb35caec6c86b04aeeecd13622 | R | 10,514 | 318 | ---
title: "2a. Opossum, Label Glutamatergic"
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$set(root.dir = dirname(dirname(rstudioapi::getSourceEditorContext()$path)))
kn... |
a2984643eb09b9a60645b95b6a4bdae08306ac920ff336a3d2b6eec4afe03079 | R | 10,529 | 247 | urmet <- read.delim("raw/urine_metabolome/urine_metabs.csv", row.names = 1, sep = ",", check.names = FALSE)
urmet <- urmet %>%
dplyr::select(!Group)
urmet[,-c(1:3)] <- urmet[,-c(1:3)] %>% t() %>% Tjazi::clr_c() %>% t()
urmet_df_long <- urmet %>%
pivot_longer(!c(ID, visit, Coffee_Type)) %>%
mutate(Visit = c... |
34f7190eb7dd6f5ea8bc0b50d50b639e82a055842a9951e65273b476bb665c1c | R | 10,564 | 156 | library(reshape2)
library(ggplot2)
my.clinical <- function()
{
id_clinical=read.delim("als_id_clinical.tsv",header=F,stringsAsFactors=F)
colnames(id_clinical)=c("ID","Individual","TargetID","Gender","Cogdx","Cogdx2","FTD","Age","Tissue","RIN","PMI","C9expansion")
id_clinical$Cogdx[grepl("ALS Spectrum MND",id... |
5b304ee1d84328af857070618ec2aca48b13c8b84264534bd0d2f8b078bbcea0 | R | 10,609 | 226 | evidence_section<-list()
evidence_section$id <- "evidence"
evidence_section$title <- "Evidence Per Gene"
evidence_section$loadData<- function(){
######create a dataframe to hold the conclusion values. This will need to contain extra info for genes on loci with multiple risk snps (like locus 1) which is why we mer... |
b61309b18f4ba0d0388477b0ed34c831d4a6eeaa66cf73970aae9f523503779d | R | 10,611 | 207 |
library(data.table)
## 2016 ####
# spatial transcriptomics ####
ST_OB_data_1 = list(
dataset = 'ST_OB1',
spatial_locs = "https://raw.githubusercontent.com/drieslab/spatial-datasets/master/data/2016_ST_olfactory_bulb/cell_locations/Rep11_MOB_0_location.txt",
expr_matrix = "https://raw.githubusercontent.com/dri... |
63977ab7a21ee38fcf0686f055c29dc1f92bd8ef8200f58cbe2adde5e15baf6d | R | 10,623 | 308 | log <- file(snakemake@log[[1]], open = "wt")
sink(file = log, type = "message")
sink(file = log, type = "output")
# IMPORTS
library(ComplexHeatmap)
library(RColorBrewer)
library(dplyr)
library(tidyr)
# pdf("TEST_R_dev.pdf", width = 20, height = 10)
pdf(snakemake@output[["pdf"]], width = 20, height = 10)
# Chromos... |
7387f15174d94f8baf5d66c08c6fa60e2fc027a2b69b0dd54d9f8232f5d358e5 | R | 10,624 | 352 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
## =============================================================================
## ==================== BATCHCORRECT UI/SERVER =================================
## ======================... |
4b20b84648c68fec6955fe684ef3c0cce8b3aeb1593d485968d2324a2a261ba8 | R | 10,644 | 274 | #########################################
### Taylor-Bateman et al., 2025 - Repurposing drugs for the prevention of vascular dementia: Evidence from drug target Mendelian randomization
### GColoc_DTMR.R requires 2 input files
### An Exposure GWAS
### An Outcome GWAS
Exposure_GWAS <-
Outcome_GWAS <-
### Column ... |
0911ec320842474595b0ea3e9a870b89566323a9bbfe76e1e982d9fa6e22954c | R | 10,685 | 334 | # Time-resolved decoder comparison using sliding-window random forests.
#
# Expected input:
# - Two CSV files (e.g. "WTdata.csv" and "DGLcKOdata.csv") with one trial per row.
# - All columns except the last are time-resolved features.
# - The last column contains the class label for each trial (e.g., "escape", "avoidan... |
7f3ca878ec65162eac6437b34bc3c1d886bb0f90db8705246a72ad2249422eb5 | R | 10,806 | 179 |
#########################################
### Taylor-Bateman et al., 2025 - Repurposing drugs for the prevention of vascular dementia: Evidence from drug target Mendelian randomization
### CisLT_DTMR.R requires 2 input files
### An Exposure GWAS
### An Outcome GWAS
Exposure_GWAS <-
Outcome_GWAS <-
### Column ... |
e88f510719e61ea4c99367f1617bbcbf82aa0ab78be2ac0db1de01d789f0976d | R | 10,842 | 339 | ---
title: "HUDECA — Figure 6: Analysis of the expression of the olfactory receptors (ORs) in the fetal human olfactory system"
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 fig... |
78ea4f0891fad657841bdcb1d745205ddde7182790775715d313a70332be207b | R | 10,851 | 399 | # %% Load libraries and load data
suppressPackageStartupMessages({
library(readr)
library(dplyr)
library(gtsummary)
library(forcats)
library(gt)
library(knitr)
library(purrr)
library(kableExtra)
})
here::i_am("code/make_variable_tables.R")
library(here)
results_path <- here("results", "reproduced")
dat... |
d74fbd043bae1c94a7762102d51f11677dcb738dec5a7231ad77cd658220b151 | R | 10,888 | 341 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
WgcnaBoard <- function(id, pgx) {
moduleServer(id, function(input, output, session) {
ns <- session$ns ## NAMESPACE
fullH <- 700 ## full height of page
rowH1 <- 250 ## row 1... |
90d6f4759ca0cd5b31c077718a4fba49a4cd053fb72508617efb0bd2599f3800 | R | 10,928 | 244 | ---
title: "Figure 1G-K: Class and Subclass Proportions"
output:
---
```{r setup, include=FALSE}
# This sets the project root based on the repo structure.
# If you move this file, you may need to set the root manually to find config.R
knitr::opts_knit$set(root.dir = dirname(dirname(rstudioapi::getSourceEditorContext(... |
6c880082a5582eb2ad37715544d71f98bb5c0d3b719038a5afcc1ce2049d49be | R | 10,948 | 253 | library(R.matlab)
library(tidyverse)
library(ggplot2)
library(gridExtra)
library(refund)
library(dplyr)
# read data and extract variable names
setwd("~/Desktop/NIMH Research/Causal/DA_adapts_learn_rate")
matdat <- R.matlab::readMat("seshMerge.mat")
matdat <- matdat$seshMerge
# indices in dataset of variables
photo_id... |
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