sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
bdd96c18f635ea3ac3dcb005f3c9733572ca007ca5118810eb2d1cfd38016626 | R | 27,430 | 489 | ---
title: "Calling Hits on Vglut 410 Data"
author: "Stephen P Plassmeyer"
date: "7/17/2020"
output: html_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = FALSE)
source('../../../code/mpra_tools/mpra_tools.r')
library(ggVennDiagram)
```
# Load and Format Data
```{r}
compiled_counts <- fread('../... |
3e20fb93ef788470a2738f00446c6acd25f8cd071421446a3ee3ff74dcaf1133 | R | 27,497 | 614 | ### for MAGMA with locus coeruleus snRNA-seq populations
# MNT 27May2022
library(rtracklayer)
library(GenomicRanges)
#BiocManager::install("liftOver")
library(liftOver)
library(jaffelab)
library(sessioninfo)
library(here)
here()
#[1] "/dcs04/lieber/lcolladotor/pilotLC_LIBD001/locus-c"
# ==
## Create gene loca... |
41cc7f4c79fb513af47ae715dcc579bf2f648217de4bb62063fa8bbaa6260af6 | R | 27,566 | 744 | #linear mixed effects models: relationship between each QC metric and each cortical phenotype (cortical thickness, volume, surface area)
#with Desikan Killianey and Glasser (HCP) parcellations
library(effectsize)
library(parameters)
library(plyr)
library(lmerTest)
library(ggpubr)
library(ggplot2)
library(ggseg)
libra... |
3a8bf804f00ede7b03ec39c11e2cbd5e41ef2c499befdf47166b3ee706a0a861 | R | 27,678 | 869 | #
# FCS conversion program
# Last Updated: 24 March 2020 by Max Qian
# Support both BD and Accuri Files
# Both FCS2.0 and FCS3.0 are now output to 0 to 4095 (previously FCS2.0 is 0 to 1023)
suppressMessages(library(parallel))
suppressMessages(library(flowCore))
suppressMessages(library(openxlsx))
suppressMessages(libr... |
87a786a720e98de9b97e92c1a7efe67e5f47a36ebd15ad1bab3a30ca066592be | R | 27,697 | 621 | ### LC snRNA-seq analysis
### Feature selection with deviance & clustering
### qrsh -l bluejay,mf=
### Initiated: MNT 31Dec2021
library(SingleCellExperiment)
library(DropletUtils)
library(scater)
library(scran)
library(scry)
library(batchelor)
library(bluster)
library(BiocParallel)
library(jaffelab)
library(gridEx... |
c23868573321dd5631ce1d82243276ee5804e91b04e04aa01e802f25890efba2 | R | 27,732 | 411 | ## Author: Youtao Lu <luyoutao@sas.upenn.edu>
## Copyright (c) 2017-2023, Youtao Lu and Junhyong Kim, Department of Biology, University of Pennsylvania
## Copyright (c) 2017-2023, James Eberwine, Perelman School of Medicine, University of Pennsylvania
## All Rights Reserved.
## This Source Code Form is subject... |
717960409c517f4e35b768afd77d7367a77f91f3cf75eb4c0ebe0f28fa5dd8a0 | R | 27,867 | 639 | # Setting Working Directory
setwd("/Users/alanx/OneDrive/Desktop/2019_killi_rna_data/2019_killi_rna_data_descriptor/count_table")
# Library Loading
library(DESeq2) # Version 1.40.1
library(ggplot2) # Version 3.4.2
library(clusterProfiler) # Version 4.8.1
library(org.Dr.eg.db) # Version 3.17.0
library(Annotat... |
a57ab50cd02d1513a37668e5dcd64469ab925038875a038f4b9892a6108f16b9 | R | 27,884 | 464 | ---
title: "Figure N Comparing Libaries 455 to 546"
author: "Anthony Fischer"
date: '2022-12-13'
output: html_document
editor_options:
chunk_output_type: console
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
source("../../../../code/mpra_tools/mpra_tools.R")
library(Hmisc) # Thi... |
4ea1fb86f145b01452b14f2be85492e6c7fa6458eebc22fc62ae6794071c4f98 | R | 28,058 | 634 | ### LC snRNA-seq analysis
### Exploration with other datasets
### qsub -l bluejay,mf=76G,h_vmem=80G
### Initiated: MNT 06May2022
library(SingleCellExperiment)
library(scater)
library(scran)
library(scry)
library(batchelor)
library(BiocParallel)
library(jaffelab)
library(gridExtra)
library(here)
library(sessioninfo... |
1aa9cffa78e9490e2c53739450ab8261660788c89e36f088678ed556b4d52f6d | R | 28,097 | 500 | ---
title: "Calling Hits on N2a 410 Data with LMM"
author: "Stephen P Plassmeyer"
date: "Last Updated: 07/11/2021"
output: html_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = FALSE)
source('../../../code/mpra_tools/mpra_tools.r')
```
Updates 08-05-2020:
* Moved threshold sele... |
b116aac9fb1e8189aaf582127061ee82f54c01a81f04a91aa7e59a2e9f8a234c | R | 28,130 | 560 | ---
title: "Evaluating Effect of DNA Normalization on Variance"
author: "Stephen P Plassmeyer"
date: "8/5/2020"
output: html_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
source('../../../code/mpra_tools/mpra_tools.r')
library(ggsignif)
library(patchwork)
library(ggpubr)
```
# Load and ... |
9b10a9ca23af9e78a0ee449f6f8ef4833d3a90dcb789e24ba1b64faff80cc457 | R | 28,276 | 413 | ## Author: Youtao Lu <luyoutao@sas.upenn.edu>
## Copyright (c) 2017-2023, Youtao Lu and Junhyong Kim, Department of Biology, University of Pennsylvania
## Copyright (c) 2017-2023, James Eberwine, Perelman School of Medicine, University of Pennsylvania
## All Rights Reserved.
## This Source Code Form is subject... |
706d78db19d698d7686b0a7cacd92ec6126c308ce50644956805ba6bf3781a6d | R | 28,312 | 888 | #
# FCS conversion program
# Last Updated: 24 March 2020 by Max Qian
# Last Updated: 19 October 2021 by Yue Liu
# Support both BD and Accuri Files; Support FCS3.1 and updated format of compensation matrix
# Both FCS2.0 and FCS3.0 are now output to 0 to 4095 (previously FCS2.0 is 0 to 1023)
suppressMessages(library(par... |
8d041e70bb169c39602120dc1b030740e69280e577087d37418e02fd82239676 | R | 28,347 | 644 |
# PACKAGES ----------
# Data Manipulation
library(tidyverse)
library(reshape2)
# Modeling & Differential Expression
library(limma)
library(edgeR)
library(variancePartition)
# Plots
library(ggpubr)
library(pals)
library(RColorBrewer)
library(wesanderson)
library(svglite)
# Other
library(doParallel)
# BEFORE USING... |
04f3a7fdedf70e73af8a76f9794ab78d5945d45db79660225c9dcd2c16653d59 | R | 28,463 | 617 | ---
title: "Cross-Experiment Correlation"
author: "Stephen P Plassmeyer"
date: "4/3/2020"
output: html_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
source('../../code/mpra_tools/mpra_tools.r')
```
```{r}
compare_experiments<-function(data, experiment_parameters){
compiled.expression<-... |
a0b1d871bf98f6c6add6f728726232cb4e36afbdd8d067126073b363a43ad8f4 | R | 28,955 | 594 | ---
title: 'Mortality analysis including main Figure 2'
author: Cas Swarte
output: html_notebook
# ==========================================================================================
# By: Weersma Group, TransplantLines (UMCG)
#
# UMCG Transplantlines Project da... |
625d59fe82bff38e4cfce6fa9369f3decb8426d5828384d34fc037e35d221e12 | R | 28,982 | 754 | ---
title: "DCN - Stage2 Analyses"
author: "<h3>by Michael Demidenko</h3>"
date: "`r format(Sys.time(), '%B %Y')`"
output:
html_document:
theme: united
highlight: tango
toc: yes
number_sections: yes
toc_depth: 2
toc_float:
collapsed: yes
smooth_scroll: yes
code_folding: hide
... |
a79d88c2379c760fbd0b47322c3bc6c2a0edd5a14484b4eb4240d7f5e309382f | R | 29,111 | 579 | #################################
#
#
#
#
#################################
##################Setting the work space##################
library(M3C)
#set the workspace:
rm(list = ls())
dev.off()
cat("\014")
#Start here
setwd("/Users/adityanatu/Library/Mobile Documents/com~apple~CloudDocs/Project_2023/Juliet_Data_Ana... |
e5535cedefdd9cd9ab64700d4d73db40be65dec6076797198b81027dc7d5dee3 | R | 29,154 | 554 | plotMisha <- function(main_f,object,targetGene,outDir=outDir,gene_track=readRDS(paste0('/home/hpc/bonev/annotations/',genome,'/',genome,'_gviz.RDS')),out_f=NULL,upstream=1e5,downstream=1e5,plotClusters=levels(object),chipTracksToExtract = gtrack.ls('scATAC.E14'),conditions='',targetEnh=NULL,plotOrder=list(scores=TRUE,a... |
03bc26479b0f271f8c22c6f1b6f287b164fc1900b048dc0895fb6cfa15b28100 | R | 29,239 | 821 | #' Repulsive textual annotations.
#'
#' \code{geom_text_repel} adds text directly to the plot.
#' \code{geom_label_repel} draws a rectangle underneath the text, making it
#' easier to read. The text labels repel away from each other and away from
#' the data points.
#'
#' These geoms are based on \code{\link[ggplot2]{g... |
eac365cabbe30077d7ea9a3208bf07808e0a3ed5108fea525746ed8396c0f778 | R | 29,274 | 597 | ## Youtao Lu <luyoutao@sas.upenn.edu>
## Copyright (c) 2017-2022, Youtao Lu and Junhyong Kim, Department of Biology, University of Pennsylvania
## Copyright (c) 2017-2022, James Eberwine, Perelman School of Medicine, University of Pennsylvania
## All Rights Reserved.
## This Source Code Form is subject to the terms of... |
d87d062eabe5d6f45405022af80787e4437be127984fbbe3add04d4aad528d7b | R | 29,526 | 601 | ---
title: "Getting started with the pwr package"
author: "Clay Ford"
date: "`r Sys.Date()`"
output: rmarkdown::html_vignette
vignette: >
%\VignetteIndexEntry{Getting started with the pwr package}
%\VignetteEngine{knitr::rmarkdown}
%\VignetteEncoding{UTF-8}
---
The basic idea of calculating power or... |
faadf49963b07ebb2eb16903fe2eaf4a504bec4b7a7e00d08eac957763748e8c | R | 30,043 | 730 | ---
title: "Simulating IVT Timecourse"
author: "Stephen P Plassmeyer"
date: "7/14/2020"
output: html_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
source('../../code/mpra_tools/mpra_tools.R')
```
```{r}
compiled_counts <- fread('../../data/compiled_counts/asd3utr_compiled_counts_as_of_0... |
97094e98822e2885b33e4e4fcebd94535ebc4b691c417929afbdbd3500965ff3 | R | 30,241 | 839 | ---
title: "Perceived sensitivity of brain data"
author: "Shenyang Huang"
date: "09/04/2023"
output:
html_document: default
word_document: default
pdf_document: default
---
Script written 07/20/2021 for first submission
Script updated 09/04/2023 for JLB revision 1
# Set up
## - R library
```{r se... |
801c98e66f459b2628454c18d10ef29f45825d2a4ec565b0c6522a3014c2ab37 | R | 30,285 | 591 | ---
title: "Mapping back variants from Mike's Library to the WES/WGS Tables"
author: "Stephen Plassmeyer"
date: "Last Updated November 23, 2021"
output: html_document
---
Update November 23, 2021:
* July 24, 2020: I re-ran the script, to pull out the sampleID or patientID from the WGS/Exome tables.
* July 24, 2020: I... |
465dff1a0512dfbdaba6d5d80dd7b9b2230ec01bda80887bc10a61bbe363e677 | R | 30,811 | 495 | library(GenomicFeatures)
library(DESeq2)
library(Rsamtools) #needed for BamFileList
library(rtracklayer) #needed to import GTF as GRanges object
library(GenomicAlignments) #used for summarizeOverlaps
library( "RColorBrewer" ) #for making heatmaps
library(gridExtra)
library("pheatmap") #used for heatmaps
library(ggrepel... |
a0ef08876461c40e77c03a9f53bc41542a9b8f570bd802c7e4bce5d524256ae4 | R | 30,966 | 828 | ---
title: "Effect Size of Null Comparisons as Function of BC Coverage"
author: "Stephen P Plassmeyer"
date: "6/22/2021"
output: html_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
source('mpra_tools.R')
library(patchwork)
#Tony's notes - rewrote code to pull files locally, and ... |
c822f7f94005ac08c0d502442600509acf867fb60b634344d872e651ca2ac96a | R | 31,013 | 520 | ## Youtao Lu <luyoutao@sas.upenn.edu>
## Copyright (c) 2017-2022, Youtao Lu and Junhyong Kim, Department of Biology, University of Pennsylvania
## Copyright (c) 2017-2022, James Eberwine, Perelman School of Medicine, University of Pennsylvania
## All Rights Reserved.
## This Source Code Form is subject to the terms of... |
26c08631f84df82c7af90cf83c590e9b7607438da8ff0ae1435cb762a4f57255 | R | 31,018 | 521 | ## Author: Youtao Lu <luyoutao@sas.upenn.edu>
## Copyright (c) 2017-2023, Youtao Lu and Junhyong Kim, Department of Biology, University of Pennsylvania
## Copyright (c) 2017-2023, James Eberwine, Perelman School of Medicine, University of Pennsylvania
## All Rights Reserved.
## This Source Code Form is subject to the... |
cce01c8831d3da64654e05935fa221f83ed1bf9697a32b2ba3af3673c605717e | R | 31,034 | 832 | ## LOAD PACKAGES ----------
# Data manipulation
library(tidyverse)
library(rlist)
library(readxl)
# Plots and visualizations
library(grid)
library(viridis)
library(ggrepel)
library(ggpubr)
library(svglite)
# Statistics
library(rstatix)
# library(emmeans)
# library(multcomp)
# library(multcompView)
# Matching samp... |
658041216c0415b865bf7dc4e27d6d7e417c0552bb1205c5f9e45224a00d65e9 | R | 31,132 | 802 | ---
title: "Streamlined GTEx"
output: html_document
author: Annika Vannan, avannan@asu.edu
date: 01/14/23
---
## Set-Up
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
options(dplyr.inform = FALSE)
```
### Load Libraries
Make sure you have the following libraries downloaded before using this script:
-... |
f9553a382287a1e9718c2f01380b27e198c1dce62e0043f984b31f372b7c877c | R | 31,273 | 638 | ---
title: "Immunosuppresive medication analysis"
author: Shixian Hu & Cas Swarte
output: html_notebook
# ==========================================================================================
# By: Weersma Group, TransplantLines (UMCG)
#
# UMCG Transplantlines P... |
ad59be13f4a2685a3b436886aa0f455f1e8c9c06e8c3bec1fdc43546ea29dc40 | R | 31,402 | 662 | cembav2env <- rlang::new_environment(
data = list(
# current L2 clustering updated at 220716
L1CMeta = data.frame(
L1Id = seq(3),
L1Label = c("NonN", "GLUT", "GABA"),
L1Reso = c(0.6, 1.0, 0.7)
),
# * update L3 clustering with the selected resolutio... |
418ca6b4b17ea06f419ee8ecadd4529a896a73c0944b79c0ccc999a04aebcb2e | R | 31,615 | 455 | ## Author: Youtao Lu <luyoutao@sas.upenn.edu>
## Copyright (c) 2017-2023, Youtao Lu and Junhyong Kim, Department of Biology, University of Pennsylvania
## Copyright (c) 2017-2023, James Eberwine, Perelman School of Medicine, University of Pennsylvania
## All Rights Reserved.
## This Source Code Form is subject to the... |
b9f5865e17012b9907546ff32d8951cc8dbb7a022b43e9808a98eba6d26d00b2 | R | 31,790 | 583 | ### R Script to analyse data for manuscript: MoGA project for Paper:
### Becker, Yu & Cabeza, 2023
## study 1: replication of Yu et al. - Solving problems with an Aha! biases the choice over monetary rewards
## study 2: fMRI study (taken from Becker, Sommer & Cabeza, 2023)
## AHA response (no AHA! moment) 1 <... |
c8cc46024b0af5d6ee53b91e96989dde328bb14826bb27216f9869ba2cc78dee | R | 31,957 | 751 | createOncoMatrix = function(m, g = NULL, chatty = TRUE, add_missing = FALSE, cbio = FALSE){
if(is.null(g)){
stop("Please provde atleast two genes!")
}
subMaf = subsetMaf(maf = m, genes = g, includeSyn = FALSE, mafObj = FALSE)
if(nrow(subMaf) == 0){
if(add_missing){
numericMatrix = matrix(data =... |
a8708f9d5c098a1ed80a65cb3b8e8b66d537c8293d369cb3eb92be844aad8ece | R | 32,095 | 824 |
#This script computes diffusion map, using deveopmental gene module to contruct pseudotime trajectories.
## ----receive input from nextflow----------------------------------------------
#Get parameters
args <- commandArgs(TRUE)
path<-args[1]
file<-args[2]
markers<-args[3]
modules<-args[4]
print(path)
set.seed(123)
... |
4613b8cefc89e5be9be08d5c79c985fff8ae64277e1ed487bdac5e712ca5c242 | R | 32,125 | 829 | ####╔═════ ═════╗####
####💠Visualizations💠####
####╚═════ ═════╝####
cli_h2("┗ [SCRIPTS] Loading vizualisation functions")
#--------------------#
####🔺Correlation ####
#--------------------#
corr_matrix_plot <- function(df, vars, title = "") {
return(df
|> mutate(
across(where(is.character),... |
cf7e0db17273330b81af5b480f57d1b2dc068a16ad755db7243536e2197b651f | R | 32,272 | 806 | #library(GSVA)
# library(singleCellTK)
# source("sergio_analysis_functions.R")
library(BiocParallel)
library(GSVA)
library(Seurat)
# library(SeuratData)
library(dplyr)
library(ggrepel)
library(ggplot2)
# to be bench marked
library(gsdensity)
library(CelliD)
# library(escape)
library(VAM)
library(DescTools)
library(GSEA... |
eb89384c026a3b16ed2a9d2d1188fe97b9de31b52bf03ef274f05917c1645006 | R | 32,334 | 578 | ---
title: "N2a 410 MPRA QC"
author: "Stephen P Plassmeyer"
date: "Last Updated: 11/18/2020"
output: html_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = FALSE)
source('../../../code/mpra_tools/mpra_tools.r')
```
# Overview
In this notebook, quality checks are run to evaluate library coverage,... |
10a9711711bd3f71607642b4f6b4beec4faad2bfdcb8607e2b3bd2737cc353d5 | R | 32,485 | 639 | ### LC snRNA-seq analysis
### Cluster agglomeration
### Motivation is that we want a less-resolved atlas for purposes of
### spatial spot-level deconvolution; something akin to the 'step 2' from
### Tran-Maynard et al. Neuron 2021 (hierarchical clustering-based)
### qrsh -l bluejay,mf=92G,h_vmem=96G
### In... |
60a55c03205db85f3311ceb4e631f2b4a27910112be2e48f7cbb173f91ebc860 | R | 32,661 | 762 | # pain vs control
merFISH_integrated = readRDS(file = "./RDS/merFISH_final.1101.RDS")
merFISH_integrated$subcluster = factor(merFISH_integrated$subcluster, levels = levels(merFISH_integrated_L3$subcluster))
#
merFISH_integrated_pain = subset(merFISH_integrated, orig.ident %in% c("Pain1", "Pain2", "Pain3", "Pain4", "... |
5949ff4abd8b428b5adfd0928f01543e40fcdd60e6ae7d01d9e18bf44d3bb91a | R | 32,934 | 515 | ---
title: "FIGURE 3 ANALYSIS"
output: html_notebook
---
###############################################
#################### SETUP ####################
###############################################
#Import packages
```{r}
library(tidyverse)
library(igraph)
library(monocle3)
library(Seurat)
library(plotly)
library(... |
bce3a7d43ead9835dc2c916382e5e57a3a424c9590ce485beaf7f96f09b61181 | R | 32,983 | 893 | # Automatically check and install necessary packages that were used in R v 4.0
if (!require("pacman")) install.packages("pacman")
pacman::p_load(simsem, plyr, tidyverse,ggdist, ggplot2, ggpubr, tidyquant, corrplot, reshape2,
data.table,ggplot2,esemComp,
Hmisc,nFactors,car,psych, paran, #fo... |
aace98955f3fb657d7b56d4ceb826260aee85eb49e104da716057b3231d75417 | R | 33,365 | 626 | library(Seurat)
library(dplyr)
library(patchwork)
library(metap)
library(ggplot2)
library(wesanderson)
library(scater)
library(DoubletFinder)
library(purrr)
library(tibble)
library(scCATCH)
library(SingleR)
library(scRNAseq)
library(celldex)
library(progeny)
library(tidyr)
library(pheatmap)
library(biomaRt)
library(Sin... |
07e5ccc73918f9f06650bb8b34aa347c6d2b32710bee34690bdecb501edd6e26 | R | 33,487 | 450 | library(GenomicFeatures)
library(DESeq2)
library(Rsamtools) #needed for BamFileList
library(rtracklayer) #needed to import GTF as GRanges object
library(GenomicAlignments) #used for summarizeOverlaps
library( "RColorBrewer" ) #for making heatmaps
library(gridExtra)
library(ggrepel) # for labeling points on plot with ge... |
90b4c914fdec3bf64faf9cb6e8512dc0ce0cf5cf3a79cdb09f1f69b96a83754e | R | 33,726 | 525 | source('scripts/config.R')
source('scripts/aux_functions.R')
source('scripts/plot_functions.R')
source(paste0(main_dir,'results/hg38/hic/config.R'))
source(paste0(main_f,'scripts/main_functions.R'))
source(paste0(main_f,'scripts/aux_functions.R'))
source(paste0(main_f,'scripts/plot_functions.R'))
source(paste0(main_f,... |
3320d9d847053b84bd1140ac87d620c4a43884c89e5dcf3670c5aa0021417724 | R | 33,771 | 856 | ---
title: "MonkeyScRNA"
author: "Xiangning Xue"
date: '2023-04-01'
output: html_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = FALSE,
eval = FALSE)
```
```{bash}
srun -n1 -t02:00:00 --pty bash
module load gcc/10.2.0 r/4.2.0
R
```
## Prepare the files
Craete HDF5Summar... |
bfe37873bd126f4b0b1b6fd46783eded1b6e7d2697eb370020083e1c92af0ab3 | R | 33,855 | 631 | ---
title: "N2a 410 MPRA QC"
author: "Stephen P Plassmeyer"
date: "Last Updated: 11/18/2020"
output: html_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = FALSE)
source('../../../code/mpra_tools/mpra_tools.r')
library(ggpubr)
```
# Overview
In this notebook, quality checks are run to evaluate l... |
bd80e5ba11638d21ea5b86187f40ebe924ae95e40d2b46a82eb9359efb17f8f3 | R | 34,021 | 666 | ---
title: "Supplemental_Table_2"
author: "Anthony Fischer"
date: '2022-06-07'
output: html_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
pkgTest <- function(x){
if (!require(x, character.only = TRUE)){
install.packages(x,dep = TRUE)
if(!require(x, character.only =... |
34a1e9a7ec21e6899b22df0fddf7665ed4023cc0385bfdc321dc3243847055c0 | R | 34,141 | 819 | ###############################################################################
# Neural substrates of parallel devaluation-sensitive and
# devaluation-insensitive Pavlovian learning in humans
# analysis for supplementary materials
# last modified on AUGUST 2023
########... |
74e686ae6c6f0f8c194da15de9b30a110f240a5363701d1e85982a58f6cf06be | R | 34,164 | 358 | library(dplyr)
library(tibble)
library(tidyverse)
library(ggrepel) #for genes points on plot
library(gridExtra)
# script to produce plot of (zonal) positions of teto-Olfr17 expressing cells along a curve of the MOE (Figure 7E)
# the curve is drawn to start medially along the septum (in zone1) and move distally (towa... |
532984adf49d3f1a3bc510dc8b8ac677b1d6dc58b581196f43b425b60c0f52e1 | R | 34,363 | 671 | ---
title: "Cross Experiment Reproducibility for Existing 410 Data"
author: "Stephen P Plassmeyer"
date: "4/17/2020"
output: html_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
source('../../code/mpra_tools/mpra_tools.R')
```
### Load Data
```{r}
compiled_counts <- fread('../../data/compi... |
7509220ff9a5457c11769250510d65eed4232c2d70e111c8499b9ce5e3082ee2 | R | 34,513 | 1,084 | #' Normalization single-nuclei methylation gene-score data (gmat).
#'
#' We will use a transform function on the gmat, then
#' log10CPM normalizaze (option, default not run), scale,
#' findvariablefeatures, and get pca with all the features.
#'
#' @return Seurat object
#' @import Seurat
#' @export
normalizeMethyGmat <-... |
dd47b28216bf3f502bbafec23afeeeb26c3291410d1cd7d05cd357abee8f0bc3 | R | 34,543 | 877 | ### some functions for spatial transcriptome
# gate points
library(gatepoints)
gate_points = function(obj, image = image){
plot(obj@images[[image]]@coordinates[, 1:2], pch=20, cex=0.1)
selectedPoints <- fhs(obj@images[[image]]@coordinates[, 1:2], mark = TRUE)
c(selectedPoints)
}
# gene ontology enrichments
li... |
96379c33a1976a145dd7df1dc38d33cb298b8ac28be52e49a26f07a816e7d3b4 | R | 34,885 | 600 | #find the assoiations between exposures and confounding variables
rm(list=ls())
gc()
####################
## Load libraries ##
install.packages('pheatmap')
install.packages("lmerTest")
install.packages("robustHD")
install.packages("fmsb")
library(data.table)
library(dplyr)
library(readxl)
library(pheatmap)
library(lme... |
94282c1393a20309264070077fc0ca5f3c8cedad4849b463734180af1eb9a41e | R | 34,971 | 1,216 | library(tidyverse)
library(fs)
library(yardstick)
library(ComplexHeatmap)
library(khroma)
library(igraph)
library(limma)
library(ggrepel)
library(patchwork)
source("scripts/styling.R")
# Load data ---------------------------------------------------------------
# for testing, since loading from original data files t... |
d16095ebd3ab8113f1becfa5a5749c4ac9760de6d920de70663be8f6367f5a45 | R | 35,255 | 499 | ---
title: "Evaluating Alignment-Based Read Filtering"
author: "Stephen P Plassmeyer"
date: "5/08/2020"
output: html_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
source('../../code/mpra_tools/mpra_tools.R')
library(ggsignif)
library(ggpubr)
```
Last Updated: May 10, 2020
# Major Takea... |
9e83179b4ade76f6d5b7b8627bbb4e2c6be3a93908fdbb96b6a8b29a873585df | R | 35,385 | 1,183 | # ============================ #
# 3. APOE interactions: SABRE #
# ============================ #
## Set up ----
filepath <- ""
setwd(filepath)
## Load libraries ----
library(data.table)
library(dplyr)
library(magrittr)
library(mice)
library(purrr)
library(tidyr)
## Read in data ----
# Principal components (EUR)
eu... |
dcd37b281eea80c00a22cbe9af4c17764da3c692afbef0e7b6d0520169d65788 | R | 35,708 | 798 | ## LOAD PACKAGES ----------
# Data manipulation
library(tidyverse)
library(rlist)
library(readxl)
# Plots and visualizations
library(grid)
library(viridis)
library(ggrepel)
library(ggpubr)
library(svglite)
# Gene annotations
library(biomaRt)
library(org.Mm.eg.db)
library(org.Rn.eg.db)
library(limma)
# Statistics
... |
80e49fbda16850b0b04870ba80e3d9da65fd48891468dc0786c82d5ef6b1c7e4 | R | 36,142 | 690 | library(tidyverse)
library(ggplot2)
library(ggpubr)
library(ggridges)
library(infotheo)
library(doFuture)
# parallel: set number of workers
cores <- 14
registerDoFuture()
plan(multisession,workers = cores)
library(doRNG)
#Process function to add condition ids and duplicate ids
process_embeddings <- function(embbedings... |
b22459568970daaaa2b86bbd135f64940c7f00098c90da70553625e17cc3dcb0 | R | 36,288 | 722 | ---
title: "Distribution of Effect Sizes for 410 Experiments"
author: "Stephen P Plassmeyer"
date: "4/21/2020"
output: html_document
---
Update May 11, 2020 -- Re-organized code, cleaned up and added run_analysis and compare.variance functions
Update May 28, 2020 -- Re-ran with re-filtered counts from May 10, 2020
Upd... |
e160ef5b3bfabbcf3bbcad47befec54516f62afd470bb2535cd3c8bc7d10c1cb | R | 36,578 | 669 | library(tidyverse)
library(gg3D)
library(ggsignif)
library(ggpubr)
samples_separation <- function(embbedings,
compare_level=c('equivalent condition',
'diagnosis',
'cell',
... |
9fc638a5d3e45d03a4a78338b3ee9afda96490f39d3f2d3a0117da9545b42fa9 | R | 37,208 | 498 | ## Author: Youtao Lu <luyoutao@sas.upenn.edu>
## Copyright (c) 2017-2023, Youtao Lu and Junhyong Kim, Department of Biology, University of Pennsylvania
## Copyright (c) 2017-2023, James Eberwine, Perelman School of Medicine, University of Pennsylvania
## All Rights Reserved.
## This Source Code Form is subject to th... |
516d976f2b92317f60838362bb184c9bedaee6ea3af59c6d1f1fb0aefe884857 | R | 37,856 | 498 | ## Author: Youtao Lu <luyoutao@sas.upenn.edu>
## Copyright (c) 2017-2023, Youtao Lu and Junhyong Kim, Department of Biology, University of Pennsylvania
## Copyright (c) 2017-2023, James Eberwine, Perelman School of Medicine, University of Pennsylvania
## All Rights Reserved.
## This Source Code Form is subject to th... |
4b3426d21c4f416a45ec426f86c7c4f79751d503508b1b03aea7e9beea68ebcd | R | 37,995 | 724 | library(tidyverse)
library(gg3D)
library(ggpubr)
#Process function to add condition ids and duplicate ids
process_embeddings <- function(embbedings,dataInfo,sampleInfo){
dataInfo <- dataInfo %>% select(sig_id,cmap_name,duplIdentifier) %>% unique()
sampleInfo <- suppressMessages(left_join(sampleInfo,dataInfo))
... |
6a85999f47ae4dba191e1a67bd047e16e3a6d612a5a8c721b035bc6c17f0d4b9 | R | 38,139 | 640 | ---
title: "Calling Hits on N2a 410 Data"
author: "Stephen P Plassmeyer"
date: "Last Updated: 11/18/2020"
output: html_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = FALSE)
source('../../../code/mpra_tools/mpra_tools.r')
library(ggVennDiagram)
```
Updates 08-05-2020:
* Moved... |
45e7d325fe5a93b87c174d42734fa5a6f742e9737c4b9aaaa876a53364b33ddb | R | 38,415 | 547 | ## Author: Youtao Lu <luyoutao@sas.upenn.edu>
## Copyright (c) 2017-2023, Youtao Lu and Junhyong Kim, Department of Biology, University of Pennsylvania
## Copyright (c) 2017-2023, James Eberwine, Perelman School of Medicine, University of Pennsylvania
## All Rights Reserved.
## This Source Code Form is subject to th... |
7308b8f233ed20d99a1ff9ffb32ef1229f43882be8409f482116634a91a42be1 | R | 38,421 | 757 | ## Author: Youtao Lu <luyoutao@sas.upenn.edu>
## Copyright (c) 2017-2023, Youtao Lu and Junhyong Kim, Department of Biology, University of Pennsylvania
## Copyright (c) 2017-2023, James Eberwine, Perelman School of Medicine, University of Pennsylvania
## All Rights Reserved.
## This Source Code Form is subject to th... |
7c029c768123c37cf57fd6f09ec100fe0da71675680585f2f65ae00ee9adb247 | R | 38,512 | 821 | ---
title: "Figure 2"
author: "Stephen P. Plassmeyer"
date: "4/24/2021, Updated 11/23/2021"
output: html_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
source('../../../../code/mpra_tools/mpra_tools.r')
library(ggpubr)
library(MASS)
library(ggrepel)
theme_set(theme_bw(base_s... |
9d1bc182818ae9d22590c1510db1b68bbdd48b635d44f3fec0d48baa04c0994d | R | 38,583 | 547 | ## Author: Youtao Lu <luyoutao@sas.upenn.edu>
## Copyright (c) 2017-2023, Youtao Lu and Junhyong Kim, Department of Biology, University of Pennsylvania
## Copyright (c) 2017-2023, James Eberwine, Perelman School of Medicine, University of Pennsylvania
## All Rights Reserved.
## This Source Code Form is subject to th... |
ac6dac877121a2a65ce8c8dc6a5510444aff09f2532820276f1b64dce76650e9 | R | 38,861 | 809 | #figure1
Seurat.harmony <- readRDS("F:/code/Seurat.harmony.rds")
##Figure1 tsne
pdf("all_cell_tsne.pdf",height=6, width=6)
p1<-DimPlot(Seurat.harmony,reduction = "tsne",label = TRUE)+theme(legend.position = "none")
plot(p1)
dev.off()
dev.new()
##major cluster
my_levels <- c("0","1","2","3","4","5","6","7","8"... |
c3806de61274d9fe102a348a0f32e9d96e2ef4854ab3df6b3ef3c73492fdc43f | R | 39,193 | 925 | ---
title: "Streamlined Conservation"
output: html_document
author: Annika Vannan, avannan@asu.edu
date: 01/07/23
---
## Set-Up
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
options(dplyr.inform = FALSE)
```
### Load Libraries
Make sure you have the following libraries downloaded before using this sc... |
168145d6e022e7495e193dd063e54ea4d6376b15fa88f89f38f1bc10ac509bb3 | R | 39,213 | 619 | ---
title: "FIGURE 1 ANALYSIS"
output: html_notebook
---
###############################################
#################### SETUP ####################
###############################################
#Install Packages
```{r}
library(tidyverse)
library(igraph)
library(monocle3)
library(Seurat)
library(plotly)
library... |
80a3c3f996bd963d2a4db64172fc59805d3091014a64f2db3eedf26eded39d54 | R | 39,312 | 560 | ---
title: "Associations_PFN_Cognition"
author: "Arielle Keller"
date: "3/21/2022"
output: html_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
options(width=250)
library(tidyr)
library(dplyr)
library(ggplot2)
library(lsr)
library(lme4)
library(lmerTest)
library(mediation)
library(ggcorrplo... |
7a3e3cfc8462e0c123dbb9205f13331fbce135a5acfb1bc96cd1cd985ca8ec82 | R | 39,358 | 1,005 | ---
title: "Pooled ASD 3'UTR Comparison — Determination of Barcode Effects"
author: "Stephen P Plassmeyer"
date: "6/2/2021"
output: html_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
source("mpra_tools.R")
theme_set(theme_bw()+theme(text = element_text(size = 10)))
```
# Pre-Processing ... |
2d66843c3bec861932050a5078652e157d0693642a8f6ae33ab421810bf109ce | R | 40,932 | 1,134 | ---
title: "Differential abundance analysis"
author: Cas Swarte
output: html_notebook
# ==========================================================================================
# By: Weersma Group, TransplantLines (UMCG)
#
# UMCG Transplantlines Project data analysis... |
f52b3b7a20db6b2a7fafd24d666b6dd9bbafcd601647aea653d384fe8ea2f85e | R | 42,437 | 689 | ---
title: "Comprehensive Analysis of ASD 3'UTR Experiments"
author: "Stephen P Plassmeyer"
date: "4/07/2020"
output: html_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
source('../../code/mpra_tools/mpra_tools.r')
```
### Load Data
```{r}
compiled_counts <- fread('../../data/compiled_cou... |
dc02936702ef29c9a246542e3c3fbf961f3a4f0831355a5d205076f5085622b2 | R | 42,453 | 1,095 | setwd(file.path(path.expand(dirname("~")), "Downloads"))
library(tidyverse)
library(lme4)
library(car)
library(zoo)
library(ggplot2)
library(qqplotr)
library(patchwork)
library(interactions)
library(effects)
library(MuMIn) # for effect size
library(sjPlot)
library(dplyr)
library(performance)
library(lmtest)
library(cor... |
70790323fd9146be09486dd7ca0d71df83decd93254c26479984a2b8a77fe773 | R | 42,908 | 903 | library(tidyverse)
library(reshape2)
library(ggsignif)
library(ggpubr)
library(scales)
library(patchwork)
library(gridExtra)
library(doFuture)
# parallel: set number of workers
cores <- 16
registerDoFuture()
plan(multisession,workers = cores)
r2 <- function (x, y) cor(x, y)^2
scientific_10 <- function(x) {
parse(te... |
cb58697e923b84ff7a2dd174e55c3c3e44222204c599d67a703836f5dab553d8 | R | 43,996 | 952 | ---
title: "Analysis of NovaSeq N2a and Vglut Data"
author: "Stephen P Plassmeyer"
date: "7/1/2020"
output: html_document
---
Updated 07-12-2020: Re-ran after fixing the aggregate.counts issue in mpra_tools.R and re-running the count compilation.
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
source('... |
1aedf0e3ba1a49c1f8f307d49ecf014c6eabb7ff0e597848849700d879cdfd17 | R | 44,250 | 891 | ---
title: "Calling Hits for 410 & 455 Data"
author: "Stephen P Plassmeyer"
date: "5/18/2020"
output: html_document
---
Updated May 26, 2020, with added annotations for pLI and LoF Intolerance.
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
source('../../code/mpra_tools/mpra_tools.R')
library(ggsignif... |
72795ca31e6aad1103f71f60f9482e20d165e8ba49bce47f62fc7e7a86b34875 | R | 45,443 | 687 | ## Author: Youtao Lu <luyoutao@sas.upenn.edu>
## Copyright (c) 2017-2023, Youtao Lu and Junhyong Kim, Department of Biology, University of Pennsylvania
## Copyright (c) 2017-2023, James Eberwine, Perelman School of Medicine, University of Pennsylvania
## All Rights Reserved.
## This Source Code Form is subject to th... |
7d9f53f245644c15ab133ceee45c3f56c67ccf9b3708c6f891534c56706ee938 | R | 45,625 | 690 | library(SeuratDisk); library(Seurat); library(dplyr); library(ggplot2); library(patchwork);library(RColorBrewer)
library(ktplots); library(pheatmap); library(viridis); library(tidyverse)
library(CellChat); library(nichenetr); library(hrbrthemes); library(circlize); library(networkD3)
readRDS("pk_all.rds") -> pk
D... |
935aaac5c99e793a8ee339e1aa9cab8503a9decc1f45395a462f4e96c9c9efa0 | R | 46,105 | 838 | ---
title: "Exploratory analyses"
author: "Regina H. Reynolds"
output:
html_document:
code_folding: hide
theme: paper
highlight: kate
df_print: paged
toc: true
toc_float: true
number_sections: true
---
```{r setup, include=FALSE}
library(DT)
library(readxl)
library(EWCE)
library(ggplot2... |
85abb4598b966c0672e73880c1caa68433f4c4452ba346542fe6c8f4ca6b9801 | R | 46,349 | 1,509 | ---
title: "Examples"
author: "Kamil Slowikowski"
date: "`r Sys.Date()`"
output:
html_document:
self_contained: false
---
```{r setup, echo=FALSE, results='hide', warning=FALSE, error=FALSE, message=FALSE, cache=FALSE}
library(knitr)
opts_chunk$set(
cache = TRUE,
autodep = TRUE,
echo = FAL... |
e1f896e47bedccfe9c3cd06566cb34ffb5135ee71c4ec368a0555f9b0768c47f | R | 46,796 | 1,086 | ---
title: "Sec_GCN_ukbec"
author: "Amy Hicks"
date: "16/12/2021"
output:
html_document:
code_folding: hide
toc: true
toc_float: true
df_print: paged
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
library(tidyverse)
library(ggplot2)
library(devtools)
library(CoExpNets)
library(CoE... |
96c169dd656a8820098377cb55f4a1c252c5dc583e3960bfc6bc54aa1a3237af | R | 46,927 | 767 | library(Seurat)
library(tidyverse)
library(patchwork)
library(reshape2)
library(cowplot) #for plot_grid
library(Matrix) #to do counts on the sparce matrix (not super important)
# script used for all analysis of plate-based scRNAseq data (Figures 1 and Supp Figure 1)
# scRNAseq was performed bt NYGC in replicate
# scr... |
4bf08b16641c0ad92cde953d83dd4ab2c85d085a0f80e08721871e81318e003f | R | 47,070 | 853 | library(SeuratDisk); library(Seurat); library(dplyr); library(ggplot2); library(patchwork);library(RColorBrewer)
library(ktplots); library(pheatmap); library(viridis); library(tidyverse); library(broom); library(tidyr)
library(BisqueRNA); library(Biobase)
library(survival); library(survminer)
### Decomposition ##... |
d2192efa2add1cc43dfd2df2a59d546e7ad878feaa018c3ef5319aa6ac567cf1 | R | 47,487 | 710 | ## Author: Youtao Lu <luyoutao@sas.upenn.edu>
## Copyright (c) 2017-2023, Youtao Lu and Junhyong Kim, Department of Biology, University of Pennsylvania
## Copyright (c) 2017-2023, James Eberwine, Perelman School of Medicine, University of Pennsylvania
## All Rights Reserved.
## This Source Code Form is subject to th... |
6fac2d1b785857804e76298b0d051f80165de3313e3b2cc89dcaa016e46ebc05 | R | 47,499 | 696 |
library("gamlss")
pop_norms <- read.csv("~/r_files/pop_norms.csv")
xsteps = (35 - 4)/31
xlim1 = 4 - xsteps
xlim2 = 35 + xsteps
ysteps = (25 - 5)/20
ylim1 = 5 - ysteps
ylim2 = 25 + ysteps
# ABCD-specific
boys_abcd = subset(pop_norms, pop_norms$Dataset != 'ABCD' & pop_norms$Gender == 1)
x_axis = make.names("Age")
y... |
ad32ad4face885e0759ec9da3c08ce7e7be0d2df857641a1ae1381b41fb13d8b | R | 47,515 | 1,044 | ### -------------------------- ###
# Phylogenetic regressions
# (PGLSs & PIC Regressions)
# N. Magielse, 2022
### -------------------------- ###
## Load packages
library(ape)
#library(geiger)
library(nlme)
library(phytools)
library(corrplot)
library(tidyverse)
library(magrittr)
library(evomap)
#library(car) #may... |
540334c206119d6fdda2253899590d99130c638d33ef056607ea310413f295ea | R | 47,681 | 1,275 | ---
title: "Filtering dataset and DEA iPSC-DA time course"
author: "J Monzón Sandoval"
date: 'Last update: `r date()`'
output:
html_document:
theme: lumen
toc: yes
number_sections: true
toc_float:
collapsed: yes
smooth_scroll: yes
---
```{r setup, include=FALSE}
knitr::o... |
19cb27e0141a6f789caae70f9d2d49f833edc374936329b121a3839d95a90469 | R | 47,894 | 740 | library(SeuratDisk); library(Seurat); library(dplyr); library(ggplot2); library(patchwork);library(RColorBrewer)
library(ktplots); library(pheatmap); library(viridis); library(tidyverse); library(broom); library(tidyr)
readRDS("pk_all.rds") -> pk_all
DefaultAssay(pk_all) <- "RNA"
# An object of class Seurat
#... |
c029a59ff6b2ca6ce0432790afae5c2b08d34511448b3252d204d02ae01d4938 | R | 48,016 | 875 | ## to replicate conda environment used in paper, install conda, and then call the following in terminal: conda env create -f environment_droplet.yml - yml file here: https://github.com/brianherb/HumanHypothalamusDev/blob/main/environment_droplet.yml
library(SingleCellExperiment)
library(Seurat)
library(scDblFinder)
li... |
19436dc7afac08fd55027580919445959c7d8fb3ca8ee6b1b66fbd222e1faf9d | R | 48,543 | 1,552 | ---
title: "Multi-omics data integration: exploring associations of transcriptomics and metabolomics data from a germ-free mouse study"
author: "Mikael Niku"
output:
html_document: default
pdf_document: default
'': default
---
# Introduction
This collection of scripts was made for the integrated anal... |
45e0582a4fd03f6159b2128a0fd0de76a8ecadc4b07cf8e564609b99366ef76c | R | 48,934 | 1,215 | setwd(file.path(path.expand(dirname("~")), "Downloads"))
library(tidyverse)
library(lme4)
library(car)
library(zoo)
library(ggplot2)
library(qqplotr)
library(patchwork)
library(interactions)
library(effects)
library(MuMIn) # for effect size
library(sjPlot)
library(dplyr)
library(performance)
library(lmtest)
library(cor... |
d1fb8c162a8c2634a51efac1e429aad099140bd7f10b047057297583987e45c4 | R | 49,161 | 722 | library(tidyr)
library(dplyr)
library(stats)
library(ggplot2)
library(truncnorm)
path<-"./"
calc_param <- function(x,y) {
det=var(x)*var(y)-(cov(x,y))^2
return(det)
}
all_pred_false<-c()
all_mse_false<-c()
for (pop in c("CLM","MXL","PEL","PUR","ASW","ACB")) {
for (bins in c("21","22")){
for (option in c("0","... |
49cfb1960f28ecf14ffee4fe4f44b177827c3b124561aca5652ce2fc54d3aa90 | R | 49,740 | 1,151 | ---
title: "Differential abundance analysis for HRQoL - Gut microbiome TransplantLines"
author: J.C. Swarte
output: html_notebook
# ==========================================================================================
# By: Weersma Group, TransplantLines (UMCG)
#
# ... |
c9a492e3a59342c26285a9c1783fbbcf31f2cddef4dc02fecf0d4efe0d670f86 | R | 50,352 | 1,246 | ---
title: "MID - Measurement Model Code"
author: "<h3>by Michael Demidenko</h3>"
date: "`r format(Sys.time(), '%B %Y')`"
output:
pdf_document:
toc: yes
toc_depth: '2'
latex_engine: xelatex
html_document:
theme: united
highlight: tango
toc: yes
number_sections: yes
toc_depth: 2
t... |
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