sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
b5af26cba0124e23c0220e630fa0a0c8d590557c06d2bc4d84b4f8caf679d00d | R | 14,432 | 455 | #' This function writes citation data to disk in different formats
#' @export
#' @import dplyr
#' @import synthesisr
#' @importFrom utils read.csv read.table
#' @importFrom rlang .data
#' @param citations A data frame containing citations - usually post-deduplication
#' @param type export type
#' @param filename output... |
7bba0874f181ae375d3b3d52affefac2cbfcb82bd0a4d42c863057c313885043 | R | 14,445 | 336 | # install.packages('ggplot2')
# install.packages('tidyverse')
# install.packages('lmtest')
# install.packages("readxl")
# install.packages("MultNonParam")
# install.packages("gtable")
# install.packages("grid")
# install.packages("gridExtra")
library(ggplot2)
library(car)
library(lmtest)
library(readxl)
l... |
be366de5987fe3f5952cda2e9f2cd3135398e13baf7f6474fd42c6b3e5eb198f | R | 14,452 | 420 | #!/usr/bin/R
# ------------------------------------------------------------
# Create a representative figure panel for each set of modules
# Updated 02/09/2022
# ------------------------------------------------------------
library(cbrbase)
set_proj('DEVTRAJ', 'multiRegion')
if (!exists("cellmeta")){
source(paste0(s... |
2739c166cff63ce799b90de7d835473aa2e89fd0dc9d4e093ec33616be24117d | R | 14,471 | 349 | ---
title: "prep_sample4_fro_scvelo"
author: "T Attenborough"
date: "10/01/2023"
output: html_document
---
The other packages are on CRAN.
```{r, message=FALSE}
library(remotes)
library(Seurat)
library(zeallot) # For %<-% that unpacks lists in the Python manner
library(DropletUtils)
library(tidyverse)
library(GGally) ... |
28bdb4c0e78e98b59a5ec67e0e1b10e40d1d09ba1bc07bf67f75d1c68fe09ee7 | R | 14,476 | 349 | ---
title: "prep_sample2_fro_scvelo"
author: "T Attenborough"
date: "10/01/2023"
output: html_document
---
The other packages are on CRAN.
```{r, message=FALSE}
library(remotes)
library(Seurat)
library(zeallot) # For %<-% that unpacks lists in the Python manner
library(DropletUtils)
library(tidyverse)
library(GGally) ... |
2c366de9f1c144bdd7e1a885145faea7012d0c8a3c93ce478e51e71539cf6b35 | R | 14,476 | 349 | ---
title: "prep_sample3_fro_scvelo"
author: "T Attenborough"
date: "10/01/2023"
output: html_document
---
The other packages are on CRAN.
```{r, message=FALSE}
library(remotes)
library(Seurat)
library(zeallot) # For %<-% that unpacks lists in the Python manner
library(DropletUtils)
library(tidyverse)
library(GGally) ... |
1d951a48ea61662a9d1ca84500771ef4e027d60773348dddfd2ce3c4b9e14749 | R | 14,484 | 333 | # install.packages('ggplot2')
# install.packages('tidyverse')
# install.packages('lmtest')
# install.packages("readxl")
# install.packages("MultNonParam")
# install.packages("gtable")
# install.packages("grid")
# install.packages("gridExtra")
library(ggplot2)
library(car)
library(lmtest)
library(readxl)
l... |
263836446f21703dcb35bf5e6860a3046878c19ce597d91b54670a00f0325513 | R | 14,518 | 381 |
library(tidyr)
library(ggplot2)
library(glmnet)
library(ROCR)
library("optparse")
# Get the passed parameters
option_list = list(
make_option(c("-f", "--featureSelection"), type="character",
default="Binary_PromOnly_Motif_Counts", #"Binary_Combined_Motif_Counts", # "Binary_Combined_Motif_Counts"... |
0d960489b22a4ae3d43e16563362f2e2544a38981f3a07e41541e7c381be4450 | R | 14,522 | 351 | ---
title: "prep_sample1_fro_scvelo"
author: "T Attenborough"
date: "10/01/2023"
output: html_document
---
The other packages are on CRAN.
```{r, message=FALSE}
library(remotes)
library(Seurat)
library(zeallot) # For %<-% that unpacks lists in the Python manner
library(DropletUtils)
library(tidyverse)
library(GGally) ... |
164c68a2dae1d41a1e7934cd4d68310b96d793bd52b5c0b99774b77be417cf78 | R | 14,542 | 372 | ## general goal: clusters of mainly GFP-positive cells are more pure than clusters of mainly GFP-negative cells
############# combine time points but keep GFP+/- separate
## this one probably works best (after 90 degree transpose)
#Generate a heatmap of cluster vs tissue+gfp+time
#all cells are represented
#install t... |
b93b5c3b8b92eede707be7209d2d3514d97bd05172004a672776d4278ff8f2b9 | R | 14,576 | 327 |
# load requirements
suppressPackageStartupMessages({
# library(ArchR)
library(monocle3)
library(dplyr)
library(ggrastr)
# library(Seurat)
})
library(tidyr)
library(plyr)
library(ggplot2)
library(Matrix)
library("lme4")
assignDonorAndSite <- function(inputCDS){
updatedColdata = separate(data... |
1139fe5fab0c12f6bf5167f1563a48a11f021c5899a59a066e8d80f12f8ff602 | R | 14,621 | 368 | # 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... |
367bec9347655adebc7e77a94b02dce9a71380feebf5dc3c2d0ab1ecb6f84df3 | R | 14,654 | 502 | ---
title: "Bilateral rhizotomy. Analyse MPA"
author: "Yaromir Kobikov <kobikov.yaromir@gmail.com>"
date: "10/25/2021"
output:
word_document: default
html_document:
toc: true
toc_float:
collapsed: false
editor_options:
chunk_output_type: inline
---
```{r setup, include=FALSE}
source("../../BayesianPValue.R")... |
995ad4c34ea1c8ca90783a1b06291d320831c7dde4fad9dc04e5d7d87092f03a | R | 14,702 | 506 | ---
title: "Vertical Analysis PAS: Ctrl, BNI, FNA (hand, machine)"
author: "Yaromir Kobikov <kobikov.yaromir@gmail.com>"
date: "Date: `r format(Sys.time(), '%d/%m/%Y')`"
output:
word_document: default
html_document:
toc: true
toc_float:
collapsed: false
editor_options:
chunk_output_type: inline
---... |
2c844bba59ae658b6ebe553dea4cf68eea944e41e04ab33e81d5ea52154d20aa | R | 14,774 | 468 | #' @keywords internal
deconvolve_inputs <- function(inputs, sep, header, out, control, njobs) {
## Helper function to deconvolve all inputs prior to running GIMME
#require(parallel) #should be moved to import in NAMESPACE for R package
#require(foreach)
#require(doSNOW)
#require(doParallel)
if (missing(n... |
5cf43bda0b1d495f773df1fe5c1579ad7a51392455a1a23a825f02ae6d5691a2 | R | 14,809 | 372 | #' helper function to create an FWE object that specifies the type of FWE correction and the
#' model outputs to which it is applied
#' @param gpa a \code{glm_pipeline_arguments} object that already contains model output information in $l3_model_setup$fsl
#' @param level an integer indicating what modeling level thi... |
21a5e8718c754436b72ad8992246638cf7ab6bdac1c9eee63e45ffc53b7b7c4a | R | 14,817 | 434 | remove_black_white_gray <- function(hex) {
tibble(r = str_sub(hex, 2, 3),
g = str_sub(hex, 4, 5),
b = str_sub(hex, 6, 7)) %>%
filter(r != g | g != b | r != b) %>%
mutate(rgb = str_c("#", r, g, b)) %>%
pull(rgb) %>%
return()
}
convert_hex_vector_to_image <- function(hex, ... |
563a090cef0bf123dc9dc8d193bda3c0c17981b9da7edbf9c7ec1c05ab87da4f | R | 14,831 | 332 | ---
title: "integr_scDART"
output: html_document
---
In this document we do the integration of the YTH and YTH-mut scDART data using the Seurat package.
We also determine the cell clusters and cell types present in the data and the markers for each cell type, aided by the tools scibet and scMCA.
Finally we plot some ... |
a01db790e4e5fe65d9f1573948e7ca8672cddf84dc4439e170918e8d1cdb61b4 | R | 14,836 | 471 | ---
title: "shinyÉPICo Workflow Report"
output:
html_document:
toc: true
toc_float:
collapsed: true
theme: sandstone
highlight: pygments
toc-title: "Table of contents"
params:
#input
rval_sheet: NA
rval_sheet_target: NA
name_var: NA
grouping_var: NA
donor_var: NA
#normalization ... |
5d6501b2a003482645ac403e6aa74f8bdc8745d08a34a9bf2ec970984918b304 | R | 14,843 | 379 | ---
title: "Quality check on unfiltered raw data - Nurr1 project"
author: "Yuvarani Masarapu"
date: '2022-11-30'
output:
html_document:
self_contained: true
number_sections: true
highlight: tango
df_print: paged
code_folding: hide
toc: yes
toc_depth: 3
toc_float:
collapsed: fa... |
0e325a8343ef4e145906f4f00ba9c071bca5345e185a7229830192b8571e9433 | R | 14,895 | 450 | ---
title: "_Cardinal 3_: Statistical methods for mass spectrometry imaging"
author: "Kylie Ariel Bemis"
date: "Revised: 1 September 2024"
output:
BiocStyle::html_document:
toc: true
vignette: >
%\VignetteIndexEntry{2. Cardinal 3: Statistical methods for mass spectrometry imaging}
%\VignetteEngine{knitr::rmarkd... |
daa1394b4bd1853c927e329532f13ac3a2addcd5bb55585733d558a992fed7f0 | R | 14,912 | 513 |
#### MSImagingExperiment ####
## ---------------------------
# Class for a MS-based imaging experiment
# _with_ aligned feature information
MSImagingExperiment <- function(spectraData = SimpleList(),
featureData = MassDataFrame(), pixelData = PositionDataFrame(),
experimentData = NULL, centroided = NA, metadata = ... |
fb8992ac234bec70d07a641540030355c0e76d0189ba6e9f2db8537ea2285ab0 | R | 14,926 | 442 | #From limma
strsplit2 <- function (x, split, ...)
{
x <- as.character(x)
n <- length(x)
s <- strsplit(x, split = split, ...)
nc <- unlist(lapply(s, length))
out <- matrix("", n, max(nc))
for (i in 1:n) {
if (nc[i])
out[i, 1:nc[i]] <- s[[i]]
}
out
}
# Funcion para construir matriz de distan... |
101dd07313256761c217ef6996b31448fdedc4633d06b1911473775bff2d6466 | R | 14,974 | 457 | ---
title: "SF, CI AI (Ctrl, NTI, Nal): Bayesian regression of smoothed stretch forces"
author: "Yaromir Kobikov <kobikov.yaromir@gmail.com>"
date: "Date: `r format(Sys.time(), '%d/%m/%Y')`"
output:
word_document: default
html_document:
toc: true
toc_float:
collapsed: false
editor_options:
chunk_ou... |
57aa0b3e0487f40d9e6d8c7e88ffffb8ca7704ee94782671e169f3b216bc1dc4 | R | 15,014 | 347 | ---
title: "clean_integration"
author: "T Attenborough"
date: "09/01/2023"
output: html_document
---
```{r}
library(Seurat) #Seurat v4.0.2
library(dplyr)
library(patchwork)
library(here)
library(ggplot2)
library(clustree)
library(SingleCellExperiment)
library(scater)
library(DoubletFinder)
library(zellkonverter)
libra... |
f4eafd480e717d7938306bcda7667bd4bc888c5331265056da0eefd6b4d1dbea | R | 15,080 | 413 | #Code for snRNA-seq analysis of thalamic and cortical organoids
#load required packages
library(Seurat)
library(voxhunt)
library(dplyr)
library(monocle3)
library(tidyr)
library(ggplot2)
library(viridis)
library(RColorBrewer)
library(NeuronChat)
library(CellChat)
library(ggalluvial)
library(SeuratObject)
... |
8b8725a7276d818ef7bbb8c1ad64fd59f758d8be3753472432636fb8cd992699 | R | 15,112 | 409 | ## Simulation --- AUC
#library
library(SingleCellExperiment);library(tidyverse);library(reticulate);library(tidyverse)
library(ggplot2);library(scmap);library(fmsb);library(ggsci);library(scibet);library(ggpubr)
library(Seurat);library(M3Drop);library(ROCR);library(cluster);library(parallel)
#Functions
simul_da <- fu... |
e9a8a4cdf2321844348262562a70eedc6301a889d4ec3d473c7e9b8aecc0fc14 | R | 15,119 | 398 |
library(tidyr)
library(ggplot2)
library(glmnet)
library(ROCR)
library("optparse")
# Get the passed parameters
option_list = list(
make_option(c("-f", "--featureSelection"), type="character",
default= "Binary_Combined_Motif_Counts", #"Binary_PromOnly_Motif_Counts",# "Binary_Combined_Motif_Coun... |
634da6c750942760f4efe560b9d6dcc2855df39adbb05c25fe1f7130950215c2 | R | 15,136 | 454 | ---
title: "SF, CI dW: Bayesian regression of smoothed stretch forces"
author: "Yaromir Kobikov <kobikov.yaromir@gmail.com>"
date: "Date: `r format(Sys.time(), '%d/%m/%Y')`"
output:
word_document: default
html_document:
toc: true
toc_float:
collapsed: false
editor_options:
chunk_output_type: inline... |
c6fb7e4df8e546d155715f5864659a10eec355ea12908763e2cb4bc98d0f0783 | R | 15,143 | 418 |
basepath = "/net/trapnell/vol1/home/readdf/trapLabDir/hubmap/results/2021_07_15_Greg_ATAC_Code_nobackup/"
dir.create(paste0(basepath, "archr/results/NB6/"))
out_dir = paste0(basepath, "archr/results/NB6/")
setwd(out_dir)
set.seed(7)
# load requirements
suppressPackageStartupMessages({
library(ArchR)
library(monoc... |
c8ae0bfb14a4ad05bb8462dde23ad696f93cefd2e5bb432107c42b2716fe2716 | R | 15,168 | 394 | #!/usr/bin/R
# ---------------------------------------------------
# Investigate differences between immune subtypes:
# Updated 03/08/2021
# TODO: Refactor as with astrocytes
# ---------------------------------------------------
library(cbrbase)
set_proj('DEVTRAJ')
source(paste0(bindir, 'multiRegion/load_metadata.R'))... |
261555bac7eab3c32f990c582086b28619277eb26f7ba25b643480e305c24b1d | R | 15,241 | 391 | ---
title: "Phosphoproteomics data set of multiple mouse tissues"
author: "Patrick Forny"
date: "2023-10-01"
---
Overview plots of the data.
Load packages.
```{r packages}
# Load packages
library(pacman)
p_load(data.table)
p_load(tidyverse)
p_load(readxl)
p_load(ComplexUpset)
```
Load the data. The data has been ... |
512520d7939f1e06c8c81cda765a6a6d044683cd48423781366dbb70f3b7a73b | R | 15,347 | 308 | ####################################################################################################
###
### File: 05_extract_peak_features.R
### Purpose: Extracting peak features from each time series
### Authors: Gabriel Rodrigues Palma, Rafael De Andrade Moral
### Date: 09/03/23
###
##########################... |
858c519841f4b2ed248114e7f82a573ecf14d423c8e5bee12755b385e90217a3 | R | 15,355 | 380 |
hardAssignClustLabels <- function(inputCDS, kVal){
if (kVal == 40){
colData(inputCDS)$cluster_label = as.character(clusters(inputCDS))
colData(inputCDS)$cluster_cell_type = colData(inputCDS)$cluster_label
colData(inputCDS)$cluster_cell_type = ifelse(colData(inputCDS)$cluster_cell_type %in... |
2503e7c55a6881a7e9761ab143faedb0a922cbd67fe91380296c647afaba0056 | R | 15,388 | 309 | library(ggplot2)
library(Seurat)
setwd("D:/Mouse_data_integration")
pbmc <- readRDS(file = "Glutamatergic_neurons_integrated_all_class_new.rds")
write.csv(pbmc@meta.data,file="Glutamatergic_neurons_integrated_all_class_new_metadata.csv")
data=read.csv("Glutamatergic_neurons_integrated_all_class_new_metadata_addi... |
06b4024539bb56bf672f165f42f92c40a6f272eac86fa72c462541f3765062a3 | R | 15,404 | 405 | #!/usr/bin/R
# ------------------------------------------------------
# Second pass of refining metadata:
# Final clusters from Hans, names for exc, removal of MB
# Updated 10/11/2020 with names / cluster 172 changes
# ------------------------------------------------------
library(cbrbase)
set_proj('DEVTRAJ')
source(pa... |
365bef0e45022c2714bb5f6e4c998f7cfb54e21bb8309feadc9e0dd0eb275a43 | R | 15,405 | 339 | ---
title: "revisions_analysis"
output: html_document
---
# Load libraries
```{r}
library(tidyverse)
library(here)
library(DeepComBat)
library(neuroCombat)
library(CovBat)
library(GGally)
library(ggfortify)
library(ggpubr)
library(umap)
library(caret)
library(matrixStats)
library(twosamples)
library(kBET)
source("... |
9e33876a858b4ba36a7a94851b0d92e01eda9f785d735e7b9b8c477db653e00b | R | 15,413 | 474 | ---
# For Vignette ---------------------------------------------------------------
title: Calibration of Quinine Fluorescence Emission
subtitle: "Example Workflow for Fluorescence Emission Dataset `flu`"
description: "flu: Example workflow for fluorescence emission dataset `flu`."
# Authors ------------------... |
3e6fcedd61db550ae73e8c39dc2f74f98a09217b033c987b0cefdb5b4531984c | R | 15,429 | 439 | ---
title: "03_plot_reval_output"
author: "Veronica Mandelli"
date: "2/8/2022"
output: html_document
---
```{r}
# load libraries
library(grid)
library(lattice)
library(ggplot2)
library(reshape2)
library(gridExtra)
library(grid)
#set paths
work_dir = "..."
codepath = file.path(work_dir,"code")
datapath = file.path(wor... |
46dee03315f1b768f4a9408d900bc03001aa686926fca1d668ebefb43edf3d64 | R | 15,446 | 472 | #!/usr/bin/R
# --------------------------
# Compute cell type modules:
# Updated: 05/25/21
# --------------------------
library(cbrbase)
set_proj('DEVTRAJ')
source(paste0(bindir, 'multiRegion/load_metadata.R'))
library(tidyr)
library(Matrix)
# For nebula:
library(nebula)
library(DESeq2)
library(RUVSeq)
library(qvalu... |
8dc9722888547705dbee15ef7888f8e06e0c0e4c586d7319c4910ef29f1b3c36 | R | 15,514 | 385 | #!/usr/bin/env Rscript
# Helper script to generate table of minGQ filtering conditions
###Set master parameters
options(stringsAsFactors=F,scipen=1000)
###################
###HELPER FUNCTIONS
###################
###Format size range table
formatSizes <- function(min.sizes,max.sizes){
#Vectorize inputs
min.vect... |
a894720e5b15547f3bc35dcaabc0a47a55bf498bdaf13d3ab575ad6d71e7b1c5 | R | 15,548 | 357 |
###########################################################################################
# Load relevant packages
# source("../../../sharedProjectCode/utility/singleCellUtilFuncs.R")
# modStatus <- loadMonoclePackages()
# print(modStatus)
# source("../../../sharedProjectCode/scRNA_Seq_Background_Code/backgroundMet... |
6f5a71e5c1a23e9d1c142c0f52f365d78981ab5f55dbe1a7306c01a0bd553ec3 | R | 15,580 | 283 |
#' archstabms_coupling_scatter_datasets
#'
#' Coupling scatterplots for multiple datasets.
#'
#' @param dataset_names character vector of dataset names (required)
#' @param base_dir Base directory (required)
#' @param output_dir Output directory (required)
#' @param stagenum stage number (required)
#' @param colour_sc... |
624ef213cc0630b8243f4785d6cd6e4e0b8fb7017f5e8f7a819f2557b37db403 | R | 15,601 | 245 |
library("ggplot2")
LOGEN_ROOT = "/lustre/projects/Research_Project-MRC148213/lsl693/scripts/LOGen/"
LOGEN="/lustre/projects/Research_Project-MRC148213/lsl693/scripts/LOGen/"
SC_ROOT = "/lustre/projects/Research_Project-MRC148213/lsl693/scripts/rTg4510/Paper_Figures/"
source(paste0(SC_ROOT, "0_source_functions.R"))
sou... |
12e9c7468a09662a71958a7f83205b925633221c5e90ee8c038bbcba9ac189ad | R | 15,623 | 407 | library(tidyverse)
library(broom)
library(quickpsy)
library(glmnet)
library(rstatix)
###########################################################################
# Load and preprocess data ------------------------------------------------
###########################################################################
data ... |
7c092ddc0ed2f96b15052deab1b260c4e4318bcfbae4bbaf672fca4731f8c43f | R | 15,686 | 360 | ###################################### paths #######################################################
pfad_o <- "/home/joern/Aktuell/PaclitaxelPainLipidomics/"
pfad_u1 <- "01Transformierte/sissignano/paclitaxel/results/"
###################################### libraries ##################################################... |
196d807b0f846ef58be8aeacdc914480345c3f0d9e149942ed9f1af8d0e4a863 | R | 15,717 | 427 |
library(tidyr)
library(ggplot2)
library(glmnet)
library(ROCR)
library(data.table)
library(monocle3)
library(gridExtra)
# Get shared functions between this and runRegressionModel.R
source("./utilityFunctions.R")
source("/net/trapnell/vol1/home/readdf/trapLabDir/sharedProjectCode/utility/singleCellUtilFuncs.R")
libra... |
37a1b335f16a78d387b453dfa81b6a0018b6a57e18c72b219e8f692ca0d3f3e6 | R | 15,843 | 446 | #############################################################################
###
### 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... |
7d66fb993059bece1b8581a72f49b48145b701318546827df785e3e77774f70c | R | 15,859 | 360 | #######################################################################################
############################### R script related to the study:#########################
############# Le Verger et al. In Prep. Goldfish Phenomics from an Evolutionary #######
############# Perspective: Commonalities and Lack of ... |
fa5571fdfe744af978e4ca0bfe354fbf629c4bc66162cc7981a139275978a29e | R | 15,906 | 317 | #' Function to perform voxelwise deconvolution on an fMRI dataset using the fMRI model arguments object
#'
#' @param niftis A vector of processed fMRI timeseries images (4D files) to be deconvolved
#' @param add_metadata A data.frame with one row per value of \code{niftis}. Columns of this data.frame
#' are added to ... |
e70dd893c2c5d286d4420cdb1dfe8a1ea75b8714efeadab062bdac7357f3c389 | R | 15,909 | 410 | # Tests for GLM backend registry helpers
test_that("get_glm_backends returns resolved backends from gpa", {
gpa <- create_mock_gpa(include_l1_models = TRUE)
gpa$glm_software <- c("fsl", "spm")
gpa <- fmri.pipeline:::initialize_glm_backends(gpa)
backends <- fmri.pipeline:::get_glm_backends(gpa)
expect_type(b... |
77ed04e265d97489835f3aa3c7373b66ace95400696c1bb3148f0d527696c52b | R | 15,916 | 451 | #!/usr/bin/R
# -------------------------------------------------------
# Region-region stage matching
# Updated: 11/010/23
# ------------------------------------------------------
library(cbrbase)
set_proj('DEVTRAJ', 'multiRegion')
source(paste0(bindir, 'multiRegion/load_metadata.R'))
library(tidyr)
library(MASS)
lib... |
1e5f451a78ce275b4cfc9b79b0e43f488287046c1d6c9772073d2e435a018ace | R | 15,963 | 460 | ---
title: "Smooth (spline) terms in sccomp"
author: "Stefano Mangiola"
date: "`r Sys.Date()`"
package: sccomp
output:
prettydoc::html_pretty:
theme: cayman
toc: yes
toc_depth: 2
number_sections: yes
fig_caption: yes
df_print: paged
abstract: >
Splines let you model non-linear compositional ... |
26c9ac720ab0c3d978b82b6c23bff6352bb86c4ec44616c407459de3161886b4 | R | 15,987 | 460 |
# TF expression profile cascade
#
# input:
# data/05_DS2_seuratLT.Rdata : DS2
# data/07_DS2_pseudot_umap.Rdata: pseudo time
# output:
# data_figs/09_DS2_tfsCascade.pdf
require(SingleCellExperiment)
require(scran)
require(dorothea)
library(pheatmap)
library(ComplexHeatmap)
library(dendsort)
options(bitmapTyp... |
560cf369f933eb630f28456b469c5946ac51b98dd0dceeea7f140fe8870de4bb | R | 16,027 | 453 | FindAllMarkers_for_MAST <- function(
object,
assay = NULL,
features = NULL,
slot = 'data',
logfc.threshold = 0.25,
min.pct = 0.1,
min.diff.pct = -Inf,
verbose = TRUE,
only.pos = FALSE,
max.cells.per.ident = Inf,
random.seed = 1,
latent.vars = c('cngeneson'),
min.cells.feature = 3,
min.cells.... |
bd5a765f306c361a964de6fb487eb10bc16b49ed98342f2af44297513b21526c | R | 16,065 | 406 | library(ANCOMBC)
library(phyloseq)
library(reshape2)
library(ggplot2)
library(dplyr)
library(magrittr)
library(ggpubr)
#obj loading
neuron_hd_obj_acc_caud <- readRDS("neuron_hd_obj_acc_caud_sub_3_28.rds")
neuron_hd_obj_cing <- readRDS("neuron_hd_obj_cing.rds")
comb_hd_cd44_pos <- readRDS("comb_hd_cd44_positive.rds")... |
d0ea2e1b1059776d64e6acc30b49dd21ba5350fffaba8a464fe6f0fbbeb47bdc | R | 16,091 | 449 | # Collected FWE results and persistent artifact manifests
fwe_result_schema_version <- function() 1L
fwe_artifact_manifest_schema_version <- function() 1L
fwe_artifact_manifest_column_classes <- function() {
columns <- c(
"manifest_schema_version", "correction_name", "method", "artifact_id",
"task_id", "ta... |
a15cc2a4da0d140e95f4ab2e70ba2de662ce2a44416607f46898de53bc1f9af3 | R | 16,115 | 396 | library(ggplot2)
library(tidyverse)
library(rstatix)
library(lmerTest)
library(openxlsx)
library(ggpubr)
library(bpnreg)
library(emmeans)
library(dplyr)
fnirs <- read.csv("your path/all_hemoglobin_data.csv")
fnirs$ID = factor(fnirs$ID)
fnirs$Epoch2 = fnirs$Epoch^2
setwd('Your directory')
# PRE SMA ... |
4fc684355603d34fdf8115dd3c397c035327eca813b86c48b6c1bd688fca2812 | R | 16,117 | 550 | ---
title: 'SF: Read and preprocess raw stretch force measurements Ctrl, BNI, FNA'
author: "Yaromir Kobikov <kobikov.yaromir@gmail.com>"
date: "Date: `r format(Sys.time(), '%d/%m/%Y')`"
output:
word_document: default
html_document:
toc: true
toc_float:
collapsed: false
editor_options:
chunk_output_... |
60df5c3e090fe77a722ec636c8fda928fcf4bf6afc5933077adfbd8838344e42 | R | 16,139 | 302 | #This script performs NNLS-based lineage specific molecular staging
#Link to MOCA and mouse gastruloid datasets are provided in https://shendure-web.gs.washington.edu/content/members/hGastruloid_website/public/
#Human gastrloid datasets from this paper are provided at National Center for Biotechnology Information (NCBI... |
2ec66ca981cea9265ffabaee78740893e74555064f81f79ecdade3809511f77a | R | 16,146 | 352 | #########################
########Licensing########
#########################
# Breathe Easy - an automated waveform analysis pipeline
# Copyright (C) 2022
# Savannah Lusk, Andersen Chang,
# Avery Twitchell-Heyne, Shaun Fattig,
# Christopher Scott Ward, Russell Ray.
#
# This program is free software: you can redis... |
01dd2cca242538dc779abf3fb57b48358345983609a0da542033173336ed41dd | R | 16,212 | 513 |
#### Peak processing ####
## ----------------------
setMethod("peakProcess", "MSImagingExperiment_OR_Arrays",
function(object, ref,
spectra = "intensity", index = "mz",
method = c("diff", "sd", "mad", "quantile", "filter", "cwt"),
SNR = 2, type = c("height", "area"),
tolerance = NA, units = c("ppm", "mz"),
... |
c3c66cdf5bfdd3aafbfd8348c65913a4df11e2c73ed641ae9ce4c93264eaa5fc | R | 16,273 | 394 |
basepath = "/net/trapnell/vol1/home/readdf/trapLabDir/hubmap/results/2022_04_03_redoATAC_proc_nobackup/"
# dir.create(paste0(basepath, "archr/results/NB6/"))
out_dir = paste0(basepath, "archr/results/NB6/")
setwd(out_dir)
# load requirements
suppressPackageStartupMessages({
library(ArchR)
library(monocle3)
libr... |
e574188b8482e44ede585233422a14744e479e968c46930cb0920d9469b089fb | R | 16,312 | 474 | # Execution of compiled familywise-error correction plans
fwe_run_schema_version <- function() 1L
refresh_fwe_method <- function(method, plan) {
method <- as_fwe_method_adapter(method)
UseMethod("refresh_fwe_method", method)
}
#' @keywords internal
#' @export
refresh_fwe_method.default <- function(method, plan) ... |
4317d292d0b6f1eaba425b09178f00517a8b48fcc2be62d072fb4e8a16e90a63 | R | 16,317 | 564 | library(dplyr)
library(tidyr)
library(sccomp)
library(ggplot2)
data("seurat_obj")
data("sce_obj")
data("counts_obj")
counts_obj =
counts_obj |>
mutate(count = count+1) |>
with_groups("sample", ~ .x |> mutate(proportion = count/sum(count)))
# Precomputed CmdStan fits: `helper-precomputed-estimates.R`
# Test for... |
eaa311b816b78724f4c1541ff9b97ae5057516c04eba9bf4b0fe22e39115d464 | R | 16,332 | 433 | # Compiled familywise-error correction plans
fwe_plan_schema_version <- function() 1L
as_fwe_method_adapter <- function(method) {
method <- normalize_fwe_method(method)
class(method) <- c(
paste0("fwe_method_", method$name),
"fwe_method",
"list"
)
method
}
compile_fwe_method <- function(method, t... |
8cccdeb51fc950540cd04137383a25a583850fcfd6d96a22bcc18743263fac77 | R | 16,400 | 369 | # VISUAL ACUITY, OPTOMOTOR RESPONSE, EXPERIMENT WITH MALES AND FEMALES, UP- AND DOWN-SELECTED FOR TELENCEPHALON SIZE,
# GENERATION 3, 5% DIFFERENCE IN TELENCEPHALON SIZE, 238 FISH
# OCTOBER - NOVEMBER 2019, DATA COLLECTED BY MADDI GARATE OLAIZOLA
#-----------------------------------------------------------------------... |
3cfc20a46a1cc3118e6a88d392bf4bb805dd97a2b626c616f57e892294b73928 | R | 16,411 | 489 | #!/usr/bin/R
# --------------------------------------------------
# Analysis of metabolic modules
# with each other / across cell types
# both at sample & cell type level
# Updated 02/07/2022
# --------------------------------------------------
library(cbrbase)
set_proj('DEVTRAJ', 'multiRegion')
if (!exists("cellmeta")... |
2754bde8739b1dd527583a03882e7b2040801f0a174674023e1eeaef825d3603 | R | 16,458 | 385 | # Description: Post-hoc QC analysis of filtered de novo SVs
# Load libraries
library(tidyr)
library(ggplot2)
library(UpSetR)
library(data.table)
library(dplyr)
library(gridExtra)
library(grid)
library(tidyverse)
library("grid")
library("ggplotify")
library(dplyr)
args = commandArgs(trailingOnly=TRUE)
input_bed <- a... |
57df9431357177e521c5b721ace0784a4dc804a9253aae9fad46098547744bd1 | R | 16,461 | 288 | ####################################################################################################
###
### File: 04_obtaining_HMM_performance.R
### Purpose: Obtain the proportion that different Hidden Markov
### Models with m = 2, 3, 4, 5 were the best based on
### AIC metric.
### Authors: Gabrie... |
3d60520e11b1f14cf38c859e8b539bd46cb03b8508ce8f9f8ec6b80197040886 | R | 16,538 | 444 |
library(tidyr)
library(ggplot2)
library(glmnet)
library(ROCR)
library(data.table)
library(monocle3)
library(gridExtra)
library(RColorBrewer)
# Get shared functions between this and runRegressionModel.R
source("./utilityFunctions.R")
source("/net/trapnell/vol1/home/readdf/trapLabDir/sharedProjectCode/utility/singleCe... |
dbf5ecb7de98dff4e8ae6e9c3da08110040c9e4d0774089236057fbf14f16bfc | R | 16,552 | 384 |
library(ggplot2)
library(dplyr)
library("optparse")
library(stringr)
library(ggrepel)
# options(ggrepel.max.overlaps = Inf)
print("Libraries loaded, starting now")
# Get the passed parameters
option_list = list(
make_option(c("-m", "--modelNotes"), type="character",
# default="_fix_Anatomical_... |
a8078abccfa511c0136e2b636dd92e724790ab68f493440c1b8053c70021a188 | R | 16,564 | 534 | # Mock Factory Functions for Unit Testing
# =========================================
# This file provides lightweight mock object creators for testing individual
# functions without requiring external data files or the full pipeline setup.
#
# Design principles:
# - Each factory creates the minimal valid object needed... |
b5385fa61d905286ec2656424d68f18af037be138380727ac227b3706ce203ef | R | 16,595 | 370 | #' wrapper class for AFNI whereami
#' @importFrom tidyselect everything
#' @importFrom dplyr select
#' @export
afni_whereami <- R6::R6Class("afni_whereami",
private = list(
pvt_method = "coord_file", # coord_file or coord_vector
pvt_coord_file = NULL,
pvt_coord_file_columns = NULL,
pvt_coord_vector = ... |
1eb2952ceeb3c68af4eb27a23c0cc164fcfaee7550182487a5a3fc0d53fd6f9c | R | 16,644 | 425 | #!/usr/bin/R
# ----------------------------------------------------------
# Plot simple predictions and top genes vs. pathology
# Last updated mid-2020 (exploratory analysis)
# ----------------------------------------------------------
library(cbrbase)
set_proj('DEVTRAJ')
source(paste0(bindir, 'multiRegion/load_metadat... |
619d6884137e6f379df9091817c1829038e2a3acdcf0e835cc446fe7cfd69ac7 | R | 16,738 | 385 | ---
title: "Compute functional connectivity and structural connectivity of Yale Brain Atlas parcels"
author: "Evan Collins"
output: html_document
date: '2024-02-06'
---
All code in this markdown document has written by Evan Collins. Any questions can be sent to evantomcollins@gmail.com.
```{r}
# Load packages
library... |
770e30658313d286a26ea8daa680aeef37ab3d320cdee5437243f4fdff9f05db | R | 16,803 | 359 |
# load requirements
suppressPackageStartupMessages({
# library(ArchR)
library(monocle3)
library(dplyr)
library(ggrastr)
# library(Seurat)
})
library(tidyr)
library(plyr)
library(ggplot2)
library(Matrix)
library("lme4")
assignDonorAndSite <- function(inputCDS){
updatedColdata = separate(data... |
32524eb3f49422b8e98e067766b9c7be64b45c9425603364f09992198eefbec7 | R | 16,804 | 519 | #' @docType package
#'
#' @section Package options:
#'
#' \pkg{Azimuth} uses the following options to control the behavior of the app.
#' Users can provide these as named arguments to \code{\link{AzimuthApp}}
#' through dots (...), specify these in the config file, or configure these with
#' \code{\link[base]{options}}... |
87102af7160c79f9d1c609dcb2531e3bd75147dee1069ca021abe987c492d317 | R | 16,822 | 525 | ---
title: "chicks_numerosity_analysis_2023"
author: "Mirko Zanon, Matilde Perrino"
date: "2023-11-21"
output: html_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
## Import libraries
```{r warning=FALSE}
rm(list=ls())
library(tidyr)
library(plyr)
library(dplyr)
library(ggplot2)
libr... |
8e96a45eb3d8a90ab3c223fdcde761cc8e87964ef30072933b2fd12a5128346e | R | 16,835 | 418 | ################################################################################
# Scrpit to plot regional brain maps of: (1) predicted centiles/effect sizes,
# (2) empirical centiles/effect sizes, and (3) molecular and micro-architectural
# features from .csv files
###############################################... |
709f51f98b5d24b30c0f2b265eaaad888fcda3c77511ba96ce3f9f37178a6ebe | R | 16,860 | 508 |
basepath = "/net/trapnell/vol1/home/readdf/trapLabDir/hubmap/results/2021_07_15_Greg_ATAC_Code_nobackup/"
dir.create(paste0(basepath, "archr/results/NB6/"))
out_dir = paste0(basepath, "archr/results/NB6/")
setwd(out_dir)
# load requirements
suppressPackageStartupMessages({
library(ArchR)
library(monocle3)
libra... |
f8be6ca9d6cdc0fd642b85945b55bce78374d46030ef6dcfb40e25e7eb31fe19 | R | 16,895 | 286 | #This script convert scRNA-seq datasets of E6.5-13.5 mouse embryos (Pijuan-sala et al., 2019, Cao et al., 2019, Qiu et al., 2022), mouse gastruloids (van den Brink et al., 2020, Veenvilet et al., 2020) into pseudobulk sample matrices
#Link to MOCA,Pijuan,mouse gastruloids and somitoids datasets are provided in https://... |
724df7a6ce18bc881b72a40f7c7003b6c3a6dcbdd17adcef115c0181bc91ed66 | R | 16,908 | 441 | #!/usr/bin/R
# -----------------------------------------------------
# Plots/stats for genes more of one pathology than other
# - Show overlap with modules, GO, ndegs, etc.
# Updated: 06/15/23
# -----------------------------------------------------
library(cbrbase)
set_proj('DEVTRAJ', 'multiRegion')
source(paste0(bindi... |
d5b018726d3afe674836346efea79fa4fec8ebe736be5ea33dda15c933a154fc | R | 16,912 | 400 | ---
# 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 --------------------------... |
8f63a38f1ce0ef53b6449c082bf7f723e7e69ab0594955f0c9aa238e201abe27 | R | 16,953 | 44 | library(testthat)
library(dplyr)
extra_pair <- tidyr::tribble(
~author1, ~author2, ~author, ~title1, ~title2, ... |
e7fc9b7778495128e8a7a4ba031c94e576e5abeed197e6b419de680e6c3f079b | R | 16,995 | 477 | #' A wrapper for cowplot's plot_grid function.
#' @param target_plots A list of plots, one for each target
#' @param nrow The desired number of rows
#' @param ncol The desired number of columns
#' @return A plot grid
.plot_all_targets <- function(target_plots,
nrow = 2,
... |
a8a658d79e44935ce837c8f20ab0812b0fee261323f7532d28a0db12782a9746 | R | 17,027 | 419 | #' Calculate the expression entropy of each gene
#' @name Entropy
#' @usage Entropy(expr, r = 1)
#' @param expr The expression matrix. Rows should be genes and columns should be cells.
#' @param r A small fixed value to avoid log(0) of mean gene expression levels. The default value of r is set to 1, but can also be set... |
42eb7fb86407e1b1a7f097f818cda815a696c5f735285df454e2cb56578b36c7 | R | 17,057 | 340 | library(dplyr)
setwd("D:/nb_hans_wkstn2/G/PFC_429_final_Spring2021/Vanshika/muscat_DecontX/Analysis_Results/Evaluate_overlap_DeJager/PermutationTest")
ct_names=read.csv("celltype_order_Mic_Ast_namesR_v3.csv")
setwd("D:/home_wkstn/F/Brain_region_project/Average_expression/Results")
AG=read.csv("AG_average_expr... |
e983e7930658373d3f6a17e297517374c7410d941dddeb8fe4e32d833ed6125c | R | 17,061 | 340 | library(dplyr)
setwd("D:/nb_hans_wkstn2/G/PFC_429_final_Spring2021/Vanshika/muscat_DecontX/Analysis_Results/Evaluate_overlap_DeJager/PermutationTest")
ct_names=read.csv("celltype_order_Mic_Ast_namesR_v3.csv")
setwd("D:/home_wkstn/F/Brain_region_project/Average_expression/Results")
AG=read.csv("AG_average_expr... |
de535dbe3a38357ae61b877491010b0d5cd5e2bd6fbaf740db7b0a4ee389e86c | R | 17,104 | 405 |
# Get functions
library(monocle3)
source("/net/trapnell/vol1/home/readdf/trapLabDir/sharedProjectCode/utility/singleCellUtilFuncs.R")
# modStatus <- loadMonoclePackages()
library(tidyr)
library(ggplot2)
# Note: Need bedtools loaded for this! bedtools/2.29.2
library(cicero)
# Add this to stop R from formatti... |
7b7209fe11d85597d13cf5a80d6fa9968c4e8459673067ad1dc86d59abdfac83 | R | 17,133 | 466 | #!/usr/bin/R
# -----------------------------------------------------------
# Use the pathology to run some tests on linear mixed models:
# Last updated mid-2020 (exploratory analysis)
# -----------------------------------------------------------
library(cbrbase)
set_proj('DEVTRAJ')
source(paste0(bindir, 'multiRegion/lo... |
f05717ea11aeea0dece368bdf9b1af9cdadf1c971aee852fbef723b5c9aca89a | R | 17,194 | 566 | ---
title: 'SF: Read and preprocess raw stretch force measurements Ctrl, NTI, Naloxone'
author: "Yaromir Kobikov <kobikov.yaromir@gmail.com>"
date: "Date: `r format(Sys.time(), '%d/%m/%Y')`"
output:
word_document: default
html_document:
toc: true
toc_float:
collapsed: false
editor_options:
chunk_ou... |
79ec87492a75b1fa74a780d3045b595386fdc73428bfd78329dbd8d4cc858a28 | R | 17,195 | 378 | #!/usr/bin/R
# ------------------------------------------------------------------------------
# Investigate the fractional content in EC/HC and other celltypes with cognition
# Plot the boxplots and scatter plots for top vuln cell types
# Updated 12/08/2022
# ------------------------------------------------------------... |
f2b76b2b82323ab9202bd0218d80bc54bba2b4234032e9ebd60b275f2f30b20c | R | 17,298 | 332 |
#' archstabms__optimal_library_design
#'
#' Library design.
#'
#' @param ddpca_outpath path to ddPCA data (required)
#' @param position_offset residue position offset (default:0)
#' @param fitness_abundance_file path to abundance fitness data (required)
#' @param fitness_binding_file path to binding fitness data (requ... |
6a41ee0d9d19f531ad7f06c96bcade0dee16c143740c147007886482203d6d51 | R | 17,459 | 699 | test_that("pVals validation works correctly", {
# Helper function to create valid test data
create_valid_data <- function() {
controlVals <- matrix(rnorm(30), ncol = 3, nrow = 10)
testVals <- matrix(rnorm(30, mean = 1), ncol = 3, nrow = 10)
intOnly <- data.frame(cbind(controlVals, testVals))
myDesig... |
d6bf8bbb38f371e126f7979dc5504952461fbb4de1a31269b38842b1f61ce2dc | R | 17,493 | 455 |
# Helper function to send a vector of fixed and random effects. Returns a string that can be converted
# to a formula that's understood by lme4
getMixedModelFormula <- function(inputFixedEffects, inputRandomEffects){
# Formatted Random Effects
fixedFormulaPart = paste(inputFixedEffects, collapse = " + ")
# ... |
aadabcea9f8c9c9b9d4dece46349b2c85b0cf343635d520d441c6d12de1befee | R | 17,711 | 366 | library(dplyr)
setwd("D:/Projects/Large_scale_snRNA_seq/Brain_region_project/Brain_region_final/Evaluate_overlap_OteroGarcia/OteroGarcia_Supplement")
celltype_list2 = c("Ex01","Ex02","Ex03","Ex04","Ex06","Ex07","Ex08","Ex10","Ex13")
for (c in 1:length(celltype_list2)){
celltype=celltype_list2[[c]]
input_fi... |
229eb31ecec27e8a539a2f75b91b2da09530b01cd8fc01e1c6b8c99b8338b482 | R | 17,715 | 366 | library(dplyr)
setwd("D:/Projects/Large_scale_snRNA_seq/Brain_region_project/Brain_region_final/Evaluate_overlap_OteroGarcia/OteroGarcia_Supplement")
celltype_list2 = c("Ex01","Ex02","Ex03","Ex04","Ex06","Ex07","Ex08","Ex10","Ex13")
for (c in 1:length(celltype_list2)){
celltype=celltype_list2[[c]]
input_fi... |
bd2d9859e099a51896ad403c5f8f77504a30c3e358b261d1871c460a7f857e2e | R | 17,719 | 453 |
library(tidyr)
library(ggplot2)
library(glmnet)
library(ROCR)
library(data.table)
library(monocle3)
library(gridExtra)
library(RColorBrewer)
# Get shared functions between this and runRegressionModel.R
source("./utilityFunctions.R")
source("/net/trapnell/vol1/home/readdf/trapLabDir/sharedProjectCode/utility/singleCe... |
542bae4b73cf29fb234aff35b3d4c848833867a31fda80f4e4cc04c6d7d86042 | R | 17,743 | 617 | #' @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... |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.