sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
8d094a541cc753e54e6463113983afa9026068a6f1c9def1f0d5cf5f8b497d37 | R | 3,166 | 132 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics Sagl. All rights reserved.
##
#' Importance plot UI input function
#'
#' @description A shiny Module for plotting (UI code).
#'
#' @param id
#' @param label
#' @param height
#'
#' @export
functional_plot_enrichmap_ui... |
58aca9916b31f249899cf4c4689083c7c6a50d207430eec53c6e31edeafbc71c | R | 3,174 | 108 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
enrichment_table_genes_in_geneset_ui <- function(
id,
title,
info.text,
caption,
width,
height
) {
ns <- shiny::NS(id)
TableModuleUI(
ns("datasets"),
info.text = i... |
89798abc325289bd32cd82941bea0fed1637c2e222778b23c06723770453348d | R | 3,187 | 111 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
mofa_table_factorenrichment_ui <- function(
id,
label = "",
title = "",
info.text = "",
caption = "",
height = 400,
width = 400
) {
ns <- shiny::NS(id)
options <- tagLis... |
2b425bcd5f7ec4ea423bc9ff2fbe4455c01f3447925310026784c3c4d4177ccd | R | 3,197 | 91 | library(data.table)
thr_p_smr <- 1e-8
thr_p_heidi <- 0.01
thr_nsnp <- 3
f_blood <- fread("Ferritin and Blood.zip")
f_brain <- fread("Ferritin and Brain.zip")
f_liver <- fread("Ferritin and Liver.zip")
mark_pass <- function(dt, panel){
setDT(dt)
setnames(dt, old = intersect(names(dt), c("nsnp_HEI... |
7f19d366da53186582a9f26c6a64f985c66fab1570b22d9cb254c22688b4e9d1 | R | 3,204 | 90 | # SPDX-License-Identifier: MIT
# Copyright (c) 2025 Yumi Kim
###############################################################################
# Main Script (updated to new function names)
###############################################################################
rm(list = ls())
# ---- Packages ----
suppressPacka... |
2cae8e6b81b582297125ea2636dfb4d2cd09a0cfea9dc5b4f9e36f980b312056 | R | 3,214 | 111 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
plot_deepnet_biomarkerheatmap_ui <- function(
id,
title = "",
info.text = "",
info.methods,
info.references = "",
caption = "",
label = "",
height = c("100%", TABLE_HEIGHT_... |
f3dd92ae9c6a6b5daffa2cb1f122ab7a3c8272b27bed73cce7b3b636cec4bc2d | R | 3,214 | 73 | #################
### Load data ###
#################
rm(list=setdiff(ls(),'params'))
basedir <- params$basedir
setwd(basedir)
savedir <- paste(params$opdir,'processed/',sep='')
dir.create(savedir,recursive=T)
data <- read.csv('Data83018/data.csv',header = TRUE,check.names = F)
connectivity.ipsi <- read.csv('Data8301... |
720993231e61e6b2e284d1c2138b3a8e14eaa33a177f0d4c18bf2d895c1f1b35 | R | 3,222 | 96 | #' @param X matrix. Rows are genes. Columns are samples. Row names are symbols.
#' @param gene_sets list. Each element is a string vector with gene symbols.
#' @param alpha numeric. Parameter for ssGSEA, the default is 0.25
#' @param scale logical. If True, normalize the scores by number of genes in the gene sets.
#' @... |
7a3028cbee0b80f33faceb5370071f15056c67da15ac26b54a6f8da95d48a903 | R | 3,229 | 115 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
signature_table_enrich_by_contrasts_ui <- function(
id,
title,
info.text,
caption,
width,
height
) {
ns <- shiny::NS(id)
TableModuleUI(
ns("datasets"),
info.text =... |
be601b96a52b0c31c175d0b4e0c7a095cce87f44218cf546539ec2f0be630cb2 | R | 3,235 | 106 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
##===================================================================
##======= Script to build PGX object from GEO dataset ===============
##==============================================... |
fa478d99a65eb8528a7d66bbb39cfcb25f9caeb25eeeae86b27fa94c8ee186a1 | R | 3,235 | 112 | ##
## 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... |
62dac0e439a9e1c83bde59c941925c032249ef1e6dc88547b7030dc8f7500c51 | R | 3,253 | 112 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics Sagl. All rights reserved.
##
#' Importance plot UI input function
#' @description A shiny Module for plotting (UI code).
#' @param id
#' @param label
#' @param height
#' @export
mofa_plot_pathbank_ui <- function(
... |
8939df1d06b750d6059a7987cd52a6f4977fc2a4cf9a12e8850dad969c224cf4 | R | 3,255 | 132 | #' Returns the first binary string with n 01 and m 1s.
#'
#' @param n The number of 0s.
#' @param m The number of 1s.
#' @author Maryam Ghareghani
#' @export
#'
#TODO This function is very short. I would define this function at the beginning of functions defined below.
initialState = function(n, m)
{
paste0(stri... |
dad61c0b8f7c0e94f61c18fe609ddd40018dac394d46e416f2ce1447f26c0d76 | R | 3,258 | 120 | test_that("normal acc: auth-code works",{
source("aux-test-functions.R")
App <- shinytest2::AppDriver$new(
normalizePath("../../dev/board.launch"),
timeout = 120000,
height = 1080,
width = 1920,
seed = 2910,
variant = shinytest2::platform_variant(),
options = list(
board = "datav... |
b0fa17fbd43b3cecd65dda020b33a94259a29bd77304091c4b553dd21490deba | R | 3,268 | 113 | #!/usr/bin/env Rscript
# Generate diverse BED files for NanoporeToBED demo
# Creates files with varying methylation levels, coverage, and CpG counts
set.seed(42)
output_dir <- "demo_data"
dir.create(output_dir, showWarnings = FALSE)
# Sample configuration with diversity
samples <- data.frame(
name = c(
"... |
d72e3e433375fb7613d7d841b4a6b6a7200637660a679d84b252a4c83806a7b1 | R | 3,275 | 113 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
connectivity_table_foldchange_ui <- function(
id,
title,
info.text,
caption,
width,
height,
label = ""
) {
ns <- shiny::NS(id)
bslib::layout_columns(
col_widths = 12... |
ad925f1746782d0fea8d72536993ba6f2f3bffdd2efa60e0998579293f51649b | R | 3,279 | 79 | # plot freg models
plot.freg <- function(fit_dat,
r,
fig = NULL,
align,
Hz,
var_name = NULL,
title = NULL,
y_val_lim = 1.1,
ylim = NULL,
... |
b453131e4e2f96607e4c4c6741f53dfbd9b36a8a46420f93d3afc5c268ff913e | R | 3,282 | 79 | ##this script is an example script that performs colocalization of lead variants in AB42 GWAS with GTEx eQTL summary statistics
install.packages("coloc")
library(coloc)
library(data.table)
library(dplyr)
gene_lookup<-fread("gene_ID_symbol_lookup_gencode.v39.annotation.txt", h=F, stringsAsFactors=F, data.table=F)
se... |
6113974f27d60c0a22ea84f22fdb225dcf6ebd68efe861db4e04c8a4fa4c935d | R | 3,283 | 106 | ---
title: "HUDECA — Extended Data Figure 9. Developmental activation of olfactory receptor programs in neuronal lineages"
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
... |
294dc8ef10a2e1826ccef5a557cf537c67572e7fdf914c3ae00fd01d07d949f7 | R | 3,289 | 77 | #!/usr/bin/Rscript
options(error = traceback)
args <- commandArgs(TRUE)
# add user defined path to load needed libraries
.libPaths(c(.libPaths(), args[6]))
suppressPackageStartupMessages(library(StrandPhaseR))
# FIXME : tmp debuging local repo
# library(devtools)
# load package w/o installing
# load_all("/g/korbel2... |
0edb343f5d7a7d5f1dd1287c43d350fdb8e5fd8c77842cf9a9b7398295ff67f7 | R | 3,306 | 124 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
dataview_module_geneinfo_ui <- function(
id,
label = "",
title,
height,
width,
caption,
info.text,
info.methods,
info.references
) {
ns <- shiny::NS(id)
a_OMIM <- ... |
b8b3312a371574ad875db555dc213a9198a0ed146dac3440c00b45f415e7e59a | R | 3,311 | 77 | args=commandArgs(trailingOnly=TRUE)
## 1) Load feature sets
##-------------------------------------------------------------------------------------
##Features: Sequence : GC%, CpG%, RT
##-------------------------------------------------------------------------------------
TSS_matrix <- read.table(args[1], header=TRUE... |
d0bbeaab674422be84f8a0277be94febcd89b7f4541d38b4d0df98843d708977 | R | 3,312 | 99 | #Statistical tools Primarily PERMANOVA, alpha diversity and the CLR transformation.
library(vegan) #install.packages("vegan")
library(iNEXT) #install.packages("iNEXT")
library(Tjazi) #devtools::install_github("thomazbastiaanssen/Tjazi")
library(lme4)
library(lmerTest)
#Data Wran... |
ed42bd52a03a339ecf3deea45761215f0df99ed0fcf511246cf198c02860a1f0 | R | 3,327 | 113 | library(GenomicRanges)
library(rtracklayer)
library(dplyr)
library(ChIPseeker)
library(TxDb.Mmusculus.UCSC.mm10.knownGene)
library(org.Mm.eg.db)
# Parse command line arguments
library(optparse)
# Create option parser with explicit dest parameter
option_list <- list(
make_option("--work-dir",
type... |
0613b926020f177b6825634804a2ba880f8b8ff2214266c6f6f381d1671a3234 | R | 3,340 | 124 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
foldchange_heatmap_ui <- function(
id,
title,
info.text,
caption,
label = "",
height,
width
) {
ns <- shiny::NS(id)
FoldchangeHeatmap.opts <- shiny::tagList(
withToo... |
5084b3aee5a30f704b317be35c7f8f39b66d395e15b6b17161a82e7fea0ac1af | R | 3,347 | 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
expression_table_gsettable_ui <- function(
id,
title,
capti... |
790c130de4f3daf8df8e4aaa9aeb32393234797627c571314bf83ed7bd625b45 | R | 3,359 | 125 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
wgcna_plot_gene_heatmap_ui <- function(
id,
label,
title,
info.text,
caption,
height,
width
) {
ns <- shiny::NS(id)
options <- shiny::tagList(
shiny::checkboxGroupIn... |
5320b54a8c9687369d099d862110e64498ea4409f73b070770a195c919e6665b | R | 3,382 | 118 | ## -------------------------------------------------------------------
## util functions
## -------------------------------------------------------------------
sendShareMessage <- function(pgxname, sender, share_user, path_to_creds = "gmail_creds") {
if (!file.exists(path_to_creds)) {
info("[sendShareMessage] WA... |
a627f2f4a669e977deadf0553935437781382a29db4132539af10ca31c0f4b54 | R | 3,392 | 128 | rm(list = ls())
library(Banksy)
library(SummarizedExperiment)
library(SpatialExperiment)
library(Seurat)
library(scater)
library(cowplot)
library(ggplot2)
# The data with format required by SpatialGlue are available from the spatialLIBD package.
SEED <- 1234
# load the data
library(spatialLIBD)
library(Experiment... |
c3744858bee607cdc361e3c5681a887c2452d1504b7da56c39df4ece25493737 | R | 3,401 | 68 | rm(list=ls())
library(ggplot2)
library(dplyr)
library(stringr)
setwd("D://work//skoltech//lipid//writing//GitHub//data")
data <- read.csv("milk_FA.normalized.csv", row.names = 1)
data <- log2(data)
info <- read.csv("milk_FA.info.csv", row.names = 1)
info$species <- factor(info$species, levels = c("HSm... |
224c785ca8fa2ae4e15a43d58bf150116a540e9fb16b8930118334ac9a26bc0b | R | 3,404 | 77 | args=commandArgs(trailingOnly=TRUE)
## 1) Load feature sets
##-------------------------------------------------------------------------------------
##Features: Sequence : GC%, CpG%, RT
##-------------------------------------------------------------------------------------
TSS_matrix <- read.table(args[1], header=TRUE... |
559d04407f40b803431895c457414c04f9b20282b1e719861ebb1a04f17a2e16 | R | 3,408 | 133 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
functional_table_reactome_ui <- function(
id,
title,
info.text,
caption,
label,
width,
height
) {
ns <- shiny::NS(id)
TableModuleUI(
ns("tablemodule"),
info.tex... |
ceb5970bf3dcabf842013a51d0a785fbaa30a0fabeb8054856da6ef3d2cf5a99 | R | 3,410 | 108 | #!/usr/bin/env Rscript
##
## Make PGX file from CSV files
##
## (c) 2023-2026 BigOmics Analytics
##
message("[create PGX process] : starting process")
args <- commandArgs(trailingOnly = TRUE)
temp_dir <- args[1]
OPG <- args[2]
if (!exists("temp_dir")) temp_dir <- getwd()
params_from_op <- file.path(temp_dir, "param... |
01004b3ff103991c8573cf9e1d786b5b592ad79f72c096b5907124fd2a4e3770 | R | 3,412 | 90 | rm(list=ls())
library(ggplot2)
library(reshape2)
library(stringr)
library(gridExtra)
library(ggrepel)
setwd("D://work//skoltech//lipid//writing//GitHub//data")
DATA.milk <- read.csv("milk_FA.normalized.csv", row.names = 1)
INFO.milk <- read.csv("milk_FA.info.csv", row.names = 1)
info.H <- read.csv("mi... |
bef05e9bdeb29e2b0883eb0a60c6588dba4d522854cc7af73a7287dfe8ca83f7 | R | 3,419 | 68 | rm(list=ls())
setwd("D://work//skoltech//lipid//writing//GitHub//data")
library(ggplot2)
library(reshape2)
library(stringr)
library(gridExtra)
DATA <- read.csv("milk_FA.normalized.csv", row.names = 1)
info <- read.csv("milk_FA.info.csv", row.names = 1)
info <- info[!(info$species %in% c("BF", "QC")), ]
... |
aee0d53c25eeb2587b8069da5762346dc1949c0c9fd6dc0768b065c48f66a699 | R | 3,432 | 133 |
library(optparse)
# Define the options
option_list <- list(
make_option(c("-d", "--data"), type="character", help="Path to pgx data files")
)
# Parse the command line arguments
opt_parser <- OptionParser(option_list=option_list)
opt <- parse_args(opt_parser)
if (is.null(opt$data)) {
stop("Please provide a path ... |
0f990a113b319fa20fa70723f11ba762d4769b97dc04b88fc14cdf3890ced430 | R | 3,435 | 126 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
#' @export
correlation_table_corr_ui <- function(
id,
title,
info.text,
caption,
label = "",
height,
width
) {
ns <- shiny::NS(id)
TableModuleUI(
ns("table"),
i... |
05c0d08d996610f0f9ac1cf5cd57296e47c870d81aa14d0c420474e4eb5e1b78 | R | 3,437 | 114 | ## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
epigenomics_plot_beta_dist_ui <- function(id,
label = "",
title,
hei... |
9c3fdeb917579f629efa0339761e4d153ebb03a7dab31e3caa41f70d418d5efb | R | 3,438 | 118 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
##===================================================================
##================ Script to build PGX object =======================
##==============================================... |
47e655fe1b543267614dff1e6b8d4bafad9afc7945a85aa662ad9d2fb08c36c4 | R | 3,442 | 83 | # plot fLME models
## Figure 4
plot.FUI <- function(r,
fig = NULL,
align,
Hz,
var_name = NULL,
title = NULL,
y_val_lim = 1.1,
ylim = NULL){
library(gridExtra)
name... |
b2d7892c87585d75641bb2465ee06c913d7830664ae5073ca55f3ebdb3f36832 | R | 3,444 | 130 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
wgcna_table_enrichment_ui <- function(
id,
label = "",
title = "",
info.text = "",
caption = "",
width,
height
) {
ns <- shiny::NS(id)
options <- tagList(
checkboxIn... |
c9835baa116bb64f7bfb9936f555ba6c91002dbb3870fe47e2d9865b4e4e18a9 | R | 3,446 | 119 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
table_deepnet_gradients_ui <- function(
id,
label = "",
title = "",
info.text = "",
caption = "",
height = 400,
width = 400
) {
ns <- shiny::NS(id)
TableModuleUI(
ns... |
79f735ca15cef2193fb76b4d771c1422aa7903fc967b78f4a2fb4955facc13cb | R | 3,454 | 101 | rm(list=ls())
library(ggplot2)
library(reshape2)
library(gridExtra)
library(cowplot)
setwd("D://work//skoltech//lipid//writing//GitHub//data")
data <- read.csv("brain_FA.normalized.csv", row.names = 1)
data <- log2(data)
info <- read.csv("brain_FA.info.csv", row.names = 1)
allSpecies <- c("HS","PT"... |
b92f7338567124c212733631471e7ba22ede9a18ddafbbe5bb4b262382bb60cd | R | 3,455 | 123 | lasagna_multipartite_nodes_table_ui <- function(id,
label = "",
title = "",
info.text = "",
caption = "",
... |
cad09b60135ce28c7e86b1145abc6dcf87a6de7cecde1f0fe6b16e71e9357abd | R | 3,462 | 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
#'
#' @export
compare_plot_compare2_ui <- fu... |
770eca11187e79ecd710cd383576de0650d3cc561a54d4aafd2f8ede7a7087f9 | R | 3,472 | 94 | # Install GIFT package
install.packages('devtools')
devtools::install_github('yuanzhongshang/GIFT')
library(GIFT)
#### load the directory containing files of summary statistics from eQTL data only
eQTLfilelocation <- $path_to_eQTL
#### load the directory of summary statistics from GWAS data
GWASfile <- $path_to_gwas
#... |
389096bb82d491c80b8eaa8ca06174f4c22752d37ecdcc35614e7b099381c95d | R | 3,478 | 100 | library(platetools)
library(ggplot2)
library(viridis)
library(dplyr)
## collect ASHLEYS prediction and count files
# ashleys_data <- read.table(file = "/scratch/tweber/DATA/TMP/labels384.tsv", sep = "\t", header = TRUE)
ashleys_data <- read.table(file = snakemake@input[["labels"]], sep = "\t", header = TRUE)
num_cells... |
100639aa504d253217e7cc77185456ed319fa426b64bfe140813b4c9ec37ddcb | R | 3,482 | 117 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
dataview_plot_phenoassociation_ui <- function(
id,
label = "",
height,
width,
title,
info.text,
info.methods,
info.extra_link,
caption
) {
ns <- shiny::NS(id)
opts <... |
09349f808f6eeacd5725f0f9a8f112e7519e6df25ff0a0523d84ce262f7043bd | R | 3,496 | 118 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
connectivity_table_similarity_scores_ui <- function(
id,
title,
info.text,
caption,
width,
height,
label = ""
) {
ns <- shiny::NS(id)
TableModuleUI(
id = ns("scores"... |
5921693d266173c4683bd9ec80d6e633245d7d25223a1893175b8ec8c0e55910 | R | 3,506 | 110 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
## Extra code for bigDash UI
##
##
## This calls the select-bigtab JS in app/R/www/temp.js
bigdash.selectTab <- function(session, selected) {
shiny:::validate_session_object(session)
... |
aa20c0ddca6c24f28faeab1fb73d89766d7db140d981dbd04ff0d49abcb162ae | R | 3,515 | 107 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
UserProfileBoard <- function(id, auth, nav_count) {
moduleServer(id, function(input, output, session) {
ns <- session$ns ## NAMESPACE
dbg("[UserProfileBoard] >>> initializing Use... |
3dec56aa744a9f220563758a8efed875d77043a8574da4ededbdf9296d5acfa0 | R | 3,524 | 101 | library(pheatmap)
library(tidyr)
library(dplyr)
library(gridExtra)
DEGs <- read.csv("/Users/osman/Documents/GitHub/PEBBLES_mouse_snRNAseq/soupx/PEBBLES_DEGs_filtered.csv")
## top DEGs
top_genes <- DEGs %>%
group_by(DEG_test, Directory) %>%
arrange(desc(logFC)) %>%
slice(1:2) %>% # Top 10 upregulated genes
bin... |
258ea6614bc7b2653713c9c073f3741193678bb10c858234ffc4116d6a6b36f0 | R | 3,539 | 110 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
wordcloud_table_leading_edge_ui <- function(
id,
title,
caption,
info.text,
width,
height
) {
ns <- shiny::NS(id)
TableModuleUI(
ns("datasets"),
info.text = info.t... |
2cae56119c55aa6600e66516586cdaf5282326a48b2de8ade87fdb8648aa327f | R | 3,563 | 119 | ##
## 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
compare_plot_compare1_ui <- fu... |
7f5e070d897db88edfe203271dc4d7a4d3db2345489c741dc2277cd150de8ac1 | R | 3,569 | 163 | # NOTE:
# DMR_summary.tsv is generated from DMR_full_results.tsv
# using scripts in 01_processing. Make sure to run the
# processing step before generating Figure 4.
# ==========================
# 0. Libraries
# ==========================
library(ggplot2)
library(dplyr)
library(patchwork)
library(VennDiag... |
b6102f04ebff2536825710d090efb9d380963aa7724072998653cc8f13348d6a | R | 3,569 | 84 | library(DNAcopy)
library(ggplot2)
library(scales)
library(gtable)
library(grid)
chrNamesLong = c("chr1","chr2","chr3","chr4","chr5","chr6","chr7","chr8","chr9","chr10","chr11","chr12","chr13","chr14","chr15","chr16","chr17","chr18","chr19","chr20", "chr21", "chr22", "chrX")
#chrNamesLong = c("chr1","chr2","chr3","chr4... |
c35bae39c32116156375b0553cb2e8c12e78add2575d0fe8431dec9a4e050169 | R | 3,601 | 141 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
functional_table_wikipathway_ui <- function(
id,
title,
info.text,
caption,
label,
width,
height
) {
ns <- shiny::NS(id)
TableModuleUI(
ns("tablemodule"),
info.... |
4ca7de49bdff373b2a9c293927cfc0d587a66f3bf56d1185c18f92f902a84aba | R | 3,602 | 107 | ## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
EpigenomicsBoard <- function(id, pgx) {
shiny::moduleServer(id, function(input, output, session) {
ns <- session$ns
shiny::observeEvent(input$board_info, {
shiny::showModal(shin... |
9cdd5deda8ae0f7d418e4749ef47e4f9086369bb3c0e9b0a4b3127205e97640c | R | 3,610 | 96 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
AppSettingsInputs <- function(id) {
ns <- shiny::NS(id)
bigdash::tabSettings()
}
AppSettingsUI <- function(id) {
ns <- shiny::NS(id) ## namespace
div(
boardHeader(title = "Ap... |
4c8f9043ee73482277eba7770a8f41be011e312a3498e66082bb2ac10786b75b | R | 3,611 | 103 | library(data.table)
library(coloc)
Ferr <- fread("Ferritin_AF0p005.mr_ready.tsv.gz")
cor_sig <- fread("Brain_Cortex.v8.signif_variant_gene_pairs.txt.gz")
cor_genes <- fread("Brain_Cortex.v8.egenes.txt.gz")
## 1) Define TOMM40 window (GRCh38)
chr_tomm <- 19L
start_bp <- 44401715L # 44,401,715
end_bp ... |
029cfc8dbc899be23c51ad62d2d71f1804c14e242cd880244ebd3ec08defc292 | R | 3,614 | 105 | rm(list = ls())
library(ggplot2)
library(patchwork)
library(scater)
library(harmony)
library(BayesSpace)
library(Seurat)
set.seed(1234)
# The data with format required by BayesSpace are available at:
# https://drive.google.com/drive/folders/1NVROB3oyBgBEzCt1yH_AJe6uSIjspDLf?usp=sharing, and
# https://drive.google.c... |
6ab7a1a5b2b174212f9cfea1a0e0bf88d7f2439851cdd171a36280ab1173608b | R | 3,620 | 95 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
SNFBoard <- function(id, pgx) {
moduleServer(id, function(input, output, session) {
ns <- session$ns ## NAMESPACE
fullH <- 700 ## full height of page
rowH1 <- 250 ## row 1 h... |
ce85c4b9ce0abb604ff370fd34b3d81d09d774ec012691e001a1e0939eed7972 | R | 3,625 | 97 | rm(list=ls())
library(ggplot2)
library(reshape2)
library(car)
library(gridExtra)
setwd("D://work//skoltech//lipid//writing//GitHub//data")
data <- read.csv("milk_FA.normalized.csv", row.names = 1)
info.shg <- read.csv("milk_FA.info.humanShangHai.csv", row.names = 1)
info.msk <- read.csv("milk_FA.info.hu... |
914c85bc74cfedaf44f44262c94b6230c6f4a8d3526c0686bdeef7ac76c10869 | R | 3,626 | 86 | ## KJH 03/19/2026:
# Hiersche, Osher, Saygin (2026) Functional Dissociation of Language and Theory of Mind in the Developing Superior Temporal Lobe. Communications Biology
# these statistics were done using "R version 4.5.1 (2025-06-13 ucrt)"
# this script provides template for calculating the rmANOVA results for ... |
935a96d922c8e85bbe43068132b4a8b4a1b4c7a5240bc7a99e92e52b700754ac | R | 3,628 | 144 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
consensusWGCNA_plot_modulecorr_ui <- function(
id,
title = "",
info.text = "",
caption = "",
label = "",
height = 400,
width = 400
) {
ns <- shiny::NS(id)
options <- shi... |
4b80fa9171257e6c27d9804f1e680d1a9570301e3bb1075083acb775dc45dfa2 | R | 3,637 | 62 | args=commandArgs(trailingOnly=TRUE)
TSS_matrix <- read.table(args[1], header=F, sep ='\t', comment.char = "")
Pred_result <- read.table(args[2], header=T, sep =',', comment.char = "")
chromosome <- c('chr1', 'chr2', 'chr3', 'chr4', 'chr5', 'chr6', 'chr7', 'chr8', 'chr9', 'chr10', 'chr11', 'chr12', 'chr13', 'chr14', 'c... |
0f4234d1258156897d911ce5bb05232ef4715d9bd81039ece780e86457d2979b | R | 3,638 | 101 | ##
## 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
TimeSeriesBoar... |
1ff99b162191c7bacdac2e03634968b235e25c2edcd8179734b08380592bf166 | R | 3,640 | 144 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
preservationWGCNA_plot_modulecorr_ui <- function(
id,
title = "",
info.text = "",
caption = "",
label = "",
height = 400,
width = 400
) {
ns <- shiny::NS(id)
options <- ... |
4c686ca641d3fb4b53a574a089fae59a6f5c3676f60b65d6b97b673bfab196aa | R | 3,640 | 117 | ---
title: "HUDECA — Extended Data Figure 5. Hierarchical annotation and compositional structure of olfactory epithelial cell populations"
author: "Mbouamboua Yvon <yvon.mbouamboua@inserm.fr>"
output:
html_document:
toc: true
toc_float: true
number_sections: true
date: '`r format(Sys.Date())`'
---
## Goa... |
cad9f39e7a4cc386a570a73dd5466bcc9c5bffb890ae5f53ca9fb4d1dc55b998 | R | 3,643 | 128 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2020-2026 BigOmics Analytics Sagl. All rights reserved.
##
UsersMapInputs <- function(id) {
ns <- NS(id) ## namespace
tagList()
}
UsersMapUI <- function(id) {
ns <- NS(id) ## namespace
fillCol(
flex = c(1),
height = 780,
tab... |
43e899b675fe5ff09ca9925f1da6b899feb72c9a8352b10267dfe785f74a548c | R | 3,645 | 111 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
## Append one row per admin action to the per-host audit log.
## Hostname is part of the filename because multiple deploys may share
## the same mounted etc/ folder; admin events must not... |
d53d62bd39154bcca48206c7fcddee24358e4934ac3baf8768a4a9853c4da715 | R | 3,670 | 113 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
##===================================================================
##================ Script to build PGX object =======================
##==============================================... |
226d1838abd97295233b6823cedadb4b6a4dc7173cb076401c2ac32613bd9cb0 | R | 3,687 | 75 | #################
### Load data ###
#################
rm(list=setdiff(ls(),c('params','grp')))
basedir <- params$basedir
setwd(basedir)
savedir <- paste(params$opdir,'diffmodel/seedspec/',sep='')
dir.create(savedir,recursive=T)
source('code/fitfxns.R')
load(paste(params$opdir,'processed/pathdata.RData',sep='')) # loa... |
7d097674aaeccaf4769517a2239c50e638482edff6ae38debbcebeb4b3a2abbe | R | 3,703 | 81 | args=commandArgs(trailingOnly=TRUE)
TSS_matrix <- read.table(args[1], header=TRUE, sep ='\t')
subclonality <- read.table(args[2], header=TRUE, sep ='\t')
##-------------------------------------------------------------------------------------
##Features: Sequence : GC%, CpG%, RT
##-----------------------------------... |
e273a83adcfcad983fd3f67fa63bf42feb7095c9da3a29e8fb82c8d95565f547 | R | 3,710 | 113 | ---
title: "HUDECA — Figure 2: Composition and development of the human olfactory system at PCW7-PCW12"
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 se... |
b0f3b95d89b1faacb3b1840021977b585d42608517e5b08038c5ae737c9e9890 | R | 3,712 | 95 | # This file is supposed to run from the root Playground folder
if (basename(getwd()) != "omicsplayground") {
stop("Please run from the OmicsPlayground root folder")
}
require <- function(pkg) (pkg %in% installed.packages()[,'Package'])
if(!require("renv")) install.packages("renv")
if(!require("BiocManager")) inst... |
dcbb37b39df0caa9147a9714b55ba9a8c24eb109e5aeef279c7b264ce9d2054e | R | 3,736 | 115 | # Median of ratios normalization
# fetch arguments
# args <- commandArgs(trailingOnly = T)
# checking arguments
# if (length(args) != 2) {
# message("Usage: Rscript GC_correction.R count-file.txt.gz gc-matrix.txt output.txt.gz")
# stop()
# }
# if (!file.exists(args[1])) {
# message(paste(args[1], "does no... |
935884befa134b7d03ff8f4f9a10f83f4e56d0a82326e0a123374929a828df79 | R | 3,754 | 84 | codingVars<-list()
codingVars$id <- "codingvariant"
codingVars$title <- "Coding Variants"
codingVars$loadData<- function(){
#read in coding variant data
coding_ld <<- fread("www/codingvars/CodingVariantLD.csv")
coding_variants <<- fread("www/codingvars/CodingVariants.csv")
#read in coding variant data ge... |
e7079a8810b4cf1bca3bfba5317512480005fdb413b78599d493619c23592919 | R | 3,782 | 138 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
admin_table_users_ui <- function(
id,
title,
height,
width = c("auto", "100%"),
caption,
info.text
) {
ns <- shiny::NS(id)
TableModuleUI(
ns("tbl"),
width = width... |
67246ab6416420ab7362b2d734b22b270ed22cacb12c840d38bd418c39d1afd1 | R | 3,788 | 115 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
enrichment_table_n_sig_gsets_ui <- function(
id,
title,
info.text,
caption,
width,
height
) {
ns <- shiny::NS(id)
TableModuleUI(
ns("datasets"),
info.text = info.t... |
bfb99bd27ec50d784bfe74033a2b8b5df4f476ac1f80f668f68ae7f370327d8c | R | 3,808 | 146 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
multiwgcna_plot_lasagna_ui <- function(
id,
title = "",
info.text = "",
caption = "",
label = "",
height = 400,
width = 400
) {
ns <- shiny::NS(id)
options <- shiny::tag... |
bced84054e01e11bfb53d1e97812d0552660f8a883e635be6c469b85b85b6896 | R | 3,827 | 163 | ---
title: "Initial Analysis of Human Cells out of Shiverer Chimeras"
author: "John Mariani"
date: "12/6/2022"
output: github_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
knitr::opts_knit$set(root.dir = rprojroot::find_rstudio_root_file())
```
```{r, echo = TRUE, message=FALSE, warning... |
a9497549cd39ba05ef2d76a69a7b43a0c58185278cd497bb04e61837e12e26e4 | R | 3,832 | 168 | ---
title: "000-HUDECA — 000-qc"
output: html_document
author: "Mbouamboua Yvon <yvon.mbouamboua@inserm.fr>"
output:
html_document:
toc: true
toc_float: true
number_sections: true
date: '`r format(Sys.Date())`'
---
## Goal
Quality control
## Setup
```{r}
knitr::opts_chunk$set(message = FALSE, warning ... |
b05e53fffb13ef7a54ad93230a3bcb3ad7ee73e9200b85fd2f9f9cabc4fdb282 | R | 3,859 | 112 | rm(list = ls())
library(circlize)
library(reshape2)
library(tidyr)
library(dplyr)
Sys.setlocale(category = "LC_ALL", locale = "Greek")
# 데이터 불러오기
mat <- as.data.frame(readxl::read_excel("[Result] Total_metabolite_correlation.xlsx", sheet = "Chord diagram_kynurenic acid_cS"))
nm <- unique(c(unlist(mat["M1.TYPE1"]), ... |
c897ccdc14a304de855e96076b689202c228ae82a38ced7c8fbaf790b1afb64c | R | 3,860 | 142 | ##
## 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
connectivity_plot_cumFCplot_ui... |
ac986f133ad54cee2a83ca687029d90f737ba8fb63ec86492f3de84f61dea610 | R | 3,870 | 154 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
preservationWGCNA_plot_moduletrait_ui <- function(
id,
title = "",
info.text = "",
caption = "",
label = "",
height = 400,
width = 400
) {
ns <- shiny::NS(id)
options <-... |
84a16ed989f7a25b4e8f3d395820b2b697411aa4921eabb472183fbbf82e5048 | R | 3,875 | 133 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
##===================================================================
##================ Script to build PGX object =======================
##==============================================... |
9ef85b8964908e0d51048cfd5660dbe58807d1a0fa5ad7e033d8218f699e7273 | R | 3,877 | 153 | ---
title: "Processing of all scRNA-Seq Data"
author: "John Mariani"
date: "3/6/2023"
output: github_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
knitr::opts_knit$set(root.dir = rprojroot::find_rstudio_root_file())
```
## Load in Libraries
```{r, message=F}
library(dplyr)
library(Se... |
e408564b12567e8ddc47cda09eb593e0875c3712edc669e367b7d02dc20221f6 | R | 3,885 | 105 | library(data.table)
library(coloc)
Ferr <- fread("Ferritin_AF0p005.mr_ready.tsv.gz")
cor_sig <- fread("Brain_Cortex.v8.signif_variant_gene_pairs.txt.gz")
cor_genes <- fread("Brain_Cortex.v8.egenes.txt.gz")
## ---- CEACAM19 window (GRCh38) ----
chr_ceac <- 19L
start_ceac <- 44119993L
end_ceac <- 4511999... |
436a2f43572571eea394ccf5970bc4028fcbfd8fc4f2339a295e136f841c3cdd | R | 3,893 | 176 |
# HuDeCA custom colors for A Single-Cell and Spatial Atlas of Early Human Olfactory Development paper
output <- "/Users/yvon.mbouamboua/Documents/projects/singlecell/hudeca/analysis/"
custom_colors <- list()
# Level 2 — Fine Cell Types (ann_level_2)
custom_colors$ann_level_2 <- c(
# Epithelium
"CycBasal" = ... |
8ca509916009d004f31519a46ef4bf4cc2525daf9457b87b024d3b9745892876 | R | 3,903 | 142 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
enrichment_plot_compare_ui <- function(
id,
title,
info.text,
info.methods,
info.references,
info.extra_link,
caption,
height,
width
) {
ns <- shiny::NS(id)
PlotModu... |
732ccf942e871f87c0ff8e96d4f35a66c97f58f9ee7998ee62ced60c108ba7e9 | R | 3,908 | 153 | ---
title: "Initial Analysis of PSC vs GPC scRNA"
author: "John Mariani"
date: "12/6/2023"
output: github_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
knitr::opts_knit$set(root.dir = rprojroot::find_rstudio_root_file())
```
```{r, echo = TRUE, message=FALSE, warning=FALSE}
library(Seu... |
3c0f04e6a9debd9252b61f4ab5c3667c70f6e3aadd2203fe46603cf625cf1ee6 | R | 3,918 | 94 | DPR <- $path_to_DPR_CVR2
EN <- $path_to_EN_CVR2
FUSION <- $path_to_FUSION_CVR2
FUSION$CVR2 <- apply(FUSION[, c("top1", "lasso", "enet", "blup")], 1, max, na.rm = TRUE)
dpr_df <- DPR[, c("TargetID", "CVR2")]
colnames(dpr_df)[2] <- "DPR_CVR2"
en_df <- EN[, c("TargetID", "CVR2")]
colnames(en_df)[2] <- "EN_CVR2"
fusion... |
1fb803c317f6ca7b854664eb19e27497132a2ddd4909969129b56897369a6969 | R | 3,929 | 130 | ##
## 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
expression_table_FDRtable_ui <- function(
id,
title,
captio... |
cb21f1294cc1a4229e16ac19abd4b0adb522320bfa527cae512f4d089ddd8b74 | R | 3,934 | 134 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
#' @param x
#'
#' @return
#' @export
visplot.PCSF <- function(
x, style = 0, edge_width = 5, node_size = 40, node_label_cex = 30,
Steiner_node_color = "lightblue", Terminal_node_color... |
63f31225309d0266aea43b51936c7931390b8c9ae87f93ddc0b21bffc178ee01 | R | 3,939 | 112 | library(data.table)
library(coloc)
library(arrow)
del <- fread("Delirium_AF0p005.mr_ready.tsv.gz")
sqtl_ctx <- read_parquet("Brain_Cortex.v10.sQTLs.signif_pairs.parquet")
sqtl_ctx <- as.data.table(sqtl_ctx)
## Case-control fraction for Delirium (NFE): 8,461 cases / 449,979 controls
case_frac <- 8461 / (84... |
8d12934b29553a298a4c7484c4de96235ef61085e7b42bddfd9da66773bed9fb | R | 3,954 | 141 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
#' Boxplots plot UI input function
#' @description A shiny Module for plotting (UI code).
#' @param id
#' @param label
#' @param height
#' @export
biomarker_plot_boxplots_ui <- function(
... |
c84badab3ea8a3bec646189640f1a05f8c7d099ce679ab7e0e0e8a432c82da29 | R | 3,960 | 126 | #!/usr/bin/env Rscript
if (commandArgs()[1] != "RStudio") {
ARGS <- c(
"tlxfiles", "character", "comma-separated list of files or dir and will grab all *.tlx",
"outputstub","character", "file path to plot to"
)
OPTS <- c(
"mh.ymax","integer",NA_integer_,"",
"mh.xmin","integer",0,"",
"mh... |
cdd4847378e26f57aa5b3deae9d6244436bc419db6f18cc3d483b6b85315b4fa | R | 3,960 | 92 | # plot fLME models
## Figure 4
plot.FUI <- function(r,
fig = NULL,
align,
Hz,
var_name = NULL,
title = NULL,
y_val_lim = 1.1,
ylim = NULL,
xlim = ... |
20490b232bcfe44590d9075a578e50bfeb6376859c62ad24567a217d7edc8acb | R | 3,964 | 117 | #load all libraries
library(dplyr)
library(purrr)
library(openxlsx)
library(glue)
library(enrichR)
#load file containing all DEGs
all_DEGs <- read.csv('all_experiments_sig_DEGs.csv')
# Get unique combinations of DEG_experiment and Cell_type
combinations <- unique(select(all_DEGs, DEG_experiment, Cell_type))
# Loop t... |
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