sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
5f6e5d43073b30abda28f4c986434bab1ba6d1c10e341412d1bf963254649a78 | R | 15,880 | 554 | # Auxiliary functions to check function arguments
#
# Package: meta
# Author: Guido Schwarzer <guido.schwarzer@uniklinik-freiburg.de>
# License: GPL (>= 2)
#
chkchar <- function(x, length = 0, name = NULL, nchar = NULL, NULL.ok = FALSE) {
if (is.null(x) & NULL.ok)
return(invisible(NULL))
#
if (is.null(name))... |
ec848c7a8717b8475ec1eb522ea23a0fa2c681a42c83975c33af329a7dc74713 | R | 15,909 | 261 | #----Figure_04_A_B_C and analysis as basis for A,F-H----------------------------
#-------------------------------------------------------------------------------
# This is the code for Figure 04 Panel A,B,C for the connectivity analysis for
# Reinhard and Fukuda et al. 2024
#---------------------------------------... |
dc4b26bcea340d967a11d7108fbc4e1c60f511480c092c845bac72be3ac37c5f | R | 15,989 | 353 | #!/usr/bin/env Rscript
#
# This script will...
#
# Gokberk Alagoz
# created on: 12.2022
#####
library(ggplot2)
library(tidyverse)
library(data.table)
library(ggalt)
library(viridis)
library(cowplot)
library(ggpubr)
if(!require(devtools)) install.packages("devtools")
#devtools::install_github("kassambara/ggpubr")
optio... |
4bb8d4a54d8f3abdb49157757502780f6e57fe0997f6a5e5b0101bf0eb524373 | R | 16,033 | 514 | #' @title Collapse/bind several `hyperSpec` objects into one object
#' @description
#' The spectra from all objects will be put into one object.
#' The resulting object has all wavelengths that occur in any of the input objects,
#' `wl.tolerance` is used to determine which difference in the wavelengths is
#' tolerated ... |
829321c45844bd7a69c7f1b40d478acda85b0c376a8703179018d1b4a7a3bfd6 | R | 16,114 | 427 | ---
title: "Variability of organ-biased genes"
author: "Bucao, Christabel Floi"
output: html_document
date: "`r Sys.Date()`"
params:
input.rds.path: "../../results/12_Organ_Bias"
output.rds.path: "../../results/13_Organ_Bias_Combined"
tau.cutoff: 0.30
qc1.only: FALSE
all.nonzero.matrix: FALSE
randomized.mea... |
2e763eab063c11ead481ec68930047fba0f5b18b0272139b8769c8eef15f7c6d | R | 16,147 | 352 | ### data from H9, HUES62 & PGP1 cells, generated by Daniella & processed by Yan before
### reprocessing using GRCh38_and_mm10 reference
### to save time, only processing the cells that are annotated as singlet by Yan's processing
setwd('/media/Scratch_SSD_Voyager/sammi/RNA_editing/')
### load cellranger output - spar... |
731dd1375935a760431dea7e43f75e23657a5665032895c470e064b9a7ecfd7f | R | 16,150 | 487 | #' Add pooled results from external analysis to meta-analysis
#'
#' @description
#' Add pooled results from external analysis to an existing
#' meta-analysis object. This is useful, for example, to add results
#' from a Bayesian meta-analysis which is not implemented in R package
#' \bold{meta}.
#'
#' @param x Meta-a... |
7f9259bba5ac77fa2d10cb4cab7352013179a934af63f06a53e854dc1f87fbb1 | R | 16,238 | 361 | ---
title: "Visualisation_BigSensitivityAnalysis"
author: "Fabienne Rössler"
date: '2023-07-14'
output: html_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
```{r, message=FALSE, warning = FALSE}
source("../DLCAnalyzer_Functions_v4.R")
source("../UnsupervisedAnalysis_Funct... |
4a45a24a175efd285bea6f85d0a84288311ba061d70343131e9b0cd43e6f68a5 | R | 16,247 | 517 | ---
title: "20240316_check_accuracy"
output: html_document
date: "2024-03-16"
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
```{r load packages}
#loaded RStudioAPI to use for selecting working directory
if("rstudioapi" %in% rownames(installed.packages()) == FALSE)
{install.packages("rstudioa... |
a0617435cb93630b37ecc0e83a8426454203f8abd98516d5feff3d4099db6558 | R | 16,254 | 301 | ---
title: "Tutorial II: Preparing gene expression data for co-expression networks"
author: "Juan A. Botía, juanbot@um.es, @juanBotiaBlaya"
date: "26/02/2018"
output:
pdf_document:
toc: yes
fig_caption: yes
html_document:
toc: yes
fig_caption: yes
---
```{r setup, include=FALSE}
knitr::opts_chunk$s... |
209429bccec7f13e186d3d3f6731f601c68cdca69628d100fcee7f896b7ba802 | R | 16,311 | 426 | ---
title: "Figure2_largeScaleClustering"
author: "Fabienne Rössler"
date: '2023-03-21'
output: html_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
```{r, message=FALSE, warning = FALSE}
source("../DLCAnalyzer_Functions_v4.R")
source("../UnsupervisedAnalysis_Functions.R")... |
b4c4ab95e136d3f37cc194e2d47b1353ae1ad47f1d05ae4f254c36d6c0135f26 | R | 16,333 | 338 | ---
title: "Tutorial for R package CTSclocks"
author:
- name: "Huige Tong"
affiliation: "Shanghai Institute of Nutrition and Health, CAS"
email: "tonghuige2021@sinh.ac.cn"
- name: "Xiaolong Guo"
affiliation: "Shanghai Institute of Nutrition and Health, CAS"
email: "guoxiaolong2022@sinh.ac.cn"
- name: "An... |
7ea3cec211d0afb0610fbde6b903ff30587450d0b269f9b65fc40d4f3b34a346 | R | 16,346 | 275 |
###Script 2
#Assess clustering techniques
library(Seurat)
library(ggplot2)
library(ggrastr)
library(dplyr)
library(ComplexHeatmap)
library(viridis)
library(RColorBrewer)
##########################
###Save allen celltypes###
dt.meta <- readRDS("output/atlas/metadata_integrated_neuronal_atlas.rds")
ou... |
aeb649b82e50c193e4f1f24e3b397d10a5ba071ddf6912ab88ed89b5ec68e38f | R | 16,355 | 482 | ---
title: "Expression Specificity"
author: "Bucao, Christabel Floi"
output: html_document
date: "`r Sys.Date()`"
params:
input.rds.path: "../../results/01_Filter_Samples"
output.rds.path: "../../results/10_Expression_Specificity"
min.cpm: 1.0
tau.cutoff: 0.30
qc1.only: FALSE
all.nonzero.matrix: FALSE
ran... |
0ddff41fc71a9e0b981973d2aba078e14b5898b3fbce9878d60504ade641fe0c | R | 16,372 | 409 | ---
title : "Neurocognitive dynamics of preparatory and adaptive cognitive control: Insights from mass-univariate and multivariate pattern analysis of EEG data"
shorttitle : "Neurocognitive dynamics of cognitive control"
author:
- name : "José C. García Alanis"
affiliation : "1"
... |
943223fa5e46780b8119ffec5f1a3f8d8514bba761ecbde7f4f92d4762980e39 | R | 16,606 | 150 | source('./scripts/01_Setup.R')
# A treemap R script produced by the Revigo server at http://revigo.irb.hr/
# If you found Revigo useful in your work, please cite the following reference:
# Supek F et al. "REVIGO summarizes and visualizes long lists of Gene Ontology
# terms" PLoS ONE 2011. doi:10.1371/journal.pone.0021... |
80fb715fc2cdb7705d8161030f08c53a0b66e4e6c1286e7a43a7141c1f04f4f6 | R | 16,610 | 451 | # Optional generic preliminaries:
graphics.off() # This closes all of R's graphics windows.
rm(list=ls()) # Careful! This clears all of R's memory!
#-------------------------------------------------------------------------------
# Load rjags library and the wiener module
library(runjags)
library(rjags)
load.module("... |
96720bbd5a6670614402cc8c1b71a12de69f9e70c99677d4a72d88f5e66bf5d6 | R | 16,694 | 413 | ## OTHER VERTEX-WISE FUNCTIONS
############################################################################################################################
############################################################################################################################
## permutation functions for random s... |
f7c109741b6de04f4dbb9224a756b6d67159718717de0b7219d8c8b16c7d76aa | R | 16,710 | 146 | source('./scripts/01_Setup.R')
# A treemap R script produced by the Revigo server at http://revigo.irb.hr/
# If you found Revigo useful in your work, please cite the following reference:
# Supek F et al. "REVIGO summarizes and visualizes long lists of Gene Ontology
# terms" PLoS ONE 2011. doi:10.1371/journal.pone.0021... |
1c9de8ed43eddee2aa07d0fe1dd32b6805577638fb48ca426090563792944e71 | R | 16,729 | 417 | ---
title: "Figure4_TransferClustering"
author: "Fabienne Rössler"
date: '2023-03-24'
output: html_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
```{r, message=FALSE, warning = FALSE}
source("DLCAnalyzer.R")
source("BFA_BFF.R")
library(sp) #tested with v1.3-2
l... |
ebc0f71cfa9a21257738fa27a83d6a42173422bc7d90d790bf17ecc2ef9b23d8 | R | 16,730 | 400 | ---
title: "PREMS -- Analyses of ANT cognitive task, balance tests and physiological measurements"
author: "Christophe Pallier"
date: "`r Sys.Date()`"
output:
pdf_document: default
html_document: default
toc: true
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
rm(list=ls())
```
```{r, echo=F... |
339c65842a0ca23bcb0d05f5fc56c76c737af4bff059a066194e89b2791ea8bb | R | 16,760 | 429 | ---
title: "`r subdir_name`"
author: "Kadi Vaher"
date: "`r Sys.time()`"
output: html_document
---
```{r setup, include=T, message=F}
subdir_name <- "microbiome_demotable_paper"
# load packages
library(tidyverse)
library(here)
library(magrittr)
library(glue)
library(ggpubr)
library(knitr)
#library(MVN)
library(tableo... |
9f5f36b69eb15e3ad4349fb6c5e11ffcb698cec17a7bca64358f78ea7d886f1a | R | 16,770 | 402 | #' Adjust for batch effects using an empirical Bayes framework
#'
#' ComBat allows users to adjust for batch effects in datasets where the batch covariate is known, using methodology
#' described in Johnson et al. 2007. It uses either parametric or non-parametric empirical Bayes frameworks for adjusting data for
#' bat... |
b841c52b8f4fa87ce1ba0f7e630394cf40b291767b35c05b1aebb057295ae46e | R | 16,772 | 556 | ---
title: "Regional astrocyte heterogeneity"
output: html_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
Import packages and set directories
```{r}
library ("data.table")
library("dplyr")
library("textshape")
require(ComplexHeatmap)
require(Seurat)
require(data.table)
require(tidyver... |
b7a6f18ac01e08ffbdc18a8b5c16cbd023bc6d07584b2e0939230ec3470b62b8 | R | 16,780 | 818 | ---
title: "SEFL10K2_Analysis"
author: "Zach"
output:
html_document:
fig_height: 4.5
fig_width: 4.5
highlight: kate
number_sections: yes
theme: readable
toc: yes
toc_depth: 6
pdf_document:
toc: yes
toc_depth: '6'
editor_options:
chunk_output_type: console
---
# Set Global Op... |
1b8457eff1cf3f6614090f25ce7296d6434cb6c6568509dec6e991278f3c9b99 | R | 16,818 | 371 |
###Script 8
#MAST DE Plots
library(dplyr)
library(snow)
library(ggplot2)
library(ComplexHeatmap)
library(RColorBrewer)
library(ggrepel)
library(ggrastr)
library(viridis)
library(enrichR)
library(future)
library(fgsea)
library(data.table)
library(msigdbr)
########################################
##... |
3de961f35362a9561aeda8f4182f196283e233ff532a5869c65525ef6bc9f10b | R | 16,856 | 407 | #### Notes ####
# Functions to compute expression variability
# See 02_Variability_Jackknife.Rmd for sample usage
#### Libraries ####
library(dplyr)
library(matrixStats)
library(slider)
#### Functions ####
#### Compute genewise summary statistics ####
# Input: expr.matrix = expression matrix (rows - genes, columns ... |
0214d816d5ded0d51cb18a79da048a7295765093e75d1bfc8b869029706835e3 | R | 16,858 | 489 | ---
title: "TEBC faecal samples: beta diversity - plots and stats"
author:
- "Kadi Vaher"
- "added 22/03: saving the sample type NMDS plot as gg-object to make a panelled figure"
date: '`r Sys.Date()`'
output: html_document
---
```{r setup, include=F, message=F}
library(tidyverse)
library(here)
library(phylose... |
a2c0d2bfda6ce57ff64787e6613e42503ad59516df41f65d32c43b590e92ab48 | R | 16,884 | 544 | #' Meta-regression
#'
#' @description
#' Meta-regression for objects of class \code{meta}. This is a wrapper
#' function for the R functions \code{\link[metafor]{rma.uni}},
#' \code{\link[metafor]{rma.glmm}}, and \code{\link[metafor]{rma.mv}} in the R
#' package \bold{metafor} (Viechtbauer 2010).
#'
#' @details
#' Th... |
9f2f1d8079aff73ae94d21658a01d36a1292e340903f1242b981c5cefe6dbdea | R | 16,893 | 399 | ---
# For vignette ---------------------------------------------------------------
title: Fitting Baselines to Spectra
subtitle: "Tutorial Explaining hyperSpec's Baseline Fitting Functions"
description: "baseline: Tutorial explaining hyperSpec's baseline fitting functions."
# Authors --------------------------... |
f1911614f999a969af7cff2e3cdce7ed35ec87975a706530f0d41f4b13c38052 | R | 16,920 | 583 | #' Bubble plot to display the result of a meta-regression
#'
#' @description
#' Draw a bubble plot to display the result of a meta-regression.
#'
#' @aliases bubble bubble.metareg
#'
#' @param x An object of class \code{metareg}.
#' @param xlim The x limits (min,max) of the plot.
#' @param ylim The y limits (min,max... |
a2dfd93e271d26f8165908c8dabc4358d2d16bb71c8c09461b88bb233c8c2beb | R | 16,923 | 499 | # #R-Script to combine datasets into one Excel (extracting peak areas), normalize and filter metabos by Rsq and CV; updated Oct 18, 2022
options(scipen = 100) #displays decimals in numeric, NOT sig-figs
remove(list = ls()) #clean-up environment first
library(dplyr) #load dependencies
library(purrr)
#library(rmarkdow... |
99c2299335fafdc5db279704ca08f481fd68b41c9e4bbc6cd4c302e2c3a046b3 | R | 16,961 | 461 | #!/usr/bin/Rscript
# Clear workspace
rm(list = ls())
# Load libraries
if(!require(NBR)) install.packages("NBR"); library(NBR)
source("https://raw.githubusercontent.com/zchuri/BilingualBrainNet/main/Code/AuxFunctions/valid_url.R")
# Read phenotypic data
info <- read.csv("https://raw.githubusercontent.com/zchuri/Bilin... |
fccacd95fe669e5d86d255c020c7c4ab117253da3bf802707317417148003f64 | R | 17,058 | 444 | ---
title: "Analysis of MEA data and plotting - per electrode"
#output: html_notebook
---
```{r}
library(ggplot2)
library(tidyverse)
library(ggpubr)
```
```{r}
# load data
#D30
run1 <- read.csv("P:\\PD_Diabetes\\MEA\\D30\\B1D30_5min.csv",
header = T, skip = 156, sep=",", ... |
7c3c454c63756e4d94282a46d9ddd28c2709d25dbc171c3d56f21e6891eb8525 | R | 17,136 | 749 | ---
title: "SEFL7c_Analysis"
author: "Zach"
output:
html_document:
fig_height: 4.5
fig_width: 4.5
highlight: kate
number_sections: yes
theme: journal
toc: yes
toc_depth: 6
editor_options:
chunk_output_type: console
---
# Set Global Options
```{r global_options}
knitr::opts_chunk$set(... |
af80eb883dca7204fad0badc10a6a3cd837e480adf0688dc88a86aaaf5498ecf | R | 17,157 | 370 | #' @title Surface plotter
#'
#' @description Plots surface data in a grid with one or multiple rows in a .png file
#'
#' @param surf_data A numeric vector (length of V) or a matrix (N rows x V columns), where N is the number of subplots, and V is the number of vertices. It can be the output from SURFvextract(), CAT12v... |
55dd8c71733297722b17314d5450598c16b109fe38ca9427a49d9c43447a179f | R | 17,161 | 359 | library(MAGeCKFlute)
library(ggplot2)
library(tidyverse)
library(dplyr)
#generate custom function for Scatter plot with SD=2
ScatterViewCustom<-function(data, x = "x", y = "y", label = 0,
model = c("none", "ninesquare", "volcano", "rank")[1],
x_cut = NULL... |
88b83d3e385f50ca1f1fffdd64049bd1f0e2d52052b1fb6a97f97f8d6cc2cc37 | R | 17,226 | 492 | # #R-Script to combine datasets into one Excel (extracting peak areas), normalize and filter metabos by Rsq and CV; updated Oct 18, 2022
options(scipen = 100) #displays decimals in numeric, NOT sig-figs
remove(list = ls()) #clean-up environment first
library(dplyr) #load dependencies
library(purrr)
#library(... |
b7dfbab690457cb8016e9bc3454f87184c553bedd38e3c780e3dacaa962c7f48 | R | 17,227 | 339 | ############################################################################################################################
############################################################################################################################
#' @title Vertex-wise analysis with random field theory cluster correc... |
8f6f330bb4cfa0743be0f482500bc3c48791ea196e4a0cc0e74720fc590e49e3 | R | 17,277 | 268 | #----Figure_03_G,H -------------------------------------------------------------
#-------------------------------------------------------------------------------
# This is the code for Figure 03 Panel G and H for the connectivity analysis for
# Reinhard and Fukuda et al. 2024
# The first run might take a bit longe... |
d018d192993e5d4ce44f9fcf425b0fa1c3d7c0b40fdd7a8f52a0ec3fbf2ff5d7 | R | 17,375 | 384 | ### this script will process single cell RNA seq from ADARKO teratoma (n=4), using non-perturbed teratoma as a reference for cell annotation,
### as well as call perturbation (which KO vs. wild type) for each cell
library(Seurat)
library(cowplot)
library(ggplot2)
library(DoubletFinder)
library(cellMapper)
input_dir ... |
de936aa32732f9106e790db122eacdbabc5975bff2efb3b211a7d4898dde1e12 | R | 17,387 | 452 | # From https://raw.githubusercontent.com/obigriffith/biostar-tutorials/master/Heatmaps/heatmap.3.R
# https://github.com/obigriffith/biostar-tutorials/blob/master/Heatmaps/heatmap.3.R
heatmap.3 <- function(x,
Rowv = TRUE, Colv = if (symm) "Rowv" else TRUE,
distfun = dist,
... |
415724203efe1d7da7b6c82cc958ef0dd9f5ac9bcd7f4f639cdc99ebb3f84106 | R | 17,432 | 212 | #############################################################################
#
# Control analysis for Temporal feature abnormality for Agitated MDD
#
# For this pipeline, we repeated the analysis of ETS and TD, but use difference
# group criteria.
#
# The control analysis include:
#. 1. Peak height difference
# 2... |
a55dcf1dfe21af98dd1f16977118884242dacc6bb36cfb03eb9db61beaa6ab1a | R | 17,434 | 321 | library(dplyr)
library(Seurat)
library(tidyverse)
library(patchwork)
library(ggplot2)
library(scCustomize)
# subset EX neurons from ACC data
ACC.new <- readRDS(".../ACC.merge.filter.rds")
Idents(ACC.new) <- "subtype"
Ex <- subset(ACC.new, idents=levels(ACC.new$subtype)[c(5,8,11,13,14,16,20)])
# VEN relat... |
0cbd72c2cac56f1195dfeb6521cedcb62c62de9539548811b011a38b941b0da0 | R | 17,471 | 501 | # #R-Script to combine datasets into one Excel (extracting peak areas), normalize and filter metabos by Rsq and CV; updated Oct 18, 2022
options(scipen = 100) #displays decimals in numeric, NOT sig-figs
remove(list = ls()) #clean-up environment first
library(dplyr) #load dependencies
library(purrr)
#library(... |
3193a1dbef2d5482835abd03a8a509b68667455020662a3341267650a69fd17e | R | 17,508 | 387 | require(matrixStats)
require(BiocParallel)
require(tidyverse)
require(energy)
gen.simulations <- function(sim_fn, paramlist=overlap.settings) {
simulations=lapply(paramlist, function(params) do.call(sim_fn, params))
names(simulations) <- names(paramlist)
return(simulations)
}
get.scatterplot_df <- function(raw... |
006e0d12c6af4484f67e1bb08e3007f6acbd67ba0da4bbe38d300c154cbaf53f | R | 17,516 | 600 | ---
title: "Supplementary material"
subtitle: "Language structure is influenced by the proportion of non-native speakers: A reply to Koplenig (2019)"
author: "Henri Kauhanen, Sarah Einhaus & George Walkden"
date: "16 December 2022"
output: pdf_document
numbersections: true
toc: true
papersize: a4
---
# Introduction
T... |
361ff077eb0df0437bed0bbde998f3379a61954d2f59f66057fe3b1ef6913d61 | R | 17,552 | 339 | paths=list(N_GEX='/sc/arion/projects/CommonMind/roussp01a/INGELHEIM/rnaseq/test/neuron_gene_norm_none_BIC_4_in_0.05_CPM_1_in_0.2/files/rev1_DAC_Analysis_dreamWeights.Rdata',
G_GEX='/sc/arion/projects/CommonMind/roussp01a/INGELHEIM/rnaseq/test/glia_gene_norm_none_BIC_4_in_0.05_CPM_1_in_0.2/files/rev1_DAC_Ana... |
32dae41acc14ab9b86a3ae5b8dc97d5950822193c097c3b3f4376299ec9f6a44 | R | 17,606 | 826 | ---
title: "SEFL10K6b_Analysis"
author: "Zach"
output:
html_document:
fig_height: 4.5
fig_width: 4.5
highlight: kate
number_sections: yes
theme: journal
toc: yes
toc_depth: 6
editor_options:
chunk_output_type: console
---
# Set Global Options
```{r global_options}
knitr::opts_chunk$s... |
bc8f2fbb28e151b64b1b3b9c4667c42983403970d2d43a7c47b9df3e27728688 | R | 17,610 | 451 | #### Markos et al
#### functions used in transitions workflow
#### Modified URD::createURD() function to use integrated data
createURD_nn<-function (count.data,norm.data, meta = NULL, min.cells = 1, min.genes = 1,
min.counts = 0, gene.max.cut = Inf, max.genes.in.ram = 5000,
verbose = T)
{
if... |
8e844b08b6595febd81e7bae15457217d44a25c5cb02c217f05f827f9878769b | R | 17,633 | 488 | #############################################################################
###
### read.ENVI - read ENVI files, missing header files may be replaced by list in parameter header
###
### * read.ENVI.Nicolet for ENVI files written by Nicolet spectrometers
### * adapted from caTools read.ENVI
###
### Time-stamp: <Cl... |
14c6731822c2b6c7dc7c7f9319b0f504d1e29d0e4da8cb339039ff534abe2c69 | R | 17,654 | 352 | ---
title: "corpus_segmentation_analysis"
author: "bezdek"
date: "3/20/2020"
output: html_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
library(tidyverse)
library(data.table)
library(lme4)
library(rlist)
library(readr)
library(stringr)
```
## Analysis
```{r load code, include=FALSE}
#... |
2e857e97e57e9fff2a7dd2184a92183dcdbaade73924d7560b4b7fa67bf996cf | R | 17,664 | 462 | ## -----------------------------------------------------------------------------
##
## Somatic variant detection in lesional focal epilepsy
## This script plots the results of the dNdScv meta-analysis
##
## Author: Dr. Christian Bosselmann
##
## Date Created: 2023-09-05
##
## Copyright (c) Christian Bosselmann, 2023
#... |
054d1be1e48e6623db1bd8c86fefdb7eca60e7551a0b7d1c25a7bf3eeab82409 | R | 17,670 | 446 | ---
title: "age_sex_analyses"
author: "Franz Xaver Mittermaier"
date: "2024-07-03"
output: html_document
---
This script contains analyses for potential age effects, as well as graphs that show data disaggregated by patient-sex.
```{r, message=FALSE, warning=FALSE}
#load libraries:
library(tidyverse)
libr... |
a726cdde85e02da291c70c8e4656ded9676db127d4dfc9717bef508e4603db29 | R | 17,726 | 623 | #' @name DEPRECATED-ggplot2
#' @concept moved to hySpc.ggplot2
#'
#' @title (DEPRECATED)
#' Spectra plotting with \pkg{ggplot2} was moved to \pkg{hySpc.ggplot2}
#'
#' @description
#'
#' These \pkg{ggplot2}-related \pkg{hyperSpec} functions are **deprecated**
#' and they will be removed in the next release of the... |
9f3756b87b9307e2566ccebbf77dffb0dbc7da91fcffaed47695e17fcd1a5c07 | R | 17,777 | 455 | # Reading of SPE files, produced by Princeton Instruments spectrometers
# File format version 2.5 (Sept. 2002)
# C. Beleites
# R. Kiselev
# July 2015
#' @name DEPRECATED-read.spe
#' @concept moved to hySpc.read.spe
#'
#' @title (DEPRECATED)
#' Import WinSpec SPE file
#'
#' @description
#'
#' These data input f... |
687bda2962b2f2e9789f2c6f3bb7945217e1e32a5c9ae34bb6f2ae9aeed8141b | R | 17,890 | 335 | ```{r load-config, incluse=FALSE}
source("config.R", local = knitr::knit_global())
```
```{r treatment-days-function}
# Create named list with treatments and their duration within a time window
treatmentdays = function(patient_id, start_date, end_date, group, treatment_data){
if(is.na(start_date)) return(NA)
days_... |
2e65029c625996d6f47c13e200f94d2b5f22169a6def426504dbb0b807b5d9e1 | R | 17,919 | 358 | library(natverse);library(reticulate);library(neuprintr); library(hemibrainr); library(nat); library(natverse); library(nat.jrcbrains); library(fafbseg);
setwd(getSrcDirectory(function(){})[1])# set the working directory to where this code is
source("Connectomics_functions.R")#library(RConnectomicsAnalysis)
#
# ###... |
f45de4fa99dc95de3f9dea72ff32314277b24024308d9801043bf265e7f483ce | R | 18,005 | 479 | ---
title: "FDR correction: check FWER under full null and in the presence of effects"
author: "Guillaume A. Rousselet"
date: "`r Sys.Date()`"
output:
# pdf_document:
# fig_caption: no
# number_sections: no
# toc: yes
# toc_depth: 2
github_document:
html_preview: yes
toc: yes
toc_depth... |
6ea7ba868a8019478a688da920d6de8481c0e42ef2f825ad6b5ae3eb966bfbab | R | 18,034 | 384 | library(MAGeCKFlute)
library(ggplot2)
library(tidyverse)
library(dplyr)
#generate custom function for Scatter plot with SD=2
ScatterViewCustom<-function(data, x = "x", y = "y", label = 0,
model = c("none", "ninesquare", "volcano", "rank")[1],
x_cut = NULL... |
27b10aa479a21cfb5e3bc4296f5692942082d5fd675ee809abfeb045292d1edb | R | 18,086 | 292 |
###Script 13
#Neuron subset atlas Cluster assignment
library(Seurat)
library(dplyr)
library(ggrastr)
library(ggrepel)
library(viridis)
library(ComplexHeatmap)
#load meta data
dt.meta <- readRDS("output/atlas/metadata_integrated_neuronal_atlas.rds")
#####################################################... |
cf16deb1a32697baaa486e0c453174f899d0f29cf0b35efff2eff8f0695548a6 | R | 18,160 | 525 | # Single cell RNA-Seq of Tlx3 WT vs KO samples
# Budhaditya Basu
library(Seurat)
library(tidyverse)
library(scCustomize)
library(SCP)
library(ggthemes)
library(RColorBrewer)
library(rstatix)
library(msigdbr)
library(clusterProfiler)
library(enrichplot)
library(org.Mm.eg.db)
library(ggrepel)
library(fgse... |
9339d6fead8f779c88086f8e6f1438cc8a944e150098c1f27bdf09d40cecc390 | R | 18,302 | 434 | ---
title: "gencor_plots"
author: "Gokberk Alagoz, L&G Dept., MPI for Psycholinguistics"
date: "`r Sys.Date()`"
output: rmarkdown::github_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
library(ggplot2)
library(corrplot)
library(reshape2)
library(dplyr)
library(tidyr)
library(tidyverse)
lib... |
0746f382bb20b43638d158e38cd1a83185c7f20f2770fa226663ad40aa85a556 | R | 18,489 | 520 | ---
title: "Figure 2 and related supplement tables"
author: "Meng-Ching Ko (MaggieMCKO)"
date: "07/17/2024"
output:
html_document:
df_print: paged
pdf_document: default
editor_options:
chunk_output_type: console
---
This [R Markdown](http://rmarkdown.rstudio.com) Notebook contain codes for reproducing Fig.2... |
83c07573fdcd7495f0f8d687d25ff675bdb4a0dcab134ac0cd92b5fcbc6cf0a0 | R | 18,531 | 459 | ---
title: "Pupilla::Assessing_Pupillary_Manifold"
author: "Elvio Blini"
date: "November 2024"
output: rmarkdown::html_vignette
vignette: >
%\VignetteIndexEntry{Pupilla::Assessing_Pupillary_Manifold}
%\VignetteEngine{knitr::rmarkdown}
%\VignetteEncoding{UTF-8}
---
## Introduction
`Pupilla` gathers several fu... |
e722906f49d7d00a21ddfd20690223f6b8c3a570ea943de2c28a911c4cad585e | R | 18,533 | 554 | ---
title: "Selection analysis (*`r params$species.name`*)"
author: "Bucao, Christabel Floi"
output: html_document
date: "`r Sys.Date()`"
params:
selectome.path: "../../data/selectome"
input.samples.rds.path: "../../results/01_Filter_Samples"
input.variability.rds.path: "../../results/03_Variability_Plots"
outp... |
2db054aa2f380722ca39f75fa8ab176a4cf967028aa0392dca9d232425841517 | R | 18,554 | 609 | #' Plotting the regulatory table from scregclust as a directed graph
#'
#' @param output Object of type `scregclust_output` from a fit of the
#' scregclust algorithm.
#' @param arrow_size Size of arrow head
#' @param edge_scaling Scaling factor for edge width
#' @param no_links Threshold value (0-10) for ... |
cbf8e570cc996c1e567abbded6e87e17f25d8c15085bcc7a70766d4e7239bcf0 | R | 18,584 | 443 | ---
title: "Rename clusters and build tree"
author: "Jeremy Miller"
date: "March 8, 2019"
output: html_notebook
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
# Overview
This script reads in the data and assigned clusters, organizes the clusters into a dendrogram, renames the clusters to incl... |
9592090b9eb02414291b3afbf5d281253ae5bc781028560ba56f1f98bd1bee24 | R | 18,622 | 589 |
#' Title
#'
#' @param netf The RDS file produced by getDownstreamNetwork()
#' @param folder This method will produce enrichment files. This variable
#' indicates where to store them
#' @param which.one Category under which the network should be installed.
#' If new, the category will be created
#' @param tissue A lab... |
225f989963a1a26060b44605efd117c8d5e4ad0bcf6d9fa66b895eca77e91651 | R | 18,639 | 582 | ---
title: "Variability of organ-biased genes (*`r params$species.name`*)"
author: "Bucao, Christabel Floi"
output: html_document
date: "`r Sys.Date()`"
params:
input.variability.rds.path: "../../results/02b_Variability_NoJack"
input.tau.rds.path: "../../results/10_Expression_Specificity"
output.rds.path: "../../... |
6aef2baf8872057576cb0371357e2e9f0974bcc7d1f264402e3ce60cbd2bd789 | R | 18,707 | 323 | .libPaths(c("/sc/arion/projects/roussp01a/jaro/programs/R_libs_4_0_3/", .libPaths(),''))
cellType= commandArgs(T)[1]
samplesToExclude=vector()
mySdCutOffForCorrelationOutliers=Inf #"Inf" means don't remove anything based on intersample correlation."Inf" means don't remove anything based on intersample correlation.
... |
e45f5436d2c37e63147382ab3d91ffd03e68a47c2b9fead5766c9d1471b90f5f | R | 18,725 | 367 | ##############################################################################
#
# eFC and agitation
#
# For this pipeline, we explored the DMN-SMN interaction with respect
# to the agitation severity.
#
# Functional connectivity was obtained from the ETS estimation and divided into
# Peak FC and Trough FC
#
# Liang Q... |
8b52cd5668720815bbb40f8874ceb16556e24ef7c68fc7d5a51aa8c6e56ba497 | R | 18,764 | 524 | #' Print results of a cumulative meta-analysis
#'
#' @description
#' Print results of a cumulative meta-analysis
#'
#' @aliases print.metacum
#'
#' @param x An object of class \code{\link{metacum}}.
#' @param prediction A logical indicating whether prediction intervals should
#' be printed.
#' @param overall A log... |
75183263a7a56eefb032b1a5c1e6bc25e497f8a923fa369161b6f1919b304c73 | R | 18,797 | 430 | #' Formatting arguments for forest plots
#'
#' @description
#' Formatting arguments for forest plots created with R package \bold{meta}.
#'
#' @details
#' In R package \bold{meta}, formatting arguments for forest plots can be
#' provided in the following named lists:
#'
#' \code{test}, \code{label}, \code{rob}, \code{... |
447db6f7473f58aa1947d11009802f083fbc1f1da9e0ff9bbb6e77f7531823fc | R | 18,864 | 474 | #!/usr/bin/env Rscript
# betaAFOutlier.R
# version 1.1
### LIBRARIES
### FUNCTIONS
parseArgs <- function(args) {
userin = list(dipn=NA, fstbar=NA, obsfreq=NA, outnames=NA, ancmethod=0, seed=NULL, qq=NULL, ancbin=0)
# parse required input
userin$dipn = as.numeric(strsplit(args[1],',')[[1]])
if (userin$dipn[1] ... |
a80cdbd1f4713ac1914bd83ef4928f5f64176982e670a8e4479c2b7f43947ddc | R | 18,893 | 631 | #' Calculate best linear unbiased predictor for \code{meta} object
#'
#' @description
#' Calculate best linear unbiased predictors (BLUPs) for meta-analysis object
#' created with R package \bold{meta}.
#'
#' @aliases blup blup.meta
#'
#' @param x An object of class \code{meta}, \code{blup.meta}, or
#' \code{estim... |
ca3975995b286563b72155b2e97754851dcfca3b1200f447f3d6dda3e5b14a9f | R | 18,935 | 505 | ---
title: "ON_2 Ambient RNA and Doublet Removal - h5 file trial"
author: "Katie Emberley, Jonathan Nelson, Greg Duncan, and Jeremiah Ryes"
date: "`r format(Sys.time(), '%d %B %Y')`"
output:
html_document:
toc: yes
toc_depth: 3
toc_float: true
number_sections: yes
theme: bootstrap
df_print: p... |
1363d66a48df5fc1e6a18376efdeae97f13050527e91b045350a7052f9daab85 | R | 19,038 | 504 | ---
title: "ON_1 Ambient RNA and Doublet Removal - h5 file trial"
author: "Katie Emberley, Jonathan Nelson, Greg Duncan, and Jeremiah Ryes"
date: "`r format(Sys.time(), '%d %B %Y')`"
output:
html_document:
toc: yes
toc_depth: 3
toc_float: true
number_sections: yes
theme: bootstrap
df_print: p... |
cbe64efdb362254f8d0f0f753a75baf12809916f87038db2d1e7837b120ba3f6 | R | 19,048 | 510 | ---
title: "ON_8 Ambient RNA and Doublet Removal"
author: "Katie Emberley, Jonathan Nelson, Greg Duncan, and Jeremiah Ryes"
date: "`r format(Sys.time(), '%d %B %Y')`"
output:
html_document:
toc: yes
toc_depth: 3
toc_float: true
number_sections: yes
theme: bootstrap
df_print: paged
code_fo... |
d2ae041073bc1adbef5b9bd712b01e9185f46682368058e66ef27a5121faa57a | R | 19,069 | 511 | ---
title: "ON_7 Ambient RNA and Doublet Removal"
author: "Katie Emberley, Jonathan Nelson, Greg Duncan, and Jeremiah Ryes"
date: "`r format(Sys.time(), '%d %B %Y')`"
output:
html_document:
toc: yes
toc_depth: 3
toc_float: true
number_sections: yes
theme: bootstrap
df_print: paged
code_fo... |
feb846d672cbefbd10cd87845a727a03b9d945adbd0c4d9a0144e51d0b568b9d | R | 19,138 | 527 | #collection of functions for the analysis of subcortical analyses from SubCortexMesh
############################################################################################################################
#############################################################################################################... |
fd4fde077ebb26de942b8ab7173476a24ba75427cf2f79ae9ebede8950cc3458 | R | 19,156 | 512 | ---
title: "ON_5 Ambient RNA and Doublet Removal"
author: "Katie Emberley, Jonathan Nelson, Greg Duncan, and Jeremiah Ryes"
date: "`r format(Sys.time(), '%d %B %Y')`"
output:
html_document:
toc: yes
toc_depth: 3
toc_float: true
number_sections: yes
theme: bootstrap
df_print: paged
code_fo... |
0e794d8b9f8e981b39ac225629c6f7c850095a1b22a284e647ca3cc3540e27f6 | R | 19,159 | 511 | ---
title: "ON_3 Ambient RNA and Doublet Removal - h5 file trial"
author: "Katie Emberley, Jonathan Nelson, Greg Duncan, and Jeremiah Ryes"
date: "`r format(Sys.time(), '%d %B %Y')`"
output:
html_document:
toc: yes
toc_depth: 3
toc_float: true
number_sections: yes
theme: bootstrap
df_print: p... |
1c2c697f8e2009baa146dcb2e2a82f8dd304fe9b95d5b1e3890925eee677ee46 | R | 19,184 | 336 | library(ggplot2)
library(data.table)
library(ggpubr)
library(dplyr)
library(ggsci)
library(UpSetR)
library(reshape)
setwd("./") # FIXME: SET TO THE FOLDER WITH UNCOMPRESSED REPOSITORY
dry_lab_dir = "dry_lab/"
wet_lab_dir = "wet_lab/"
outDir = "output_dir"
dir.create(outDir)
mpdf = function(x, width=7,height=7, outDir... |
177f3da03e357fa5b13659b0c8fa10cc12ec8de0755059df39937b97f8fed4e9 | R | 19,192 | 520 | ---
title: "ON_4 Ambient RNA and Doublet Removal"
author: "Katie Emberley, Jonathan Nelson, Greg Duncan, and Jeremiah Ryes"
date: "`r format(Sys.time(), '%d %B %Y')`"
output:
html_document:
toc: yes
toc_depth: 3
toc_float: true
number_sections: yes
theme: bootstrap
df_print: paged
code_fo... |
7cde428b5909dce8911b58703be658757a35eab80940e48fbc618cebf856c7a7 | R | 19,202 | 457 | ---
title: "Estimating group onsets using cluster statistics: simulation using EEG-like noise"
author: "Guillaume A. Rousselet"
date: "`r Sys.Date()`"
output:
# pdf_document:
# fig_caption: no
# number_sections: no
# toc: yes
# toc_depth: 2
github_document:
html_preview: yes
toc: yes
t... |
5cfae8d980edc001d4daecb7e04ade85628d24fd69f4f0d6f860ce1cfd0eface | R | 19,239 | 514 | ---
title: "ON_6 Ambient RNA and Doublet Removal"
author: "Katie Emberley, Jonathan Nelson, Greg Duncan, and Jeremiah Ryes"
date: "`r format(Sys.time(), '%d %B %Y')`"
output:
html_document:
toc: yes
toc_depth: 3
toc_float: true
number_sections: yes
theme: bootstrap
df_print: paged
code_fo... |
b6d310ff8295cf7cee8a0fa3d37b50f5a49125a0a053eff70dc777cc084963c0 | R | 19,358 | 629 | #' Calculate expected proportion of comparable studies with clinically important
#' benefit or harm
#'
#' @description
#' Calculate expected proportion of comparable studies with clinically important
#' benefit or harm which is derived from the prediction interval.
#'
#' @aliases cidprop cidprop.meta
#'
#' @param x An ... |
b6812b64f03e20a2b76d545507bb1f2778529149a2ab1c94673faeb85a93ebc3 | R | 19,439 | 385 | rm(list=ls(all=TRUE))
bin=function(x){
bins=c(0,(7:18)*2)
bin=numeric(0)
for (i in x){
bin=c(bin,max(which(bins<=i))-1)
}
return(bin)
}
path='C:/Users/Christoph/Documents/ETH/git/dslab/summaries/validation_results/validation_results__fold'
data=data.frame()
for (fold in 0:9){
data=rbind(data,read.csv(p... |
ae2120fac50d6a21cf2e4f5965600a07b58425fdc2ad5285412f49b360f519e5 | R | 19,470 | 677 | setlistname <- function(x, name) {
if (!is.list(x))
x <- list(x)
#
if (!is.null(name) & is.null(names(x)))
names(x) <- name
#
x
}
setname <- function(x, name) {
if (!is.null(x) &&
is.null(names(x)) &&
!(is.null(name) || all(name == ""))) {
nx <- length(x)
#
if (length(name) ... |
eae18315ae2d711944995a317806d2bda326522ea4babdee3c4790558b98e20b | R | 19,504 | 702 | meta2meth <- function(x, outclab = NULL) {
list(sm = x$sm,
method = x$method,
method.random = x$method.random,
three.level = replaceNULL(x$three.level, NA),
#
k = x$k,
k.study = x$k.study,
k.all = x$k.all,
k.TE = x$k.TE,
#
level = x$level.ma,
... |
4f9a37136e1ab578c89d4ad6f4b5abed72a87f41e6e8a5b6c3785eaa62684ada | R | 19,577 | 259 | library(cowplot)
library(ggplot2)
library(Seurat)
library(stringr)
library(dplyr)
library(cowplot)
library(limma)
library(edgeR)
library(stats)
### per cite RNA editing levels
### run detecting RNA editing pipeline with rediportal editing site table for reference GRCh38
load("/media/Scratch_SSD_Voyager/sammi/RNA_e... |
62c7291a58b1cdbc5632b2a9ed7b1d4291d8f5ca94cf74e6d1c0cde6258d06f7 | R | 19,595 | 725 | library(dplyr)
library(purrr)
library(ggplot2)
library(forcats)
library(tidyr)
library(broom)
### Functions
snakemake@source("__models__.R")
nested_tibble_to_coeff_tibble <- function(data) {
data %>%
mutate(model = map(model, broom::tidy)) %>%
unnest(cols = c(model))
}
base::save.image("debug.RData")
# MA... |
ae5d3575a74bb26c3d151841acc13117ac23db419dc9c3c8afd0e8e451657612 | R | 19,604 | 532 | #========================================================================================#
# Written by James M Roe, Ph.D.
# Center for Lifespan Changes in Brain and Cognition, Department of Psychology
# University of Oslo, Norway
#========================================================================================... |
d97360606f29a290a58ee58983d4d7c29ebfc7fd97421036f17e7afe88f3e926 | R | 19,635 | 408 | ---
title: "20240116_invitro_inhibitory_plots"
output: html_document
date: "2024-01-16"
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
```{r load libraries}
library(tidyverse)
library(ggplot2)
library(agricolae)
library(ggsignif)
library(multcomp)
library(nlme)
```
```{r load data}
manual_s... |
46839aebae161e55a2c342cc513ac49ddaa54a852640618711a74850b4d44a05 | R | 19,672 | 408 | ---
title: "20240116_invitro_inhibitory_plots"
output: html_document
date: "2024-01-16"
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
```{r load libraries}
library(tidyverse)
library(ggplot2)
library(agricolae)
library(ggsignif)
library(multcomp)
library(nlme)
```
```{r load data}
manual_s... |
4f8aa23797adeba516702d28659fc6cd24c3303656fbd68373f051e87bc24df1 | R | 19,718 | 303 | #!/usr/bin/env Rscript
#options(stringsAsFactors=F, scipen = 999)
options(stringsAsFactors=F)
library(SAIGE)
BLASctl_installed <- require(RhpcBLASctl)
library(optparse)
library(data.table)
library(methods)
print(sessionInfo())
option_list <- list(
make_option("--vcfFile", type="character",default="",
help="Path... |
22bac40f18379c29dc5dce93c2e4d9bfefbd69a2faafb9ea736f3e40c76e3dbd | R | 19,777 | 571 | ---
title: "Variability - No Jackknife (*`r params$species.name`*)"
author: "Bucao, Christabel Floi"
output: html_document
date: "`r Sys.Date()`"
params:
gene.metadata.path: "../../data/gene_metadata"
input.rds.path: "../../results/01_Filter_Samples"
output.rds.path: "../../results/02b_Variability_NoJack"
spe... |
fc0392ec892e6a778c70de94874f4fe1ba5aa575a36b21431395a3627140a83a | R | 19,828 | 483 | ---
title: "Figure2_largeScaleClustering"
author: "Fabienne Rössler"
date: '2023-03-21'
output: html_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
```{r, message=FALSE, warning = FALSE}
source("DLCAnalyzer.R")
source("BFA_BFF.R")
library(sp) #tested with v1.3-2
... |
efcabcf1281dced6763719387e07c88d1bccd75b4752d6f63af823d718a4e0f7 | R | 19,856 | 429 | ### data from Muotri et. al. cortical organoids, time point 1mo, 3mo, 6mo, 10mo
### cellranger using GRCh38 reference
### to save time, using cell type annotations from Muotri et. al.
# ----------------------------------------------------------------------
### couldn't find metadata - already emailed Alysson, but let'... |
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