sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
3229655690baa4bf75e7e4299d9f120129ccca65373605d49a02dce679aeba04 | R | 6,520 | 209 | ##
## 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
functional_plot_go_network_ui ... |
2f6c1d1379f653aa755dcbfeb8cbd455641c62c01164fa167fec388eb0eae36a | R | 6,539 | 216 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
##===================================================================
##================ Script to build PGX object =======================
##==============================================... |
514474da371e7ae1cb2a407ebe892f720fd612ea66f6f50c2ff008a576be1c1d | R | 6,550 | 206 | suppressMessages(library(dplyr))
suppressMessages(library(data.table))
suppressMessages(library(assertthat))
# addCountsPerSegment
# Given segments + a large count table, calculate W/C counts per segment and cell.
#
# df = table with segments / cells.
# counts = table with raw counts
#
# returns an updated df
#
# Int... |
39f525cac12213fd96a4ee1d7dd37a0110ba147d2f75b1acfc042842cd2d3bc7 | R | 6,566 | 205 | ##
## 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_genetable_ui <- function(
id,
title,
info.... |
1611702ef7e32851db013ab1ad6a64454b254e4590231128fc5ee32ab40a06d8 | R | 6,571 | 195 | ---
title: "HUDECA — Figure 1: Single-nucleus RNA sequencing of the developing human olfactory sensory epithelium from post-conceptional weeks (PCW) 7 to 12"
author: "Mbouamboua Yvon <yvon.mbouamboua@inserm.fr>"
output:
html_document:
toc: true
toc_float: true
number_sections: true
date: '`r format(Sys.Da... |
730ed8b8228db9d869f3d12dec6382bcb896394d5b924d62a948953c79a8554f | R | 6,573 | 136 | args <- commandArgs(trailingOnly = TRUE)
output_filename <- args[10]
pdf(output_filename, width = 11, height = 10)
prefix <- strsplit(output_filename, "scNOVA_result")[[1]][1]
prefix <- substring(prefix, 1, nchar(prefix) - 1)
if (nchar(prefix) == 0) {
prefix <- "."
}
print(prefix)
library(pracma)
Deeptool_chr_l... |
037051e01ff14b775f28b13d1c78ab2a3408da1621befdf24c7afaa113d151bd | R | 6,586 | 224 | ##
## 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_fcfc_ui <- functi... |
3b6183cd331d330be57bc4892b6fcbfdc16d14e18905c37d910084e9a88f9f76 | R | 6,590 | 244 | ---
title: ""
subtitle: "Check overlap with eQTm results"
author:
- Wei Zhang^[University of Miami]
- Lily Wang^[University of Miami]
date: "`r Sys.Date()`"
output:
rmarkdown::html_document:
highlight: pygments
theme: yeti
toc: true
number_sections: true
df_print: paged
code_download: fal... |
514c2588571253d3e343cde6c524054bbad7d1c6233572ab7b0bcdca44171ce0 | R | 6,610 | 232 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
enrichment_plot_freq_top_gsets_ui <- function(
id,
title,
info.text,
info.methods,
info.extra_link,
caption,
height,
width
) {
ns <- shiny::NS(id)
topEnrichedFreq.opts... |
d562e4a5b3ac3bf9ccb4e776b5ad5d96b524f32470d94485bd4e67fb2dffcdb1 | R | 6,650 | 246 | #ESK Reduction (Scenario 1)
install.packages("heemod")
library(heemod)
pacman::p_load(data.table, dplyr)
par_mod <- define_parameters(
c_3rdOP = 1165,
c_4thOP = 1341,
c_5thOP = 1686,
c_3rdIP = 405,
c_4thIP = 405,
c_5thIP = 572,
c_AD = 12.5,
c_ESK_SOPC1 = 9520,
c_ESK_SOPC2 = 4760,
c_ESK_SOPC3 = 2... |
1e73333ea3dd6870887c62f26bafca69d4aa91650867a4deb40d0a610dd4c723 | R | 6,692 | 121 | #' AnnotateFeatures
#' Annotate features in a Seurat object with additional metadata from databases or a GTF file.
#' @param srt Seurat object to be annotated.
#' @param species Name of the species to be used for annotation. Default is "Homo_sapiens".
#' @param IDtype Type of identifier to use for annotation. Default i... |
aaf7fe2a207e18b889ed826dfd06601d67d1192cf1c4c894bda53368c7259332 | R | 6,697 | 114 | ---
title: "Photometry FLMM Guide Part II: Testing changes within-trial - cue vs. baseline periods"
author: "Gabriel Loewinger, Erjia Cui"
date: "`r Sys.Date()`"
output:
html_document:
df_print: paged
toc: yes
pdf_document: null
vignette: "%\\VignetteIndexEntry{fastFMM Vignette} %\\VignetteEncoding{UTF-8} %\\... |
d5650d758df57d95232a69be17a988265ecb582f25197cd7d6e380bd64283f3e | R | 6,728 | 130 | #################
### Load data ###
#################
rm(list=setdiff(ls(),c('params','grp')))
basedir <- params$basedir
setwd(basedir)
savedir <- paste(params$opdir,'diffmodel/',sep='')
dir.create(savedir,recursive=T)
dir.create(paste(savedir,'roilevel',sep=''),recursive = T)
source('code/fitfxns.R')
load(paste(para... |
57e06594e9286b8a2ab1d3a0ac242ff75b8618de668d22944cdf1ee96cd0c955 | R | 6,747 | 256 | ##
## 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... |
7032e95022f834ab773edb11c208da569b6204e6f4aef3503cbca8ef0781d759 | R | 6,767 | 213 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
##===================================================================
##================ Script to build PGX object =======================
##==============================================... |
6215d688884c5c9cf85747452236246f7277ac4a16b9122d227ce770c9dac4a4 | R | 6,796 | 213 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
##===================================================================
##================ Script to build PGX object =======================
##==============================================... |
96ef4d62e3a54b1da654920a085a003bd31307e170e856b3f36dee0c34e47a6b | R | 6,805 | 234 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
dataview_plot_tissue_ui <- function(
id,
label = "",
title,
height,
width,
caption,
info.text,
info.methods,
info.references
) {
ns <- shiny::NS(id)
PlotModuleUI(
... |
0ee18e7fbd4ff121ad441e04742e61a58cce79a637b54bad9238ccde1793c30b | R | 6,807 | 159 | args=commandArgs(trailingOnly=TRUE)
output_filename <- args[9]
pdf(output_filename, width = 11, height = 10)
prefix <- strsplit(output_filename, "scNOVA_input_user")[[1]][1]
prefix <- substring(prefix, 1, nchar(prefix) - 1)
if (nchar(prefix) == 0) {
prefix <- "."
}
print(prefix)
library(pracma)
Deeptool_result_... |
fade0c1935fe881e25a03acf00a24535f9d83874b06b35ff9190d674129ed8c2 | R | 6,821 | 225 | ---
title: "Omicsplayground Theme + Scales for ggplot2"
author: "Cédric Scherer"
date: "`r Sys.Date()`"
output:
html_document:
theme: united
highlight: kate
toc: true
toc_float: true
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE, message = FALSE, warning = FALSE,
... |
9f18ff7c0d4c66890daa204320889fb0344600e222bb2e4cb53712c8ac8cd78d | R | 6,824 | 173 | # ===================================================================
# Final Analysis Script (positive_slope outer group)
# ===================================================================
# --- Step 1: Clean Environment & Load Libraries ---
rm(list = ls())
library(plyr)
library(dplyr)
library(stringr)
... |
8d9fda1271155f5469883e5b262cd87c5505e1b3904088c2ca1cc7eb2ceab78f | R | 6,825 | 252 | ---
title: "Integration of in vitro hGPCs and Fetal scRNA-seq"
author: "John Mariani"
date: "07/30/2025"
output: github_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
knitr::opts_knit$set(root.dir = rprojroot::find_rstudio_root_file())
```
```{r, echo = TRUE, message=FALSE, warning=FALSE... |
7c44400cc5e5390a1c7c7562b2cd510d3c91bfa0bfb3d1f0a9d7ae6b98432b7d | R | 6,843 | 216 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
#' Importance plot UI input function
#'
#' @description A shiny Module for plotting (UI code).
#'
#' @param id
#' @param label
#' @param height
#'
#' @export
connectivity_plot_enrichmentGr... |
b9b5f1004604ed9cca884db2ac904ffd23c4372b8817de1d4a796cc2231c2262 | R | 6,874 | 187 | ---
title: "Figure S1A: Cell Ranger QC Metrics Across Genome Versions"
output:
---
```{r setup, include=FALSE}
# This sets the project root based on the repo structure.
# If you move this file, you may to set the root manually to find config.R
knitr::opts_knit$set(root.dir = dirname(dirname(rstudioapi::getSourceEdito... |
86137a5cc739ad0593c9bff7d18f63feec0bb49a813cb89a4df2a4382c206ed2 | R | 6,892 | 158 | args <- commandArgs(trailingOnly = TRUE)
output_filename <- args[8]
pdf(output_filename, width = 11, height = 10)
prefix <- strsplit(output_filename, "scNOVA_result")[[1]][1]
prefix <- substring(prefix, 1, nchar(prefix) - 1)
if (nchar(prefix) == 0) {
prefix <- "."
}
print(prefix)
subclone_list <- read.table(... |
1434c0cc3ee6ed1592e762bff15a63693a3f6fe7c035c4d61311d31057ba9400 | R | 6,902 | 234 | ##
## 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_connectivity... |
18e9e5b69409046e7d3ea2959c06d89fab15f5563f1dcf019e14bbc95a1e426f | R | 6,930 | 255 | #Combination - 20 years
install.packages("heemod")
library(heemod)
pacman::p_load(data.table, dplyr)
par_mod <- define_parameters(
c_3rdOP = 1165,
c_4thOP = 1341,
c_5thOP = 1686,
c_3rdIP = 405,
c_4thIP = 405,
c_5thIP = 572,
c_SOPC = 1190,
c_COM = 25,
u_remission = 0.85,
u_response = 0.72,
u_nre... |
b92f94de05823f66f313d750e1176aa4ecb9679321f85303322cedd05f8ea0b0 | R | 6,935 | 103 | library(Hmisc)
# for categorical variables -- remap everything to 0/1 for the models in Python
relabel_binary.fn = function(x) {
if(class(x) == "logical") {
x <- factor(as.integer(samples$logical_col), levels = c(0, 1))#, labels = c("Yes", "No"))
}else {
x <- factor(x, levels = c(1,0))#, labels = c("Yes", ... |
3e7a4f300557a93a26778d324e0d0a68b5a410cfcb719195101c9448f863475d | R | 6,944 | 236 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
enrichment_plot_barplot_ui <- function(
id,
title,
caption,
info.text,
info.methods,
info.references,
info.extra_link,
height,
width
) {
ns <- shiny::NS(id)
options ... |
29d6372a92a3e2f184e2d91c2d54aa4fa484c27eda198d863e380a8a9d9d61b9 | R | 6,991 | 249 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
#' Expression plot UI input function
#'
#' @description A shiny Module for plotting (UI code).
#'
#' @param id
#' @param label
#' @param height
#'
#' @export
signature_plot_enplots_ui <- f... |
106c28d691bc548731814d5d52da2a052474f3c1f5b270504e9f58f70e9110cc | R | 6,996 | 153 | #!usr/bin/Rscript
## Collect arguments
args <- commandArgs(TRUE)
## Default setting when no arguments passed
if(length(args) < 4) {
args <- c("--help")
}
## Help section
if("--help" %in% args) {
cat("
Calculate area under the curve threshold for CUT&RUN peaks
Arguments:
--exp=someValue - Inp... |
3da19ff03b2249a92f0074819f908837a8c0d8548ca9b16a95a12651664b59dc | R | 7,003 | 171 | rm(list=ls())
library(dplyr)
library(stringr)
library(car)
setwd("D://work//skoltech//lipid//writing//GitHub//data")
data <- read.csv("brain_FA.normalized.csv", row.names = 1)
info <- read.csv("brain_FA.info.csv", row.names = 1)
info <- info[info$species != "QC", ]
level.s <- c("HS", "PT", "MM", "CA",... |
95bcb22efd0af7ae584bf657ea7433005bf9451ef4a97a16bda5944ab9c019f8 | R | 7,010 | 209 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
BIGOMICS_CONTACT_US_URL <- "https://bigomics.ch/contact-us/"
BIGOMICS_PRICING_URL <- "https://bigomics.ch/pricing/"
contact_us_callback_js <- function() {
sprintf(
"function(value) ... |
d07cb68bf02e597e0a173f832028b1992c927c11f08540d7c6be504d120f951d | R | 7,018 | 151 | ## Jun 27, 2018 ADS
## function to generate SV_Consistency barplots from Mosaicatcher outputs
SVplotting <- function(inputfile, outputfile.byPOS, outputfile.byVAF) {
library(cowplot)
library(ggplot2)
library(data.table)
library(GenomicRanges)
# ***********************************************
ash12rai... |
21629a52a143dde3c6849cbb9ab2cef3b3aac2db523e0d17f4b4d599ab2c99eb | R | 7,029 | 237 | ##
## 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 heightt
#' @param width
#' @export
expression_plot_barplo... |
c2c9f2540baf6c7c61dc6b30ebf29f8c349fb606344dac8a1af9a24c93b0af01 | R | 7,034 | 188 |
args=commandArgs(trailingOnly=TRUE)
#---------------------------------------------------
#Single-cell CN normalization (Roadmap DHS resize 2kb) and chromVAR analysis (R_chromVAR.Rmd)
#---------------------------------------------------
##Load annotation of Roadmap cell-type promoters and enhancers
DHS_annot_resize ... |
e955778f01c5a61d0e9f7d5c4eeb96f14cc75fc09c439fe0814030c27070f6b9 | R | 7,040 | 163 |
##This script recreates supplementary figure 16 from the manuscript
library(data.table)
library(dplyr)
library(readxl)
##get common vars
Abeta_sub <- fread("Abeta42_sub.csv")
pTau_sub <- fread("pTau_sub.csv")
Diagnosis_sub <- fread("Diagnosis_sub.csv")
##do correlation plot for each
merged_for_cor<- merge(Abeta... |
a49885c3d33666a69d9ddb34c3cf0ffe59e644de032d2b9fba759505e7e56a77 | R | 7,048 | 212 | ---
title: "HUDECA — Extended Data Figure 3: Sex assignment quality control Detection of maternal erythroid contamination"
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
... |
8ffcc5d84c42461a6887cd576b110f9f288f7613ddf6d3cc3b468b228808ffe9 | R | 7,057 | 205 | # This file QCs the res_verdicted, e.g. to see
# problems with normalization etc.
library(stringr)
library(ggplot2)
library(optparse)
library(reshape2)
library(tibble)
library(matrixStats)
library(grid)
library(dplyr)
make_barplot_invwise <- function(rv_f, samples_f) {
number <- 1
### Define events again ###
re... |
042a5e708dab91cafbdf5ca570964eb8331f6c256eea350ddba360bc0bd0aed0 | R | 7,060 | 265 | #Psychotherapies - 20 years
install.packages("heemod")
library(heemod)
pacman::p_load(data.table, dplyr)
par_mod <- define_parameters(
c_3rdOP = 1165,
c_4thOP = 1341,
c_5thOP = 1686,
c_3rdIP = 405,
c_4thIP = 405,
c_5thIP = 572,
c_SOPC = 4760,
c_PSY = 12600,
u_remission = 0.85,
u_response = 0.72,
... |
0ae34b701a9dda4a9564af6be848b471e3b3f9af9f21279ae04cbe68b8c191e6 | R | 7,075 | 187 | suppressMessages(library(dplyr))
suppressMessages(library(data.table))
suppressMessages(library(assertthat))
# addCountsPerSegment
# Given segments + a large count table, calculate W/C counts per segment and cell.
#
# df = table with segments / cells.
# counts = table with raw counts
#
# returns an updated df
#
# Int... |
b3d0e7f7063062f2c95dd532ec92a7d94f02d535f30da47ebf5a311a162fc669 | R | 7,079 | 266 | #Psychotherapies + AD - 20 years
install.packages("heemod")
library(heemod)
pacman::p_load(data.table, dplyr)
par_mod <- define_parameters(
c_3rdOP = 1165,
c_4thOP = 1341,
c_5thOP = 1686,
c_3rdIP = 405,
c_4thIP = 405,
c_5thIP = 572,
c_SOPC = 4760,
c_AD = 12.5,
c_PSY = 12600,
u_remission = 0.85,
... |
e21d2f26416fc21b86995e07b89f3e45ba012ff3bc56da77e17adbe01b2959d4 | R | 7,097 | 241 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
loading_tsne_ui <- function(
id,
title,
info.text,
info.references = NULL,
info.methods = NULL,
info.extra_link = NULL,
caption,
label = "",
height,
width
) {
ns <- s... |
af9d93379e8bd75279cb0156036d2dfd82e0d771d346d5da8a9a88d1f85429c5 | R | 7,104 | 321 | ---
title: "Omicsplayground Corporate Colors and Palettes"
author: "Cédric Scherer"
date: "`r Sys.Date()`"
output:
html_document:
theme: united
highlight: kate
toc: true
toc_float: true
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(
echo = TRUE, message = FALSE, warning = FALSE,
de... |
de29fad3e60a71abb2a2cb672157316e13d872c71125c4670d4269b34d010271 | R | 7,114 | 167 | # Whoeps, 23 Oct 2020
# Function(s) needed to create a vcf file that will be saved as a final result of arbigent
oldw <- getOption("warn")
options(warn = -1)
#' Take a callmatrix and make a vcf out of it.
#' @param callmatrix
#' @return list: [all header lines, all data lines]
#' @author Wolfram Hoeps
#' @export
vcfi... |
e51620a6044c24e70267aeb346e34e36d05279a3b68469d2a70876a05beda0d6 | R | 7,132 | 244 | ---
title: "Firth Cox Regression"
output: html_document
date: "2025-12-02"
---
```{r setup, include=FALSE}
library(coxphf)
library(dplyr)
library(survival)
```
```{r}
data_dir <- "/home/sak0914/MtbQuantCNN/analysis/TRUST/processed_data"
df_trust_patients <- read.csv(paste0(data_dir, "/df_trust_patients_for_outcomes.... |
0bf39e6d6a4826f8bd10930aef07f64e638c671304afe79a5a412925ec14fd2f | R | 7,138 | 236 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
#' Mechanism-of-action plot UI input function
#'
#' @description A shiny Module for plotting (UI code).
#'
#' @param id
#' @param label
#' @param height
#'
#' @export
drugconnectivity_plot... |
644d233a50566e1021b0b1390a7babae66a08dc8db8bc950a0fa5138517c83b7 | R | 7,153 | 247 | ---
output:
md_document:
variant: gfm
---
<p align="justify">
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r setup, include = TRUE, echo = FALSE}
knitr::opts_chunk$set(echo = TRUE)
knitr::opts_chunk$set(dev = 'svg') # set output device to svg
```
```{r load and prep, include... |
aa041e3520e480867505c6436c9f39436e4279f3a1c008b6df04f54b4acf1065 | R | 7,170 | 218 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
##===================================================================
##================ Script to build PGX object =======================
##==============================================... |
942c2a46044e79125b69b9c94def5eabfa91a8fd73863f3c912d842006add0f0 | R | 7,195 | 142 | library(data.table)
library(coloc)
library(knitr)
# Load GWAS Datasets
ferr <- fread("Ferritin_AF0p005.mr_ready.tsv.gz")
del <- fread("Delirium_AF0p005.mr_ready.tsv.gz")
# 1) Delirium case fraction
N_cases <- 8461
N_ctrls <- 449979
case_frac <- N_cases / (N_cases + N_ctrls)
# 2) Clean basic types
for ... |
14e9dd31e9ec5541165a48ac303e5814f7ddf926e7743c3530ef982dd9e5cb19 | R | 7,248 | 149 | #' Plot the results from FUI
#'
#' Plot the estimated fixed effects from the Fast Univariate
#' Inference (FUI) approach.
#'
#' @param fuiobj A object returned from the \code{fui} function
#' @param num_row An integer that specifies the number of rows the plots will be displayed on. Defaults to p/2.
#' @param align_x A... |
9bbb6856be70c562252a3ee4d7e31994b92f193dcb05427f4abd59be9691c737 | R | 7,318 | 268 | #rTMS - 20 years
install.packages("heemod")
library(heemod)
pacman::p_load(data.table, dplyr)
par_mod <- define_parameters(
c_3rdOP = 1165,
c_4thOP = 1341,
c_5thOP = 1686,
c_3rdIP = 405,
c_4thIP = 405,
c_5thIP = 572,
c_SOPC_TMS1 = 23800,
c_SOPC_TMS2 = 11900,
c_AD = 12.5,
c_rTMS1 = 60000,
c_rTMS... |
ac02ff44b215564e621ad81fb769b18d998124711aae3c4ac828a2eadf6c1375 | R | 7,329 | 276 | # AUG - Lifetime horizon 20 years (260 cycles of 4 weeks)
library(heemod)
pacman::p_load(data.table, dplyr)
par_mod_aug20 <- define_parameters(
c_3rdOP = 1165,
c_4thOP = 1341,
c_5thOP = 1686,
c_3rdIP = 405,
c_4thIP = 405,
c_5thIP = 572,
c_SOPC = 1190,
c_AUG = 109,
u_remission = 0.85,
u_respo... |
8064a106d80011d73428c3a6a12b8c0c3c574d75d10f6422297445d1901283d3 | R | 7,367 | 217 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
##===================================================================
##================ Script to build PGX object =======================
##==============================================... |
43eb0cb1913ea573cc26509dab4741221fabc12c3bc5917f5e4ad21ab59bf437 | R | 7,391 | 198 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
##===================================================================
##================ Script to build PGX object =======================
##==============================================... |
bebee99b41eaf0c6b9384ef91d9ee98fe369f3b4216a52f5179b4760f2d85093 | R | 7,406 | 225 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
PreservationWGCNA_Board <- function(id, pgx) {
moduleServer(id, function(input, output, session) {
ns <- session$ns ## NAMESPACE
fullH <- 700 ## full height of page
rowH1 <- ... |
9263beb52c23f08efde7cbff8900e72b897bac7c6e9ae8cfdff23fe69527b63a | R | 7,435 | 222 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
##===================================================================
##================ Script to build PGX object =======================
##==============================================... |
ed6858343502c2bb9a88fb3059f837dc85dfd1ef60de7a913f08606743324af3 | R | 7,465 | 266 | #ECT + AD - 20 years
install.packages("heemod")
library(heemod)
pacman::p_load(data.table, dplyr)
par_mod <- define_parameters(
c_3rdOP = 1165,
c_4thOP = 1341,
c_5thOP = 1686,
c_3rdIP = 405,
c_4thIP = 405,
c_5thIP = 572,
c_SOPC_ECT = 65520,
c_AD = 12.5,
c_ECT1 = 77760,
c_ECT2 = 38880,
u_remissi... |
8c7e729ab5932527e9ea4d05eeb3cdc27f6c51be4e344892b01a1ca924d2fc8e | R | 7,473 | 133 | ## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
EpigenomicsInputs <- function(id) {
ns <- shiny::NS(id)
bigdash::tabSettings(
shiny::conditionalPanel(
condition = sprintf("input['%s'] === 'Methylation ideograms'", ns("tabs")),
... |
07ccc6ec1286cdd8313cd7dacad47628a6e6b5861732cf2cec611d84221005b6 | R | 7,479 | 228 | ## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
dataview_plot_boxplot_ui <- function(
id,
label = "",
height,
title,
caption,
info.text
) {
ns <- shiny::NS(id)
options <- shiny::tagList(
shiny::radioButtons(
inputId... |
522a626c69db3f0f242084c63eacb285ea7439058f817e1250c48653ee826824 | R | 7,495 | 155 | set.seed(1)
##################EIB part
#read in the data
setwd("./EIBResult/csv_1000/trainedACC_CSV/")
for (i in 0:19) {
if (i == 0) {
EIB_acc<-read.csv(paste0("trainedACC_1000_",i,".csv"),header = T, na.strings = "NA")
} else {
EIB_acc<-rbind.data.frame(EIB_acc,read.csv(paste0("trainedACC_1000_",i,".csv")... |
77ae76493dd623c56459c0678f68c57cd08e3c04c44e0a67e846ccf3b06fdda9 | R | 7,496 | 297 | #==========
# univariate twin analysis
# used to test liability threshold models for experiment-level missing
#
# author: Giorgia Bussu
# project: BT missing data
# version: June 2024
#==========
rm(list=ls())
require(OpenMx)
source('C:/Users/myfolder/twin_modelling/tutorial/miFunctions.R')
##########... |
09799f573ff6cf007ec1490234689bf6dc99e15d9248e4e4e9be29cc343c111a | R | 7,497 | 157 | args=commandArgs(trailingOnly=TRUE)
Deeptool_result_final <- read.table(args[1], header=TRUE, sep ='\t', comment.char = "")
CNN_matrix <- Deeptool_result_final[,1:4]
DHS_matrix_for_CN <- cbind(c(1:nrow(CNN_matrix)), CNN_matrix)
#1) Calculate copy number for CN for 150 bins of 19770 genes
sv_calls <- read.table(args... |
7edc9d65f267f925ce15f76ebb5f09283352b3caa4d927312b0df0be4ab8e0b6 | R | 7,571 | 248 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
#' Create UI for gene plot enrichment visualization
#'
#' @param id Id prefix for namespace
#' @param title Plot title
#' @param caption Plot caption
#' @param info.text Info text to disp... |
451dbf63735c36af95ec5ee5aae9c35aa7618d82d614c000ae8b552580b0ce0b | R | 7,590 | 236 | ---
title: "Figure 2Q: IT Subclass Gene Expression Correlations"
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$set(root.dir = dirname(dirname(rstudioapi::getSourceEditor... |
afef590d611fc43988b91abd7acdfe9309060a4313b4842b8c252f6026bfbe1e | R | 7,591 | 239 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
MultiWGCNA_Board <- function(id, pgx) {
moduleServer(id, function(input, output, session) {
ns <- session$ns ## NAMESPACE
fullH <- 700 ## full height of page
rowH1 <- 250 ## ... |
cfad21ad58a4b74ec658e371b6b1a46d71fc7df4b8ba51a513eeb08852f4d084 | R | 7,602 | 276 | #ESK S7 - Life time horizon 20 years
install.packages("heemod")
library(heemod)
pacman::p_load(data.table, dplyr)
par_mod <- define_parameters(
c_3rdOP = 1165,
c_4thOP = 1341,
c_5thOP = 1686,
c_3rdIP = 405,
c_4thIP = 405,
c_5thIP = 572,
c_AD = 12.5,
c_ESK_SOPC1 = 9520,
c_ESK_SOPC2 = 4760,
c_ESK... |
258e3fce87f8ef6e55def585205b4a906b388898f9447f3c123068c45d270708 | R | 7,666 | 207 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
require <- function(pkg) (pkg %in% installed.packages()[,'Package'])
scan_packages <- function(path='R') {
## ---------------------------------------------------------------------
... |
c0448b7e71f74886e2ccd3db4479833fe75eefd0f30a8b8783d5c108957d2b3b | R | 7,679 | 268 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
enrichment_plot_volcanomethods_ui <- function(
id,
title,
info.text,
info.methods,
info.references,
info.extra_link,
caption,
height,
width
) {
ns <- shiny::NS(id)
... |
dc409c51e94e75b2198fcfb16589289562f6baf53338249aed443897f0b2d368 | R | 7,682 | 239 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
##===================================================================
##================ Script to build PGX object =======================
##==============================================... |
37b049b20f2d7ae7d093abab84e648860937c33f8795efcaebee7a0250447aaf | R | 7,716 | 147 | library(ggplot2)
library(dplyr)
library(reshape)
library(ggsci)
library(colorspace)
PROJECT_ROOT <- "." # put your working directory
setwd(PROJECT_ROOT)
avg_depth_total=read.table("data/depth_data.txt", header=T)
avg_depth_total$batch=factor(avg_depth_total$batch, levels=c("1","2","3","4","5","6"))
npg <... |
8e44094d89e929dad0ca2a9019a15558a1ce52278aa61f0006d97412877b9c7f | R | 7,717 | 230 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
DrugConnectivityBoard <- function(id, pgx) {
moduleServer(id, function(input, output, session) {
ns <- session$ns ## NAMESPACE
fullH <- 750
rowH <- 660 ## row height of pane... |
05df3bcfe42606a8d2f43f5def80271ec20a572edc4b6b9e820c2154abcd9295 | R | 7,727 | 215 | #!/usr/bin/env Rscript
# RNA-seq Pipeline Step 5: Differential Expression Analysis with DESeq2
# This script performs differential expression analysis between Control and Mutant conditions
suppressPackageStartupMessages({
library(DESeq2)
library(tidyverse)
library(pheatmap)
library(RColorBrewer)
l... |
be8371b118f8bd5a9edbd356ae3a3a9d271bcb18d7c1853b98d6d0147e391ccc | R | 7,751 | 247 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
#' Enrichment Scatter Plot UI
#'
#' @description
#' Creates the UI for the enrichment scatter plot module.
#'
#' @param id Module ID string
#' @param title Plot title
#' @param label Plot... |
687c45f0c678dec1109efb86283c2faf1a8657265389617f0747ea6fc0141cfc | R | 7,787 | 215 | library(data.table)
library(susieR)
library(coloc)
library(SNPRelate)
library(gdsfmt)
## ---------- inputs ----------
fer_file <- "Ferritin_AF0p005.mr_ready.tsv.gz"
pqtl_file <- "prot-a-131.vcf.gz"
## APOE ±500 kb (GRCh38)
chr_apo <- 19L
start_apo <- 44421094L
end_apo <- 45421094L
## sample siz... |
3623c612b2736f216b987677ede289d0677551342a75c02f80420a03458939b9 | R | 7,796 | 244 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
compare_plot_expression_ui <- function(
id,
label = "",
height = c(600, 800),
title,
info.text
) {
ns <- shiny::NS(id)
PlotModuleUI(
ns("plot"),
title = title,
p... |
492db9663277b53f09490bdd8e66f2150a6725cbca422b576dd4563fe0fdc37f | R | 7,830 | 257 | ---
title: "Processing of data for species integration"
author: "John Mariani"
date: "3/6/2023"
output: github_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
knitr::opts_knit$set(root.dir = rprojroot::find_rstudio_root_file())
```
## Load in Libraries
```{r}
library(dplyr)
library(Seura... |
0a4071c241c0279c9b59395ce188680aa496f78c15f2942bbf0df77121ad4a53 | R | 7,891 | 165 | # load libraries
packages <- c("tidyr", "openxlsx", "glue", "magrittr", "Seurat", "dwtools", "devtools", "dplyr", "patchwork", "scCustomize")
stopifnot(suppressMessages(sapply(packages, require, character.only=TRUE)))
#Load data
setwd("/Users/osman/Documents/GitHub/PEBBLES_mouse_snRNAseq/07_mosiacism/")
load("../06_hd... |
a89ba58433bb4afa28196082d68e1d5c9776b67b85d92ea25cbb038eac31dc53 | R | 7,928 | 246 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
dataview_table_rawdata_ui <- function(id,
width,
height,
title,
... |
73c5218f2245ad53ea62dcac51ca009d94411cbb349cb7cdb9ff7cba99012de1 | R | 7,982 | 266 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
dataview_plot_correlation_ui <- function(
id,
label = "",
title,
height,
width,
caption,
info.text,
info.methods,
info.extra_link
) {
ns <- shiny::NS(id)
PlotModuleU... |
f4987d456a33ed7a318a85c8690e79b63b3a2fbd297c369c057cc805c8283894 | R | 8,045 | 244 | library(data.table)
library(dplyr)
library(viridis)
#BiocManager::install("clusterProfiler")
library(clusterProfiler)
#BiocManager::install("org.Hs.eg.db")
library(org.Hs.eg.db)
#BiocManager::install("enrichplot")
library(enrichplot)
library(ReactomePA)
BiocManager::install("DOSE")
library(DOSE)
library(scales)
##
G... |
a992b8aef5f6fb9adee0d0db02ac101694bbf29783b9ea0124d95d7d8a9da103 | R | 8,068 | 174 | ### Function to automatically add accordions and help buttons to the section UIs in the browser. Input is the section's list
accordionFormatUIObj <- function(object){
accordion(inputId = paste0(object$id),
accordionItem(
title = span(paste0(object$title,":"),class="accordionheader"),
... |
9384a3361302e101d1585cd0f3fb17a34fa91b187f0e50fbf6d143f123ffbb82 | R | 8,076 | 209 | #
# Copyright (c) 2018 German Cancer Research Center (DKFZ).
#
# Distributed under the MIT License (license terms are at https://github.com/DKFZ-ODCF/AlignmentAndQCWorkflows).
#
# example call: R -f /home/hutter/workspace_ngs/Roddy/analysisTools/qcPipeline/coveragePlot.R --no-save --no-restore --args /icgc/dkfzls... |
d25c966e8af153c77f56a1a85cb36e1833bff25493aed14997bcb32a1945930b | R | 8,114 | 251 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
biomarker_plot_featurerank_ui <- function(
id,
title,
info.text,
info.methods,
info.references,
info.extra_link,
caption,
label = "",
height,
width
) {
ns <- shiny::... |
ac2d8e8f841b56910207eb8410f646dcd6a3bfa3b28bd1f120d166d19957174b | R | 8,135 | 167 | #' Default FUI plotting
#'
#' Take a fitted \code{fui} object produced by \code{fastFMM::fui()} and
#' plot the point estimates of fixed effects. When variance was calculated, the plot
#' function also returns 95\% pointwise and joint confidence intervals.
#'
#' @param fuiobj A object returned from the \code{fui} funct... |
5f61dc6a15da45033135a3f23fb4c64fc22036462a4dc37049b9861c82aee4be | R | 8,162 | 262 | ---
title: "Mouse Spatial Section Labeling: Integrate and Label with snRNA-seq"
output:
---
```{r setup, include=FALSE}
# This sets the project root based on the repo structure.
# If you move this file, you may to set the root manually to find config.R
knitr::opts_knit$set(root.dir = dirname(dirname(rstudioapi::getSou... |
c4c7d796ef2d3081c667832427eaefaa1c87b18d0571e7d2a4f52a43171566b8 | R | 8,196 | 318 | ---
title: "Integration of in vitro hGPCs and Fetal snRNA-seq"
author: "John Mariani"
date: "08/22/2025"
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... |
14d6efcbbfdf8a30aedc3080a1df29713788f38493bb096f8472b2bf8c7d27d3 | R | 8,221 | 151 | ## Complete Pipeline for Network Construction from Transcriptome Dataset ##
############### Step 0: Preparation ###############
# Load NetBID2 package
library(NetBID2)
# Define main working directory and project name
project_main_dir <- './test' # user defined main directory for the project, one main directo... |
9cc07cd1cc9e61dc44fbdd1ca297a094cb7ac7d92ad7119c9eb836470ecada7f | R | 8,234 | 304 | ---
title: "Compare of previous studies"
subtitle: "MIAMI-AD"
author:
- Wei Zhang^[University of Miami]
- Lily Wang^[University of Miami]
date: "`r Sys.Date()`"
output:
rmarkdown::html_document:
highlight: pygments
theme: yeti
toc: true
number_sections: true
df_print: paged
code_download:... |
898d9139c59854b25a7243f40a093dcf3f13f27b526f1fab9c8b6f158fa07427 | R | 8,252 | 208 | library(data.table)
library(coloc)
library(knitr)
## files
del <- fread("Delirium_AF0p005.mr_ready.tsv.gz")
ctx_sig <- fread("Brain_Cortex.v8.signif_variant_gene_pairs.txt.gz")
ctx_genes <- fread("Brain_Cortex.v8.egenes.txt.gz")
## Region (GRCh38): CEACAM19 ±500 kb -> chr19:44,162,645–45,162,645
ch... |
e2093faff6d00ea50e7f2bc7d195ded3945e5b03429f2a047154f77c5c9af2b8 | R | 8,264 | 260 | ---
title: "Opossum Spatial Section Labeling: Integrate and Label with snRNA-seq"
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$set(root.dir = dirname(dirname(rstudioapi::getS... |
847e6bd48526c33644cf0692cdc29daa55deecb7b2f314def52553fc8a18ae92 | R | 8,308 | 193 | library(data.table)
# ===========================
# INPUTS
# ===========================
INPUT_FILES <- c("Delirium and Blood.zip")
# Optional: write outputs (leave NULL if you only want objects in memory)
OUT_DIR <- NULL
# OUT_DIR <- "smr_bonf_outputs"
# Canonical filters (match colleague)
P_HEIDI_MIN <... |
605c908e4fae8320ccb8fa73582b621bc968c638e065ebfac7d8b5e391894206 | R | 8,403 | 271 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
clustering_plot_phenoplot_ui <- function(
id,
title,
info.text,
info.methods,
info.extra_link,
caption,
label = "",
height,
width
) {
ns <- shiny::NS(id)
phenoplot.... |
b213f28254b397f1d67cdd5ab3cc65e0b16b0892e19dbcb0658290ba1fef63cd | R | 8,429 | 246 | library(tidyverse)
library(optparse)
library(GenomicRanges)
library(org.Mm.eg.db)
library(clusterProfiler)
# Add package installation checks and installation if needed
required_packages <- c("VennDiagram", "tidyverse", "optparse", "GenomicRanges",
"org.Mm.eg.db", "clusterProfiler")
for (package... |
df0491eb782a839f75605617a503a46892df877227039aba4c1055da7b3e2d0c | R | 8,446 | 320 | ---
title: "how-to-use"
output: rmarkdown::html_vignette
vignette: >
%\VignetteIndexEntry{how-to-use}
%\VignetteEngine{knitr::rmarkdown}
%\VignetteEncoding{UTF-8}
---
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>"
)
```
```{r setup}
library(RepliSeq)
```
# readRS(paths_data,... |
83c6eb89232d3a52b048a4bd21283097319d4d2267de69490cf73deb501d7cd9 | R | 8,451 | 284 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
enrichment_plot_volcano_ui <- function(
id,
title,
caption,
info.text,
info.methods,
info.references,
info.extra_link,
height,
width
) {
ns <- shiny::NS(id)
PlotModu... |
cc9fadcc2b1ee4222ce5586368ea91e742f1c533b008bc0ffc38ea35020662be | R | 8,501 | 251 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
BiomarkerBoard <- function(id, pgx) {
moduleServer(id, function(input, output, session) {
ns <- session$ns ## NAMESPACE
fullH <- 800
rowH <- 320
imgH <- 260
pdx_inf... |
14714d2c782f993bdcacc7e5f96ae480e44d7b7733eed7ebb59c2bc53856fe79 | R | 8,528 | 172 | ---
title: "Label Transfer Figure Generation"
author: "John Mariani"
date: "07/30/2025"
output: github_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
knitr::opts_knit$set(root.dir = rprojroot::find_rstudio_root_file())
```
```{r, echo = TRUE, message=FALSE, warning=FALSE}
library(Seurat)... |
c60bf4a252c4fb2414049bd6d5ea69e123cf0aa8203fe5a6245d820fd1fdb953 | R | 8,530 | 318 | ---
title: "Brain blood correlation"
author:
- Wei Zhang^[University of Miami]
- Lily Wang^[University of Miami]
date: "`r Sys.Date()`"
output:
rmarkdown::html_document:
highlight: pygments
theme: yeti
toc: true
number_sections: true
df_print: paged
code_download: false
toc_float:
... |
29122d80171092d7155b59c50c228671f6968f00aba68aca2d91700b4f1b3e41 | R | 8,566 | 280 | ##
## 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_scatterPlot_... |
3725486a11e73ccefa0e28196068dcc5fc1ebc30ed10624ddff0abe58d78a291 | R | 8,606 | 263 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
admin_table_credentials_ui <- function(
id,
title = "User Credentials",
height = c("100%", 800),
info.text = "",
caption = ""
) {
ns <- shiny::NS(id)
if (length(height) == ... |
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