sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
0c630b1b7321c6c15c2001fc6d78cdd1a29f5e8488287fbd8e3db06e0a15d09f | R | 15,034 | 339 | #library(ggalluvial)
library(modelsummary)
library(tidygraph)
library(ggraph)
# df_long_cog
# df_long_MB
# df_long_MX
df_tot <- urmet_df_long %>%
dplyr::select(c(ID, Coffee_Type, visit, name, value, caffeine)) %>%
filter(Coffee_Type != "NCD") %>%
group_by(name) %>%
mutate(value = c(scale(value))) %>%
un... |
e9e73d9c0c6cc9698407817cad6bfe94a8ae8b06658632dbf8bc138d2e5b547c | R | 15,266 | 387 | ##############################
## Upset plot of KEGG terms ##
##############################
# Author : Osman Sharifi
#############################
## Load required libraries ##
#############################
library(UpSetR)
library(dplyr)
library(enrichR)
library(openxlsx)
library(glue)
library(ggplot2)
library(purrr)... |
fa90425628844b30babdf2beb3ed8326147f5799cb22fe3ec130ee336ea1d8f5 | R | 15,446 | 479 | args <- commandArgs(trailingOnly = TRUE)
## ---------------------------------------------------------------------------------
## DESeq after filtering out NE from deepCNN (final checking!! 20210723)
## ---------------------------------------------------------------------------------
## ------------------------------... |
b42004aaaa92b16c4040833d9f90bef6221cc55d3a7d5eaefe27170348216569 | R | 15,538 | 454 | library(dplyr)
library(ggplot2)
library(lmerTest)
PROJECT_ROOT <- "." # put your working directory
setwd(PROJECT_ROOT)
variant_count_matrix_per_indiv=read.table("data/variant_count_matrix_per_indiv.txt", header=T)
variant_count_matrix_per_indiv$batch=factor(variant_count_matrix_per_indiv$batch, levels=c("1","... |
d8eb5d47c5d839ef7b33fd87788501ee0e7692f0affce2e50263d13adcb41385 | R | 15,580 | 337 | #!/usr/bin/Rscript
#
# This file is part of the AlignmentAndQCWorkflow plugin.
#
# This script is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 or 3 of the License.
#
# This script is distribut... |
a160cf61aaf198bbd85c451a58a43b59c234f20ee7068cce9af4facd33e52d1d | R | 15,627 | 521 | #SA - AUG VS ESK
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_AD = 12.5,
c_AUG = 109,
c_ESK_SOPC1 = 9520,
c_ESK_SOPC2 = 47... |
68233dd4124cc146fba3654363adea7dd243672303fe4d931d2181765301ac12 | R | 15,783 | 349 | # Cue aligned Experiment 1
library(data.table)
library(dplyr)
library(parallel)
library(lme4)
library(mgcv)
# fGLMM code
source("/Users/loewingergc/Desktop/NIMH Research/Photometry/code/existing_funs.R") # for time align functions
source("~/Desktop/NIMH Research/git_repos/fast_univ_fda/code/fui.R") # function code
s... |
d0084814dd0b2a6909db7c43f1940bba02aabde6799554be42de4f53eb1acc55 | R | 15,940 | 410 | # Whoeps, 31 May 2020
# This is a perfectly input-output-oriented script.
# Input: - probabilities.R
# - bed file with groups
# - outdir
# - CN_mapabilty per segment
#
# Output: - table with classifications, respective CN and mapability
# - dumbbellplot
# - beeswarmplots
# setwd('/... |
43dac0fba76f987733f52fbd8226dd26de5f79b3c887a1abfdbe62ca20a0d2b0 | R | 15,988 | 540 | #SA - mPSY VS ESK
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_SOPC = 1190,
c_SOPC_PSY = 4760,
c_PSY = 12600,
c_ESK_SOPC1 = 9... |
7304c4ff14ce9c5a823b30000cc66e18155c800484fdb3b043f2afec3a26d5c9 | R | 16,049 | 543 | #SA - cPSY VS ESK
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_SOPC = 1190,
c_SOPC_PSY = 4760,
c_PSY = 12600,
c_ESK_SOPC1 = ... |
cb40dda9e3c190acd3d56873ad47e7de1ee17d326989fc5e658ce3465369ac97 | R | 16,058 | 325 | library(circlize)
library(dplyr)
library(RColorBrewer)
library(colorspace)
library(ggseqlogo)
library(ggplot2)
library(grid)
library(IRanges)
scale_breaks = function(x) {
breaks = seq(0, max(x), 1e8)
names(breaks) = paste0(breaks/1e6, "Mb")
breaks
}
scale_breaks_1 = function(x) {
breaks = seq(floor(mi... |
f3198d4d3abc56fb73a393f6715f812fccb20e93737c356272c2f5f5a30f9855 | R | 16,227 | 524 | #SA - COM VS ESK
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_AD = 12.5,
c_COM = 25,
c_ESK_SOPC1 = 9520,
c_ESK_SOPC2 = 4760... |
f9766da28d6560db90e9c77f01f2609f113d9e6d12993927664dfa5cb6c157ee | R | 16,318 | 438 | #' fit diffusion model (for internal use)
#'
#' Fit parameters of the diffusion model.
#' This function is only intended for use with a diffusion model object,
#' and should not be called directly outside of the diffusion model class.
#'
#' @usage model$fit(use_bounds=TRUE, transform_pars=FALSE, ...)
#'
#' @param use... |
e53a055e0e56a76d0fa32c4b4331c7eca46e7687b3706dc3c06d6efe6911a66c | R | 16,350 | 544 | #SA - ECT VS ESK
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,
c_ESK_SOPC1 =... |
7f38cfc03276ab7333fbfeebaf3041a0323609ab075bd45aabff64808b788b84 | R | 16,367 | 522 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
CompareBoard <- function(id, pgx, pgx_dir = reactive(file.path(OPG, "data", "mini-example")),
labeltype = shiny::reactive("feature")) {
moduleServer(id, function... |
319e23b46d1a7831bcad49e697b2f72de62eb10ca951b9f32dc1a7f85f0a7fa0 | R | 16,448 | 419 | # 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, Men... |
834d10920257031086f26609667e3c75823c26e137bf6b63c22a5e0a762353c0 | R | 16,635 | 457 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
LoadingBoard <- function(id,
pgx,
auth,
limits = c(
"samples" = 1000, "comparisons" = ... |
e5182d480fd0a32b789e926fb3ff24e3830b90fca50ceb988ce2ee422bdceea3 | R | 16,675 | 397 | library(R.matlab)
library(tidyverse)
library(ggplot2)
library(gridExtra)
library(refund)
library(dplyr)
# fGLMM code
source("/Users/loewingergc/Desktop/NIMH Research/Photometry/code/existing_funs.R") # for time align functions
source('~/Desktop/NIMH Research/git_repos/fast_univ_fda/code/plot_fReg_new.R')
source('~/Des... |
fbc392fdf23eab4f30e097be84d2fbd378366d7fdabaea69f170bc37ee585e96 | R | 16,927 | 349 | # show temporal correlation figures
# Lick aligned Experiment 1
# Final Version
library(data.table)
library(dplyr)
library(ggplot2)
# fGLMM code
source("/Users/loewingergc/Desktop/NIMH Research/Photometry/code/existing_funs.R") # for time align functions
source("~/Desktop/NIMH Research/git_repos/fast_univ_fda/code/lf... |
bad38b1767e769e6628b7118bdf240ef831506504f50cea3ccee497c7f574912 | R | 16,948 | 530 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
admin_table_datamanager_ui <- function(
id,
title = "Data Management",
height = c("100%", 800),
info.text = "",
caption = ""
) {
ns <- shiny::NS(id)
if (length(height) == 1... |
8d3ab4ce2bd38eaec6ddfd089a8b6ada5ef7bb1234a7134a8d74e2aeeaf5bd9d | R | 17,020 | 461 | library(data.table)
library(arrow)
library(susieR)
library(coloc)
library(SNPRelate)
library(gdsfmt)
## ---- file inputs ----
del_file <- "Delirium_AF0p005.mr_ready.tsv.gz"
sqtl_file <- "Brain_Cortex.v10.sQTLs.signif_pairs.parquet"
sgenes_file <- "Brain_Cortex.v10.sGenes.txt.gz"
vcf_file <- "chr19.E... |
0596d98ac2608e5188e170f9d240d571236b2aa301d66d7ece890f969be40a52 | R | 17,105 | 423 | # simulate data from fLME - multiple random effects
photo_stimulate <- function(X = NULL, # design matrix
Z = NULL, # design matrix for random effects
N = NULL, # target sample size
include = NULL, # extra data to include
... |
ae4afc903a155fd6c600aed2bac8a5251029f51c4e23a0b6a3df17d986e3828f | R | 17,144 | 283 | #!/usr/bin/env Rscript
suppressMessages(library(dplyr))
options(dplyr.summarise.inform=F)
suppressMessages(library(stringr))
suppressMessages(library(tidyr))
suppressMessages(library(spatstat))
suppressMessages(require(parallel))
source("utils.R")
make_bedgraph = function(i, args_df, path_output) {
suppressMessages... |
3632f9ddfd8055fbe29fd3468cb240973c9bd4e73fcbc6e4f0d0b548393df7fa | R | 17,187 | 382 | # Lick aligned Figure 4
library(data.table)
library(dplyr)
# NOTE: "sub-HJ-FP-M6_ses-Day22.nwb" file had an unequal number of reward cues and
# rewards and so I removed the session from the folder.
# fGLMM code
source("/Users/loewingergc/Desktop/NIMH Research/Photometry/code/existing_funs.R") # for time align f... |
6474e31fb2cf0852602c25355d5bf2a2f7d34ceb686e0749aeb101148d8d769b | R | 17,248 | 560 | #SA - TMS VS ESK
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_rTM... |
6e577c2ee9ef6b8820d127508e54d5a0989104f4b5cc9869c957c5d32624ba84 | R | 17,314 | 326 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
ClusteringInputs <- function(id) {
ns <- shiny::NS(id) ## namespace
topmodes <- c("sd", "pca", "marker")
settings_items1 <- tagList(
withTooltip(
shiny::selectInput(ns("h... |
1c2e4bea3bf6bc43ee06b932d5ef8e18376e882a365bc250b7b67102a17d2d32 | R | 17,478 | 174 | ---
title: "Photometry FLMM Guide Part V: Interactions -- Probing Learning and Changes over Time"
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} %\\Vi... |
b45ac17595718f7e75e68b5a15f1a5b4afde5b35d1704c7976479be4a116c5dd | R | 17,508 | 524 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
visPrint <- function(visnet, file, width = 3000, height = 3000, delay = 0, zoom = 1) {
is.pdf <- grepl("pdf$", file)
if (is.pdf) {
width <- width * 600
height <- height * 600
... |
9444269b920d4541663d904629f018661dd200170a3ec304ec4706da0c32742b | R | 17,527 | 310 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
ExpressionInputs <- function(id) {
ns <- shiny::NS(id) ## namespace
bigdash::tabSettings(
withTooltip(shiny::selectInput(ns("gx_contrast"), "Contrast:", choices = NULL),
"Sel... |
d745acf3316e7308278541d86f30d105f61037a78f3e7e43863240a876a99a29 | R | 17,662 | 295 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
MultiWGCNA_Inputs <- function(id) {
ns <- shiny::NS(id) ## namespace
bigdash::tabSettings(
shinyjs::hidden(
shiny::selectInput(ns("phenotype"), "Phenotype", choices = NULL)
... |
7dcb7934d2205eeaf00db49eaa0dfe0355edddaa6af0a6f618c6d2cfc5523ae0 | R | 17,667 | 426 | # simulation figures-used to make figures in appendix
######################################################
# compare different delay lengths for power
######################################################
source("/Users/loewingergc/Desktop/NIMH Research/Photometry/fLME_methods_paper/Figures/sims/Final/Code/Utility F... |
403d79a4f75c09a5f07d323d054d81fac11f74a6867fce238a6ee0e0012a37cb | R | 17,713 | 438 | ---
title: "Plot_heatmap_RNA_chromatin"
output: github_document
date: "2024-07-12"
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
knitr::opts_knit$set(root.dir = rprojroot::find_rstudio_root_file())
```
### load library
```{r, warning=FALSE, message = FALSE}
library(dplyr)
library(tidyr)
library(... |
4a95fa083ef8b1829f341d22dff719f212d828bc63a7696951f1336a8b38b6d1 | R | 17,734 | 478 |
split.by.chr <- function(gr) {
split(gr,seqnames(gr))
}
myCountOverlaps <- function(bins, tlx.cumsum) {
return(as.numeric(tlx.cumsum[end(bins)] - tlx.cumsum[pmax(start(bins)-1, 1)]))
}
calculate_local_significance <- function(bins, tlx.cumsum, bin.width, bg.width) {
if (length(bins) < 1) return(numeric())
... |
d792cbcde70c0dedfddfe970d8934013fb7d6e8aa3c551f21d51cb59816805e9 | R | 17,765 | 383 | ###############
## libraries ##
###############
library(ggplot2)
library(Seurat)
library(dplyr)
###############
## load data ##
###############
load("/Users/osman/Documents/GitHub/PEBBLES_mouse_snRNAseq/07_mosiacism/PEBBLES_parsed.RData")
xist_data_total <- FetchData(PEBBLES_soupx, vars = c("Xist", "Group", "Mecp2_all... |
6699cf4cf932f67cafb7a9dfc4ffbdd8616fdcddca061ba3770848e779f03227 | R | 17,927 | 334 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
MofaInputs <- function(id) {
ns <- shiny::NS(id) ## namespace
bigdash::tabSettings(
shiny::selectInput(ns("selected_factor"), "Select factor:", choices = NULL),
shiny::selectiz... |
fa60339770a0daafcb974cd33cde55590c48825e15088e2b3e3dd9ce5d60e39b | R | 18,065 | 539 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
upload_module_makecontrast_ui <- function(id) {
ns <- shiny::NS(id)
bslib::layout_columns(
col_widths = 12,
height = "100%",
row_heights = c(3, 3),
bslib::card(
f... |
22fbccff4fab2f90424a65aa7e9e2da3111c3f8ca36dc9901508d6237ef3572a | R | 18,305 | 458 | library(R.matlab)
library(tidyverse)
library(ggplot2)
library(gridExtra)
library(dplyr)
library(ggbrace)
library(latex2exp)
# read data and extract variable names
setwd("~/Desktop/NIMH Research/Causal/DA_adapts_learn_rate")
matdat <- R.matlab::readMat("seshMerge.mat")
matdat <- matdat$seshMerge
# indices in dataset ... |
8ff39a6661bb10d9a16e5e937f9014c771fbdde509196ac0ca269db92f589b66 | R | 18,363 | 430 | qtl_section<-list()
qtl_section$id <- "qtl"
qtl_section$title <- "QTL Evidence"
qtl_section$loadData<- function(){
#read in the csv file containing info about all the plots
qtl_info <<- fread("www/qtl/all_qtl_info_new.csv")
#list to map feature/dataset short names to the full feature/dataset name
qtl... |
56822afef4d25de1d8aa509bd513f6c00214ccd1011eda64aa03d7f6f62fd1e6 | R | 18,373 | 448 | # 1=NCD 0=F
# 2=CD 1=M
# F =Decaf
# S =Caf
unstim <- read.delim("raw/cytokines/cytokines_unstim.csv", sep = ",")
stim <- read.delim("raw/cytokines/cytokines_stim.csv", sep = ",")
unstim_df <- unstim %>%
pivot_longer(!c(Screening.ID, Group, Coffee.ID, Timepoint)) %>%
mutate(Legend = case_when(Group == 1 ... |
32a991cc7b6829ef9746487e339b899d4b3ffd4a1c8d03f5c50f0b00a2f2c2c9 | R | 18,552 | 470 | library(tidyverse)
library(Seurat)
library(extrafont)
library(cowplot)
library(ComplexUpset)
library(ggrepel)
library(ggplotify)
library(ggrastr)
loadfonts()
setwd('~/Dropbox/share_paper/paper_Visium_DCN/')
set.seed(2023)
# A: Upsetplot of unique DEGs per region
# B: Quadrant plot showing DEG results in DCN
# C: Spat... |
96a4b675a3b87c1bb078ad93f1be239cb5e74dc8509ed438d0018169bbbe86f1 | R | 18,592 | 344 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
#' DataView module UI Input function
#'
#' @description A shiny Module. Renders the input parts (sidebar contents) for the module.
#'
#' @param id Internal parameters for {shiny}.
#' #'
#... |
4da7d73b1b8c4e51a57c441bc4356df918bec2ce7220eb4f28d577a8b87b7e0a | R | 18,764 | 474 | #
# Copyright (C) 2017 Sascha Meiers
# Distributed under the MIT software license, see the accompanying
# file LICENSE.md or http://www.opensource.org/licenses/mit-license.php.
suppressMessages(library(data.table))
suppressMessages(library(assertthat))
suppressMessages(library(ggplot2))
suppressMessages(library(scale... |
d06b14331717c190e7ce82e4b5566bf69b81457d0b6edf31553e3fc843145ad2 | R | 18,885 | 448 | #####################################
# Helper functions for diffusion model object
check_ddm_constraints <- function(){
par_matrix_names = names(private$par_matrix)
checks = 0
if ("a" %in% par_matrix_names)
checks = checks + sum(private$par_matrix[, a <= 0]) # a
if ("t0" %in% par_matrix_names)
checks ... |
23c07cd8488d640a02d30477a24237849d51a5d430414de137e6d1d6b6aaa355 | R | 18,949 | 542 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
ConnectivityBoard <- function(
id,
auth = NoAuthenticationModule(id = "auth", show_modal = FALSE),
pgx,
reload_pgxdir = reactive(auth$user_dir)
) {
moduleServer(id, function(inpu... |
c011bf9dbf37944799105dfbfe9aba7a8e3fb76ace3bd97dd7ea2df1c1685ad1 | R | 19,238 | 595 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
upload_table_preview_samples_ui <- function(id) {
ns <- shiny::NS(id)
uiOutput(ns("table_samples"), fill = TRUE)
}
upload_table_preview_samples_server <- function(
id,
orig_sample... |
4c63c6e66bbedb91cf541aa4c9dd81913e2c4cbff8b856ecd2c9e11345ee6d5e | R | 19,310 | 444 | # Lick aligned Experiment 1
# Final Version
library(data.table)
library(dplyr)
library(parallel)
library(lme4)
library(mgcv)
library(latex2exp)
# fGLMM code
source("/Users/loewingergc/Desktop/NIMH Research/Photometry/code/existing_funs.R") # for time align functions
source("~/Desktop/NIMH Research/git_repos/fast_univ... |
ee5c74a8dca0d8f1e4deab30bfa4460eb858cdbd5c1fe37aa7dfd8fc360b6cdf | R | 19,395 | 589 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
#' Clustering plot UI input function
#'
#' @description A shiny Module for plotting (UI code).
#'
#' @param id
#' @param label
#' @param height
#' @param width
#'
#' @export
clustering_plo... |
65e9179f7f0451fc26c455a1cbbbd1be3953aa388d2d0e7f91e1f8a8c65e2baf | R | 19,651 | 359 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
WgcnaInputs <- function(id) {
ns <- shiny::NS(id) ## namespace
bigdash::tabSettings(
## data set parameters
shiny::selectInput(ns("selected_module"), "Select module:", choices... |
235a92bc20ae338d45f0b45d5950aed81387d559a09d69ad3d0009a1e54f696f | R | 19,809 | 244 | ---
title: "Photometry FLMM Guide Part I : Data Formating and Binary Variables"
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} %\\VignetteEngine{knitr... |
e8a0d9cb171c78dcbc7f28555ee2f7ebdb4817d56ab2c36cffd7616c58f3974f | R | 19,881 | 549 | ---
output: github_document
---
```{r opts, include = FALSE}
knitr::opts_chunk$set(
cache = FALSE,
collapse = TRUE,
tidy = FALSE,
comment = "#>",
results = "hide",
message = FALSE,
warning = FALSE,
fig.path = "man/figures/",
fig.height = 5,
fig.width = 10,
fig.align = "center",
dpi = 300,
out... |
f57697a60a6e34f3aed7799f27e56f0b6ed5a55028c839a70d7ff014832a9510 | R | 20,056 | 632 | #!/usr/bin/env Rscript
# RNA-seq Pipeline Step 7: Generate Visualizations
# This script creates publication-quality plots for RNA-seq analysis
suppressPackageStartupMessages({
library(DESeq2)
library(tidyverse)
library(pheatmap)
library(RColorBrewer)
library(ggrepel)
library(viridis)
libra... |
8dfdbae34453848be44e2d8bebad4327f59b3e109ebca627fe88b35845f0612c | R | 20,254 | 548 | # This program will perform hdWGCNA analysis on single cell data
# single-cell analysis package
library(Seurat)
library(tidyverse)
library(cowplot)
library(patchwork)
library(WGCNA)
library(hdWGCNA)
library(dplyr)
library(UCell)
library(magrittr)
library(igraph)
# using the cowplot theme for ggplot
theme_set(theme_cowp... |
cafa98fe44fa24b7c388d02cf83933394d7f7f0af6307a0c6f1b670613b297a5 | R | 20,992 | 459 | tutorialLogic <- function(session,input,output){
observeEvent(input$tutorial.activate, {
if (input$tutorial.activate == T) {
#render the popup
output$tutorial <-renderTutorial(pageOutput,selectOutput)
#set the states of the tutorial popup
runjs("setTutorialPage('Start')")
... |
13b588884112d8fb225ee31dc97f93aa3b43e8595a4809aebdc2edad23abc687 | R | 21,019 | 407 | library(tidyverse)
library(ComplexHeatmap)
library(ggrepel)
library(stringr)
library(Seurat)
library(extrafont)
library(rtracklayer)
library(zellkonverter)
loadfonts()
setwd('/data1/Spatial_DCN/')
# Import data
seu <- readRDS('Tables/Data/final_data/spatial_dcn_3samples_after_finalannot_20240319.rds')
sce_sc <- readH... |
47ed3bd70ad99c5c97fef24279d78b4c2fe3b512ca29dbd7159741019d97149e | R | 21,404 | 429 | # 1=NCD 0=F
# 2=CD 1=M
s1 = readxl::read_xlsx("raw/cognition/raw_xlsx/V2 - SPSS Template.xlsx")
s2 = readxl::read_xlsx("raw/cognition/raw_xlsx/V2 vs V3 - SPSS Template.xlsx")
s3 = readxl::read_xlsx("raw/cognition/raw_xlsx/V2 vs V4 - SPSS Template.xlsx")
s4 = readxl::read_xlsx("raw/cognition/raw_xlsx/V3 vs V4 - SPSS Te... |
542c99bd72e87c55360306e5d1fc2a2ffcbe1c0f20c3413f018eb2e92f342422 | R | 21,491 | 463 | # Lick aligned Experiment 1
# Final Version
library(data.table)
library(dplyr)
library(parallel)
library(lme4)
library(mgcv)
library(latex2exp)
# fGLMM code
source("/Users/loewingergc/Desktop/NIMH Research/Photometry/code/existing_funs.R") # for time align functions
source("~/Desktop/NIMH Research/git_repos/fast_univ... |
6123734fc6b2376874b3dd7952c839877bfb6311a31b034503e689c315ac174d | R | 21,537 | 638 | ---
title: "HUDECA — Figure 3: Lineage inference and developmental dynamics of the human fetal olfactory epithelium"
author: "Mbouamboua Yvon <yvon.mbouamboua@inserm.fr>"
output:
html_document:
toc: true
toc_float: true
number_sections: true
date: '`r format(Sys.Date())`'
---
## Goal
Final figures
## Se... |
db180b3c86a362945dde595ac8b6d5991977d671306cf96b406d77b083b05b99 | R | 21,562 | 533 | ---
title: "Make Supplemental Tables"
output: github_document
date: "2024-07-12"
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
knitr::opts_knit$set(root.dir = rprojroot::find_rstudio_root_file())
```
### load library
```{r, warning=FALSE, message = FALSE}
library(xlsx)
library(data.table)
libr... |
05e192d2ef2bcb4c577ecaeadcd491e53dfde9526f26a13495d888aedb0c7030 | R | 21,756 | 513 | # Lick aligned Figure 4--check whether activity falls with trial-- Photobleahing?
library(data.table)
library(dplyr)
# NOTE: "sub-HJ-FP-M6_ses-Day22.nwb" file had an unequal number of reward cues and
# rewards and so I removed the session from the folder.
# fGLMM code
source("/Users/loewingergc/Desktop/NIMH Res... |
39beb7654c62df335af6f0dd84f271884c2d7fa59b725bb9d8509ebebfa593b3 | R | 21,846 | 662 | ---
title: "Mouse Spatial Labeling: Iterative Integration with snRNA-seq Reference"
output:
---
```{r setup, include=FALSE}
# This sets the project root based on the repo structure.
# If you move this file, you may need to set the root manually to find config.R
knitr::opts_knit$set(root.dir = dirname(dirname(rstudioap... |
0755d0f2b181c0e87229eca98645ef671d7951893220e9479ba4fbbf0d1ea3b1 | R | 21,903 | 468 | # Lick aligned Figure 4
library(data.table)
library(dplyr)
library(fastFMM)
library(lme4)
# fGLMM code
source("/Users/loewingergc/Desktop/NIMH Research/Photometry/code/existing_funs.R") # for time align functions
source("~/Desktop/NIMH Research/git_repos/fast_univ_fda/code/fui.R") # function code
source('~/Desktop/NIM... |
1b313dab510f802f69d519f49d4d650ccf41311a89b6c73aec13afe4f37a4313 | R | 21,918 | 251 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
DeepNetInputs <- function(id) {
ns <- shiny::NS(id) ## namespace
bigdash::tabSettings(
## data set parameters
shiny::selectInput(ns("select_pheno"), "Select phenotype:", choice... |
e061e8ed339efb20d581cdef371c6664b4d5c6316037930b3c2a7d198b2d1d64 | R | 22,002 | 611 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
EnrichmentBoard <- function(id, pgx,
selected_gxmethods = reactive(colnames(pgx$gx.meta$meta[[1]]$fc))) {
moduleServer(id, function(input, output, session) {
... |
d272308d1696eea4e8ee9f7e2bae130c9c63a0757db1fac2b2101bb81785749b | R | 22,115 | 784 | #
# Copyright (C) 2017 Sascha Meiers
# Distributed under the MIT software license, see the accompanying
# file LICENSE.md or http://www.opensource.org/licenses/mit-license.php.
# options(error = function() traceback(3))
# while (!is.null(dev.list()))
# dev.off()
suppressMessages(library(dplyr))
suppressMessages(libra... |
71391f8ad2ea308056b145bafb1fdf4f0905509934e78e30e3f5d257edc9f3d7 | R | 22,141 | 538 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
SignatureBoard <- function(id, pgx,
selected_gxmethods = reactive(colnames(pgx$gx.meta$meta[[1]]$fc))) {
moduleServer(id, function(input, output, session) {
... |
f6a9d89b18790417ba151d27f41b73f085fbd212f5592eef69956934a0171583 | R | 22,227 | 541 | ## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
upload_module_normalizationSC_ui <- function(id, height = "100%") {
ns <- shiny::NS(id)
uiOutput(ns("normalization"), fill = TRUE)
}
upload_module_normalizationSC_server <- function(id,
... |
a25e755804a447c240fdf5ab8bee7506f0cd49553ff3cfaabe142f8fe5d5ef1a | R | 22,248 | 742 | ---
title: "Simulations Vaccines Paper"
author: "Niklas Hartung"
date: "`r Sys.Date()`"
output: html_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
## Preliminaries
Number of individuals to simulate for each scenario
```{r}
nrep <- 50
```
### Aim
Simulation of AL exposure in child... |
1741de2013ca915647a3ddc164457b27ed2b7b1f7e5b9103deaec3572368e515 | R | 22,487 | 600 | #####################################
# Helper functions for pulse model object
pulse_fp_obj <- function(pars,
dat=NULL,
transform_pars=F,
check_constraints=T,
debug=F,
...){
### check cons... |
e0aff57c114e0a994fa524029520a4e3906b10f2b6da9e48ff208501b5adaf0b | R | 22,543 | 681 | ---
title: "Opossum Spatial Labeling: Iterative Integration with snRNA-seq Reference"
output:
---
```{r setup, include=FALSE}
# This sets the project root based on the repo structure.
# If you move this file, you may need to set the root manually to find config.R
knitr::opts_knit$set(root.dir = dirname(dirname(rstudio... |
497d3939969311c9e98dcd36ac6feed5061d88db1e9dabae85864cc336e9dd7b | R | 22,613 | 638 | ---
title: "000-HUDECA — 002-annotation"
output: html_document
date: '`r Sys.Date()`'
---
## Goal
Cell type annotation
## Setup
```{r setup, message=FALSE, warning=FALSE}
knitr::opts_chunk$set(message = FALSE, warning = FALSE)
root <- '/Users/yvon.mbouamboua/projects/singlecell/000-hudeca'
outdir <- file.path(root, '... |
0663ccfb56c3b22e79829014791cf2de28fdf05d16ea825afb3e5c9bfe7a54f0 | R | 22,673 | 598 | # This program will perform hdWGCNA analysis on single cell data
# single-cell analysis package
library(Seurat)
library(tidyverse)
library(cowplot)
library(patchwork)
library(WGCNA)
library(hdWGCNA)
library(dplyr)
library(UCell)
library(magrittr)
library(igraph)
# using the cowplot theme for ggplot
theme_set(theme_cowp... |
6caf48c3d3d168be976c2859334794f1908f7b50440388429c5cd379666586bb | R | 22,787 | 842 | ---
title: "Objects preparations"
author: "Rasmus Rydbirk"
date: "2024-11-29"
output:
html_document:
toc: yes
toc_float: yes
---
# Setup
```{r setup, message=FALSE}
library(qs)
library(cacoa)
library(conos)
library(magrittr)
anno.major <- qread("anno_major.qs")
```
# All cells
## Conos object
The easie... |
d8a953e894be7633a98c025c75018451b0c043174a58529b33f78ba33e36b605 | R | 22,861 | 562 | #=========================================================================================================
# Main for project: Genetic influences on missing data across experimental measures in infancy
#
# used to run multivariate twin model and plot results
#
# author: Giorgia Bussu
# project: BT missing data
... |
e176687d5cdfba3cfc82e4b53f553f04e1d54e01d5110bbd2120226f982f071f | R | 22,969 | 567 | library(R.matlab)
library(tidyverse)
library(ggplot2)
library(gridExtra)
library(refund)
library(dplyr)
# read data and extract variable names
setwd("~/Desktop/NIMH Research/Causal/DA_adapts_learn_rate")
matdat <- R.matlab::readMat("seshMerge.mat")
matdat <- matdat$seshMerge
# indices in dataset of variables
photo_i... |
3fc9f5cae52bf77d8532d7c7bbe49fe04b85035857a98fcbaacd1cf46db66339 | R | 22,987 | 609 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
app_ui <- function(x) {
if (identical("/cookie", x$PATH_INFO)) {
value <- x$HTTP_HEADER_USER_COOKIE
return(cookies::set_cookie_response(
cookie_name = "persistentOPG",
... |
82bb40a1fc569042697e798e4f96d21ed91e473abab15b29e0151bc24f8a36b7 | R | 22,996 | 514 | # Lick aligned Experiment 1
# Simpsons Paradox
library(data.table)
library(dplyr)
library(parallel)
library(lme4)
library(mgcv)
# fGLMM code
source("/Users/loewingergc/Desktop/NIMH Research/Photometry/code/existing_funs.R") # for time align functions
source("~/Desktop/NIMH Research/git_repos/fast_univ_fda/code/fui.R"... |
89e6894eccfd7b8e1828093ae93ae21eeebbf0a4b4edc6466a31741de7a43304 | R | 23,040 | 638 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
## ---------------------------------------------------------------
## Editor Helper Functions
## ---------------------------------------------------------------
## Centralised helpers that... |
eb97fcb071a0eaaeec3a6245edad6f8b7d128bc2af9d90a8f56ee99bc6e21b69 | R | 23,566 | 691 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
ExpressionBoard <- function(id, pgx, labeltype = shiny::reactive("feature")) {
moduleServer(id, function(input, output, session) {
ns <- session$ns ## NAMESPACE
fullH <- 780
... |
eafb00de3602cbf7575ebc18336a865d4cd352132cb2245ba037305013fc3c17 | R | 23,570 | 382 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
EnrichmentInputs <- function(id) {
ns <- shiny::NS(id) ## namespace
bigdash::tabSettings(
withTooltip(shiny::selectInput(ns("gs_contrast"), "Contrast:", choices = NULL),
"Sel... |
e288d47f4ef56594d393703a64b3d7a89a0e1ba6a8765b91d95b19374f0fac77 | R | 24,482 | 659 | ---
title: "Analysis of Cultured hGPCs"
author: "John Mariani"
date: "10/26/2025"
output: github_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
knitr::opts_knit$set(root.dir = rprojroot::find_rstudio_root_file())
```
```{r, echo = TRUE, message=FALSE, warning=FALSE}
library(Seurat)
li... |
84e7d0544d09b69993c7b06d0fb211fb4953fdf6d10fbba634a6c354dd24caca | R | 24,752 | 500 | #' Run doublet-calling with scDblFinder
#'
#' This function performs doublet-calling using the scDblFinder package on a Seurat object.
#'
#' @param srt A Seurat object.
#' @param assay The name of the assay to be used for doublet-calling. Default is "RNA".
#' @param db_rate The expected doublet rate. Default is calcula... |
27d93275f589f00aa5de68eebf6e57be0e066e09d295ce69d49e538e86f03e63 | R | 24,772 | 629 | #######################################################################################################
# =================================================================================================== #
# Function for annotation and inflation adjusted
# ============================================================... |
2488db4537eee3592b787089e46f95502a471a18b6b828f238b415fcc6beae03 | R | 25,336 | 609 | #!/usr/bin/env Rscript
# NanoporeToBED Pipeline - Summary Statistics and Plots
# Version: 1.6.0
# Author: Markus Hodal Drag
#
# Changes in 1.6.0:
# - Added comprehensive qualimap BAM statistics (27 fields)
# - Improved aggregation for re-sequenced samples
# - All plots use aggregated data when duplicate sample I... |
221d71e89f9441fb2355a77e215f2b4df949e5b161c24c3b2fbe623eecf140d6 | R | 25,413 | 938 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
local({
# the requested version of renv
version <- "0.15.4"
# the project directory
project <- getwd()
# figure out whether the autoloader is enabled
enabled <- local({
... |
05cf5ca9e642220e259dcbc7680b677605b9b7577262201a34ecd1d24fef320f | R | 25,510 | 688 | ---
title: "Opossum Genome 3' Extension"
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:... |
7ea4a4864f173d50b627935052db2658f120cc6db7e332e74e5dd7f74db07f64 | R | 25,909 | 692 | #######################################################################################################
# =================================================================================================== #
# Single CpG assocation test
# =================================================================================... |
540c2a701952f11aaaabe46e4a1bcfdecf532b78a7de1af6ea656438e8a59787 | R | 26,247 | 553 | # simulations using Science paper's data for data-driven sims
# this R code is saved in: /gpfs/gsfs8/users/loewingergc/photometry_fglmm/code
library(lme4) ## mixed models
library(refund) ## fpca.face
library(dplyr) ## organize lapply results
library(progress) ## display progress bar
library(mgcv) ## smoothing in step ... |
7803e8fb555b8639f5bed6f5111d281e7602623b2c398455d2a93e8710c1a42a | R | 26,460 | 596 | ######################################################
# simulation figures
######################################################
source("~/Desktop/NIMH Research/Photometry/fLME_methods_paper/simulations/photometry_sim_fLME_fn_multi.R") # simulations
wd <- "/Users/loewingergc/Desktop/Research/sims_delays" # simulation... |
3666c8c8f25b36ef06f93872437c518d0d72611db106a4464c959218bf9b343f | R | 26,530 | 369 | ## Generated automatically: do not edit by hand
message("source all called from wd = ", getwd())
if (!file.exists("00SourceAll.R")) {
message("WARNING: not in source folder. skipping.")
} else {
message("Note: sourcing all code...")
source("app/R/utils/auth.R", encoding = "UTF-8")
source("app/R/utils/database.... |
6e1eb9286cedfb15544fed93832e961669d29871110ed211d6bea0933bc42fae | R | 26,705 | 689 | # Make a table
make_table_sc_separated <- function(pg_f) {
library(reshape2)
# library(reshape)
n_sites <- dim(unique(pg_f[, c("chrom", "start", "end")]))[1]
haps_to_consider <- c("1010", "0101", "1001", "0110", "1000", "0010", "0000", "1110", "1011", "1111")
# Cut down to interesting haplotypes
pgi2 <- ... |
a89833f241d33b8e1ad8a42280a8db01626e809dbac4cc48023429c6babf7efb | R | 26,768 | 523 | library(tidyverse)
library(extrafont)
library(cowplot)
library(ggrepel)
library(ggplotify)
library(dplyr)
library(ggplot2)
library(ggrastr)
library(Seurat)
loadfonts()
setwd('~/Dropbox/share_paper/paper_Visium_DCN/')
set.seed(2023)
# A: Anatomical & spatial plot of purkinje layer
# B: Volcano plot of DEG result comp... |
76f1555a47434aa433b32dc2a47e9e72da486fc229707039baf8d54c205d608b | R | 26,985 | 548 | library(tidyverse)
library(Seurat)
library(extrafont)
library(cowplot)
library(ComplexUpset)
library(ggrepel)
library(ggplotify)
library(ggrastr)
loadfonts()
setwd('~/Dropbox/share_paper/paper_Visium_DCN/')
set.seed(2023)
# A: UMAP of DCN snRNA-seq data
# B: Barplot showing number of LRT DEGs for each cell type
# C, ... |
94b305dee345136ee4153254a19a9a1d731e2407d6e7c89e172160aa71047606 | R | 27,046 | 629 | 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_i... |
e5a5b663a0e7e72df856b12b7ad3d0b983e44ab185d3214cb89d10bb25f311c3 | R | 27,184 | 436 | # Generated by using Rcpp::compileAttributes() -> do not edit by hand
# Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
#' Collapsing boundary functions
#'
#' @description evaluate diffusion model boundary using the hyperbolic ratio or weibull functions
#'
#' @param t vector; time points to evaluate boundary
#'... |
ee092dc870f16215248150795f20da61728689df92036ce6200df505a44f59ad | R | 27,380 | 413 | ## Complete Pipeline for Advanced Analysis and Visualization ##
############### Preparation ###############
# Load NetBID2 package
library(NetBID2)
# Give file path to reload `ms-tab` RData from driver estimation step
analysis.par <- list()
# Here we use demo data from NetBID2 package
analysis.par$out.dir.... |
3401cac1e9653ca3aa19c559a37f284aaef9479a40be3c2809bf63f3debd4506 | R | 27,503 | 639 | # Lick aligned Figure 4 - Include Inset to explain figure
library(data.table)
library(dplyr)
library(mgcv)
library(lme4)
# NOTE: "sub-HJ-FP-M6_ses-Day22.nwb" file had an unequal number of reward cues and
# rewards and so I removed the session from the folder.
# fGLMM code
source("/Users/loewingergc/Desktop/NIMH ... |
f340f62b241bbc0c07577a37d1800f9757a218964c147cbe3d9093c5c5e3f4c6 | R | 27,777 | 613 | ---
title: "Analysis"
output: html_document
---
Setting up the notebook
```{r}
library(lme4)
library(lmerTest)
library(dplyr)
library(ggplot2)
library(stringr)
library(lattice)
library(tidyverse)
dataset_full <-read.csv('/Volumes/data/MoL_clean/outputs/story_matrix_withHipp.csv')
dataset_full$subses <- paste(dataset... |
9c5faa505a3258c9e50e975b26ab874669e653bc80650c11f4d67037db62a12f | R | 28,620 | 564 | Variant_anno_Exome_V9_T2p = function(){
#load library
library(xlsx)
library(myvariant)
library(plyr)
library(stringr)
library(rtracklayer)
library(kableExtra)
library(dplyr)
library(tidyverse)
#load file
Gene_Panel <- read.csv(file = "File/Gene_Panel.csv", header = TRUE, sep = ","... |
18422c9b1659bae0222610e0ce8e22b5d9ac612dab0060c8acd65e8df4a6dfff | R | 28,624 | 563 | Variant_anno_Exome_V9_T2 = function(){
#load library
library(xlsx)
library(myvariant)
library(plyr)
library(stringr)
library(rtracklayer)
library(kableExtra)
library(dplyr)
library(tidyverse)
#load file
Gene_Panel <- read.csv(file = "File/Gene_Panel.csv", header = TRUE, sep = ",")... |
9d6e4ad1af9b88f6d05284460d8c8158efa05703db93c7ad5fabd4283890e958 | R | 28,698 | 725 | library(Seurat)
library(SeuratDisk)
library(ggrepel)
library(tidyverse)
library(SingleCellExperiment)
library(knitr)
library(limma)
library(Matrix)
library(DESeq2)
library(scater)
library(ggpubr)
library(cowplot)
library(clusterProfiler)
library(grid)
library(writexl)
library(extrafont)
loadfonts()
setwd('/data1/Spati... |
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