sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 17k | content stringlengths 1 200k |
|---|---|---|---|---|
e7b3f7e9502158972500934999e82959702b868193832025d61dccb3d44d60dc | R | 21,335 | 628 | ---
title: "R Notebook"
output: html_notebook
---
<!--
# Per-event somatic actin intensity at wave emergence vs before
# (3-timepoint paired comparison). Feeds Fig 2d.
## What this file does
Reads ``wave_soma_int*.csv`` files and computes per-wave-event somatic
actin intensity at 3 timepoints (line 85: ``rep(1: (nro... |
8f9551bac0b1beb72871d0acbe5de46a825fb531a0c5b465b28aa73e15baee14 | R | 21,410 | 490 | userGWAS <- function(covstruc=NULL, SNPs=NULL, estimation="DWLS", model="", printwarn=TRUE,
sub=FALSE,cores=NULL, toler=FALSE, SNPSE=FALSE, parallel=TRUE, GC="standard", MPI=FALSE,
smooth_check=FALSE, TWAS=FALSE, std.lv=FALSE,fix_measurement=TRUE,Q_SNP=FALSE,
... |
14918f95e50da63c8e854d3f80609a5fdb5b073ab4cecb06ebd7c2efdc06f110 | R | 21,595 | 656 | # Auto-correlation script
library(readr)
library(dplyr)
library(pracma)
library(lmtest)
library(signal)
env_hopp_lp <- read_csv("C:/Users/tnguyen/OneDrive - Fondazione Istituto Italiano Tecnologia/IIT_Postdoc/WP4/Deeplabcut/TinyDancer_PM/AcousticStim/env_hopp_lp.csv",
col_names = FAL... |
e0acba8f92525dce22cb2d9bf3a8b9da0e9ca4f57cc26651bf1164289ebe1660 | R | 21,622 | 613 | ---
author: "Sayeh Kazem"
title: "Fig4"
date: "`r Sys.Date()`"
output: github_document
---
## Fig4 : Rare and common variant architectures across complex traits ( + S20, S21, ST11).
#### -- Figure legend -- ####
A)Example of genetic and phenotypic correlations between fluid intelligence (FI) and 6 traits, with each ... |
9fddaee7d46d1faa06061ab023bbab4e3aa97d4365a902a40523221e09eac8e5 | R | 21,953 | 583 | ldsc <- function(traits, sample.prev, population.prev, ld, wld,
trait.names = NULL, sep_weights = FALSE, chr = 22,
n.blocks = 200, ldsc.log = NULL, stand = FALSE,select=FALSE,chisq.max = NA) {
time <- proc.time()
begin.time <- Sys.time()
if(is.null(ldsc.log)){
logtrait... |
cd09220c193006d3efae1c9e7ea2ca68248673a412acad3a3c3ec9f313d1f1ac | R | 22,078 | 450 | ---
title: "Fig2"
output: github_document
---
## Fig. 2: Heatmap of effect sizes for whole body tissue, cell type gene sets across traits (& Figure S2, S3, S13, S14, S17, S18)
#### -- Figure legend -- ####
Legend:
Heatmap displays a representative set of the most significant associations between 5 categories of tra... |
80da1870d32c7fb43bef0ac9483b8a0f4cf9c5bc8fe1fa183d861234749aacf9 | R | 22,136 | 258 |
---
title: "CellChat inference and analysis of spatially multimodal cell-cell communication from spatially multiomics data"
author: "Suoqin Jin & Chenfeng Mo"
output:
html_document:
toc: true
theme: united
mainfont: Arial
vignette: >
%\VignetteIndexEntry{CellChat inference and analysis of spatially multimo... |
897e65e4a23c8874eb7af8502841b43d4bf768e5c09b43151d27fa938f7f49a1 | R | 22,436 | 541 | ---
title: "Fig5"
author: "Saye Kazem"
output: github_document
---
## Fig. 5: Rare and common variant architectures across complex traits.
#### -- Figure legend -- ####
**Legend:** (A) Example of genetic and phenotypic correlations between fluid intelligence (FI) and 6 traits, with each point color-coded by correlati... |
fcce8c7fa5a3ae836f6184610f4e58660dd2341b62cbf8dd49301dbd5c420ac3 | R | 22,484 | 507 | #' Show the description of CellChatDB databse
#'
#' @param CellChatDB CellChatDB databse
#' @param nrow the number of rows in the plot
#' @importFrom dplyr group_by summarise n %>%
#'
#' @return
#' @export
#'
showDatabaseCategory <- function(CellChatDB, nrow = 1) {
interaction_input <- CellChatDB$interaction
geneIf... |
70de0cfd68c8f398173dde71885df4049de16bc98ab3b2d69794d4c822d678cb | R | 22,681 | 668 | #' @include generics.R
#'
NULL
#' @param seu A Seurat object. Only applicable for the Seurat method.
#' @param group.by A variable from `meta.data` for grouping or a character vector of equal length as the number of cells. Only applicable for the Seurat method.
#' @param split.by A variable from `meta.data` to bifurca... |
7912bf7142de6c974d340d83cccdf12c532bd90114abfbc5a6c15dfd47afc25e | R | 22,933 | 650 | ---
title: "R Notebook"
output: html_notebook
---
<!--
# PA-Rac1-induced actin intensity difference at growth cones / soma / lamellipodia
## What this file does
Reads Fiji "Batch ROI measurement" CSVs (`*measurements.csv` via `list.files`
at lines 60-63) for PA-Rac1 photoactivation movies, including the dominant-
ne... |
a1cfa02e3d40a0d465531432d39d91e43317034c90ac7ce086b97dde143b4a00 | R | 23,054 | 484 | ---
title: "Trajectory and Pseudotime Analysis"
author: "Yichao Hua"
date: "`r Sys.Date()`"
output: rmarkdown::html_vignette
vignette: >
%\VignetteIndexEntry{Trajectory and Pseudotime Analysis}
%\VignetteEngine{knitr::rmarkdown}
\usepackage[utf8]{inputenc}
---
## Table of Contents
1. [scVelo Tutorial for Trajec... |
77699881f3b99357013f3b915a131ed2fa7c01b4b199435b459376333ea4d966 | R | 23,129 | 607 | ### CALCULATE CPMs, RUN DESeq2, AND MSsatsTMT AND CALCULATE CLUSTERS ####
#
library(dplyr)
library(tidyr)
library(arrow)
library(edgeR)
library(DESeq2)
library(MSstatsTMT)
library(stringr)
library(rtracklayer)
######################
# CALCULATE TRANSCRIPT- AND GENE-LEVEL CPM
#####################
... |
c0ce44fd14b9673076b10173b6a9e34121a87b4e61e09272adaae86dc629d71e | R | 23,247 | 722 | ---
title: "HumanPilot: Clustering using PCA, UMAP, marker genes, spatial coordinates"
author: "Lukas Weber"
date: "`r format(Sys.time(), '%Y-%m-%d')`"
output: html_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
# Introduction
This script contains code for several attempts at cluste... |
c0a495ffcd81242a53076b6bb6ede73af27b5fc37ffceb61386471b88d242c52 | R | 23,397 | 718 | ---
title: "R Notebook"
output: html_notebook
---
<!--
# Lag cross-correlation: DMSO-control WT neurite-tip velocity vs soma actin
## What this file does
Reads per-cell kymograph CSVs (`list.files(...)` at lines 52, 87 for the
170515 + 170522 imaging batches) for DIV-1 WT neurons treated with DMSO
vehicle. For each ... |
1fe359264aa2d6dfe79878d29fefc05bf25acb23cbdaf70c2b8185e3e938adea | R | 23,440 | 585 | #setup ----
#set library paths and load libraries:
.libPaths(c("/lisc/data/scratch/molevo/agcole/R/libs/seurat4/","/lisc/data/scratch/molevo/agcole/R/libs/course24/"))
setwd("/lisc/data/scratch/molevo/agcole/R/Aurelia_51k/Ac_manuscript_revision_ACOE")
library(Seurat,quietly=T)
packageVersion('Seurat') #che... |
49a810ddf0cdbcb9a96be2dfbc2a8f9dbb8a91149c152db6cdeff9abfe1ff1db | R | 23,474 | 463 | ################################################################################
### Modifier Interval Candidate Gene Pipeline Part 4:
### Imprinting: are any genes within modifier intervals shown to be imprinted?
################################################################################
### Import librarie... |
031ddd3a4ca61e0bc739847203d498561993e79bbeb33e7a0285995b1fa34fb5 | R | 23,643 | 646 | ---
title: "HeLa Endo-lyso imaging eval"
output: html_document
date: "2025-08-10"
chunk_output_type: console
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
# I. Load packackes
```{r}
library(devtools)
# Core data manipulation
library(tidyverse)
library(readr)
library(dplyr)
library(stringr)... |
ab835cfbc55c9a40da3280db632f8ae331bfece4434ede8f9eefad80570b5877 | R | 23,756 | 581 |
#' Creates a dotplot that shows how genes (columns) are expressed in different clusters (rows)
#'
#' @param object A Seurat object
#' @param genes.use A vector of genes to plot
#' @param use.counts A boolean indicating whether to use raw counts or scaled data
#' @param ident.use Which ident to use for plotting cluster... |
eabdb090280ae4e4d63167a77a4744963d822cbd4377dac3b2b4590286517437 | R | 23,774 | 649 | ##### QAPA ######
library(dplyr)
library(rtracklayer)
library(DESeq2)
library(stringr)
library(tidyr)
library(arrow)
classification <- read_parquet("./data/final_classification.parquet")
# PREPARE FOR QAPA BUILD --------------------------------------------------
ORFanage_replaced <- rtracklayer::import("... |
58d02ab2b1fbd6108e99282bddf1e2405c50159ec4cd1ffeed4ad2607d89ee8a | R | 24,295 | 535 | #!/usr/bin/env Rscript
# =============================================================================
# run_methylation_subgroup_limma.R
# =============================================================================
# Full per-subgroup methylation analysis following the NBIS Array Tutorial:
# https://nbis-workshop-... |
02d065f30c1dbfaba7b385f9b8e1e9c407e0b81c31faa114b2fe44d2efd948b1 | R | 24,663 | 585 | #!/usr/bin/env Rscript
#
# PhysMAP cross-dataset transfer evaluation.
#
# Fits PCA + UMAP on the TRAINING dataset, then projects the PREDICT dataset
# into that same embedding space. Trains a KNN on training embeddings and
# evaluates it on the projected predict embeddings.
#
# This mirrors the HIPPIE cross-dataset pr... |
4fbc95d9a4f81d9180403170bb1bb2d01b9467b07a909b16759b1f6c6bad28ab | R | 24,754 | 523 | ################################################################################
### Sox10Dom Pedigree GWAS Population Plotting
################################################################################
### Import packages:
library(ggplot2)
library(stringr)
library(dplyr)
library(gdmp)
library(factoex... |
ee0259c69bbcc3c296a96b9ea5e1b9ab4b12727965e53d9aa5537cb9d5cf4573 | R | 24,842 | 494 | ################################################################################
### Modifier Interval Candidate Gene Pipeline Part 5:
### Stavely et al., 2023 Differentially expressed genes from Migratory Wavefront
### at 11.5dpc: Are there any genes within modifier intervals that overlap with
### these genes diff... |
d61a05079e2e26581b0ba0536bd9f6ccae8d1c086ba5da6c9d9fc57ade9411eb | R | 24,872 | 294 | ---
output: github_document
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r 'setup', include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%"
)
library('BiocStyle')
library('spatialLIBD')
## Bib setup
library... |
18f22dca6ef4bef079dc29155c3c7b335d215eb10a68322515b1d1c329c87f4c | R | 25,033 | 300 |
---
title: "CellChat inference and analysis of spatially proximal cell-cell communication from spatially resolved transcriptomics"
author: "Suoqin Jin"
date: "`r format(Sys.time(), '%d %B, %Y')`"
output:
html_document:
toc: true
theme: united
mainfont: Arial
vignette: >
%\VignetteIndexEntry{CellChat infere... |
cd911eae2f3cd131848c4304a988aa4fd364cc9c1e844f49e684a22b85691cdf | R | 25,137 | 661 | library(ggplot2)
library(scico)
library(patchwork)
library(reshape2)
library(dplyr)
library(emdist)
library(readxl)
# Import data
Wt_E8_data <- as.data.frame(read_excel("Data_1.xlsx", sheet = "Wt_E8.5_data", col_names = TRUE))
NMPoutlines <- as.data.frame(read_excel("Data_1.xlsx", sheet = "WtE8_NMP_ROI_outlines", col_... |
0e65173fbbca5dc9c146ec09e916f794bed8b0effa0285a484b7e5d9d2adffa4 | R | 25,185 | 755 | ################################################################################
### Pre-GEMMA Genome-Wide Scan Data Organization from Old Files from 2011
### Data import, fixing data formatting, UCSC LiftOver from mm6 to mm10,
### writing files for covariates, phenotypes, making ped files.
### Not excluding any c... |
939481476dcd5d13cc02305fa3d283b57e71b6ca26817635622f8d2346a13a9e | R | 25,532 | 338 | # Plot LDSC results for 'adjusting for baseline' analyses
# code adapted from Peter Hickey (https://github.com/hansenlab/BrainEpigenomeNN/blob/master/SLDSR/scripts/plot_ldsc.baseline_adjustments.R)
# qrsh -l bluejay,mem_free=100G,h_vmem=100G,h_fsize=500G
### ------------------------------------------------------------... |
669e4420eb919ffd4fa9769f42a6f4bf1208b40dea455cbda3bdc99f186ad2b4 | R | 25,537 | 672 | library('SingleCellExperiment')
library('here')
library('readxl')
library('limma')
library('grid')
library('gridExtra')
library('sessioninfo')
dir.create('pdf', showWarnings = FALSE)
dir.create('rda', showWarnings = FALSE)
## Load data
load(here(
'Analysis',
'Human_DLPFC_Visium_processedData_sce_scran.Rdata'
... |
c7a5799d45284a5008ad712cd603023b9d8cac5449798bfd247bbe13a7d5c8bb | R | 25,889 | 586 | #!/usr/bin/env Rscript
#
# PhysMAP-PCA: induction-safe multi-modal PCA + KNN benchmark.
#
# Parallel to physmap_script.r / physmap_script_holdout.r but replaces
# Seurat WNN (which requires all cells in one object and cannot project
# held-out animals inductively) with plain prcomp() + predict().
#
# Modes
# -----
# ... |
f0800f3e37ef2f41167fa7a6929a869d1ffe3ad5284209b7db4b2719f1b1638c | R | 25,919 | 577 | # ==============================================================================
# Script: 7_never_always_LPR25.R
# Manuscript relevance: 3.4, Table S3
# ==============================================================================
# PURPOSE:
# Test whether persistently elevated LPR patients exhibit distinct linear ... |
df384d01b190511e879393fd969953f0731b619bf0c0f68c5de7206b5d2e9024 | R | 26,022 | 572 | # ==============================================================================
# Script: 8_substrate_lpr_fidelity.R
# Manuscript relevance: 3.5, Fig. 5
# ==============================================================================
# PURPOSE:
# Elucidate the relationship between substrate delivery (glucose), the l... |
bcc26d06d41319234ee48c67a24e614dc6b4ba35a5693bda1cefd2fb3884b2f1 | R | 26,053 | 710 | #========================================================================================#
# Author: James M Roe, Ph.D.
# Center for Lifespan Changes in Brain and Cognition, University of Oslo
#
# Purpose: Calculate AB deposition maps and rank order of regional deposition
#==============================================... |
d2eecabe401f67f880cefe08ddd4e80d1b428c31739dd5f1a2096a34f470ae84 | R | 26,613 | 784 | ---
title: "SpatialDE genes analysis"
author: "Lukas Weber"
date: "`r format(Sys.time(), '%Y-%m-%d')`"
output:
html_document:
toc: true
toc_depth: 2
---
```{r setup, include = FALSE}
knitr::opts_chunk$set(echo = TRUE, cache = TRUE)
```
# SpatialDE genes analysis
Analysis of SpatialDE gene lists... |
8994da56f61a52977ba7bbd143c3d18ab85e2955ccec2c6b64e8a14b0c795eee | R | 26,709 | 696 | ---
title: "Fig3"
author: "Sayeh Kazem"
output: github_document
---
## Fig. 3: Whole-body cell type-specific associations of CNVs with complex traits.
#### -- Figure legend -- ####
**Legend:** (A) Heatmap displays a representative set of association effect sizes between five categories of traits (x-axis) and deletion... |
8cce0db1fc9a35a312be3d0e50c96e6d5084af0880b3472fbc2ba6bd29e03f24 | R | 26,990 | 458 | ################################################################################
### Overlap between GWAS-close genes from multiple GI GWAS and the final
### candidate genes
################################################################################
### Import packages:
library(Seurat)
library(Signac)
... |
e71510205cf996638fa668582c2265887370b0593253ea504312a12c26bce586 | R | 27,133 | 611 | enrich <-function(s_covstruc, model = "",params,fix= "regressions",std.lv=FALSE,rm_flank=TRUE,tau=FALSE,base=TRUE,toler=NULL,fixparam=NULL){
time<-proc.time()
##determine if the model is likely being listed in quotes and print warning if so
test<-c(str_detect(model, "~"),str_detect(model, "="),str_detect(model, ... |
faeea25b8ec4175faf3094c496029c3fac6f05feaa1e8b4991b8b77ff3dbfccc | R | 27,328 | 744 | ### APA ###
library(rtracklayer)
library(seqinr)
library(Biostrings)
library(dplyr)
library(tidyr)
library(arrow)
library(edgeR)
library(stringr)
library(purrr)
setwd("")
classification <- read_parquet("nextflow_results/V47/final_classification.parquet") #182371
# PREP FILEs -----------------------... |
3eebb67a13b673f15dfa42c7f4711d15e6e100c13c21fac2c2dd2ac777e0ced1 | R | 27,387 | 973 | # screen -S image
# qrsh -l bluejay,mem_free=30G,h_vmem=30G,h_fsize=100G -pe local 4
# module load conda_R/3.6.x
library('SingleCellExperiment')
library('ClusterR')
library('BiocParallel')
library('ggplot2')
library('cowplot')
library('sessioninfo')
dir.create('pdf_image', showWarnings = FALSE)
dir.create('rda_image'... |
7dcbb2a289c9aa2ca2af53be4039f08f93d0732bfeb18d20d9a0e10afca81efc | R | 27,388 | 473 | library(data.table)
library(DBI)
library(stringr)
library(ggplot2)
library(pals)
library(confintr)
# set model paths
aamod <- '$dbdir/AA_Whole_Blood.db'
allmod <- '$dbdir/All_Whole_Blood.db'
mamod <- '$dbdir/MX_Whole_Blood.db'
prmod <- '$dbdir/PR_Whole_Blood.db'
gtmod <- '$dbdir/PrediXcan_Whole_Blood.db'
gtbmod <- '$d... |
d715b10681059a1e0328113f4fdf2bd223434054665ff6bd33d0d70a161be140 | R | 27,566 | 677 | ---
title: "Single-cell cluster robustness analysis"
output:
BiocStyle::html_document:
toc: true
date: "2023-07-28"
params:
filepath: "../../Ortho_Objects/vertebrateAC_v2_100.rds"
nPermutations: 50
nCores: 1
method: "seurat"
group.by: "species"
proportion: 0.8
run.perm: TRUE
---
```{r setup, inclu... |
5cc25bed86d2c6d290195876526d36db6aa5a51922b0a21e29b20e70d7d083fd | R | 27,615 | 657 | #!/usr/bin/env Rscript
# --- Progress logging helpers + perf CSV -------------------------------------
assign(".start_time", proc.time(), envir = .GlobalEnv)
# Event counter
assign(".__event_idx", 0L, envir = .GlobalEnv)
# In-memory performance log (data.frame)
assign(".__perf_log", data.frame(
event_id = int... |
9ab8394affa6165b190c767df8f00e678c8398eb106a961ce06d7beca69040ea | R | 27,631 | 828 | ---
title: "R Notebook"
output: html_notebook
---
<!--
# Slice DIV-3 neurite growth profiling + neurite-tip / soma-actin CCF
## What this file does
Reads kymograph TIFFs and per-cell neurite-tip / soma-actin CSVs (`list.files`
patterns at lines 59, 89, 94) from cortical-slice DIV-3 movies of neurons
expressing LynTM... |
c0aeb849247008a2b71450487e47cee5e4485e60f89e5427b3af74ba570fc74e | R | 27,689 | 804 | ---
title: "R Notebook"
output: html_notebook
---
<!--
# Microperfusion of CK-666 or para-aminoblebbistatin: actin intensity + neurite-length response timecourse
## What this file does
Reads per-experiment ROI intensity CSVs (`*int.csv` via `list.files` at line
60, loaded line 63) and per-experiment neurite-length C... |
4f6fbc74baaf7a3a6da88fbb8f1a9bf187ab27c3ebcdf1351205c919d280549a | R | 27,703 | 829 | ---
title: "R Notebook"
output: html_notebook
---
<!--
# Lag cross-correlation of neurite-tip velocity vs soma actin (2D culture + cortical slice)
## What this file does
Reads kymograph TIFFs and per-cell neurite-tip / soma-actin CSVs (`list.files`
patterns at lines 59, 89, 94) from 2D-culture and cortical-slice DIV... |
e742cadfcb6985202606b8425b227797d2ecfb6c20825fe38a0f2d46a7380768 | R | 27,703 | 787 | #' 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... |
3b326ffc6b34c78ffb8b8c0e9b0e602c188c7ed2421c3884e6d6a205045f8e3a | R | 28,040 | 380 |
---
title: "Comparison analysis of multiple datasets using CellChat"
author: "Suoqin Jin"
date: "`r format(Sys.time(), '%d %B, %Y')`"
output:
html_document:
toc: true
theme: united
mainfont: Arial
vignette: >
%\VignetteIndexEntry{Comparison analysis of multiple datasets using CellChat}
%\VignetteEngine{k... |
911230921f505487414202621bfa80681d2ca01b6d5ad57fb550fcbc8abe1126 | R | 28,066 | 831 | ---
title: "CURCI Figures"
output: html_document
date: "2024-06-08"
---
```{r setup, include=FALSE #Libraries and fonts}
knitr::opts_chunk$set(echo = FALSE)
library(readr)
options(readr.show_col_types = FALSE)
library(tidyr)
library(influence.ME)
library(MuMIn)
library(car)
library(reshape2)
library(gda... |
71d7f4490c1b36e11bf12c0bd589a0de1bcabcdd57c11009b1a6967f7a0bebc9 | R | 28,171 | 717 | library(dplyr)
library(Rmisc)
library(ggplot2)
library(ggpubr)
library(stringr)
library(ggforce)
library(paletteer)
library(ggsci)
##### ADNI #####
epsilons <- c(5, 10, 50, 100, 200, NA)
samples <- c(rep(100, length(epsilons)-length(which(is.na(epsilons)))), 18)
file_paths <- paste0("~/Python/WASP-DDLS/SE-benchmark/a... |
61cd9a6f4ee53e1ad8ba0025a6bc8c9fc7dca4bfa25061d13b42c7af97edad66 | R | 28,495 | 618 | #' @title Convert Seurat Object to AnnData and Generate scVelo Plots for Single-Cell RNA Velocity Analysis
#' @description This set of functions converts a Seurat object and associated Velocyto loom file(s) into an AnnData object and generates visualization plots for RNA velocity analysis using scVelo. The AnnData obje... |
630c21f6e9b1f10d359c1ed75da7d1a0acdc2d3eea8c928b423e7c1a032e9bc5 | R | 28,560 | 681 | #' @title Enhanced Dot Plot for Single-Cell Data Visualization
#' @description Creates an enhanced dot plot for visualizing gene expression across different cell types or clusters in single-cell data, with support for split visualization.
#' @param seu A Seurat object.
#' @param features A vector of gene names or a lis... |
5190f761c3e0557fb238d788d3fee0a2a54a4111eb2b06b963590a02f454892d | R | 28,816 | 845 | #
# Copyright (c) 2020 The Broad Institute, Inc. All rights reserved.
#
## install pacman and cmapR packages
if(!require(pacman)){install.packages("pacman");library(pacman)}
## make sure 'rhdf5' is loaded BEFORE 'cmapR'
if(!suppressPackageStartupMessages(require(rhdf5))){
source("https://bioconductor.org/biocLite.R"... |
a2788c96c391a4c3ecf7ee7fefdc2b31c73fe431bfa196165bf27483013cdc13 | R | 29,308 | 568 | ---
title: "Fig3"
output: github_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE, warning = FALSE)
```
## Fig. 3: Dissecting pleiotropy, gene function, and genetic constraint. ##
## Markdown for generating panel figures and statistics ##
## --------- Figure legend --------- ###
Legend: A)... |
fc34dba91f468c3b73f726b7576601216d483fa76d7a78746cbd1a6bcd023a0d | R | 29,388 | 651 | ---
title: "Non-parametric test for difference in mean"
author: "Christoph Hafemeister"
date: "`r Sys.Date()`"
output:
html_document:
toc: true
toc_float: true
code_folding: hide
highlight: pygments
df_print: kable
link-citations: true
references:
- id: phipson2010
title: "Permutation P-values ... |
1cb19f9ce5effac3d8e8558a31e029efb3456541652cccebf4ff4ba9d061e88a | R | 30,034 | 884 | ---
title: "R Notebook"
output: html_notebook
---
<!--
# Lag cross-correlation: blebbistatin-treated WT neurite-tip velocity vs soma actin
## What this file does
Reads per-cell kymograph CSVs (`list.files(...)` at lines 51, 85, 121 for
the 170515 + 170522 imaging batches) for DIV-1 WT neurons treated with
20 uM bleb... |
8635d8ed6ac404456d66de67eed7a574ac4d5dae754242b7b63157ec97d2402c | R | 30,092 | 771 | # This is a copy of the file 'utils.R' downloaded from https://github.com/cmap/cmapR GitHub repository on Oct 1, 2019.
# BSD 3-Clause License
#
# Copyright (c) 2017, Connectivity Map (CMap) at the Broad Institute, Inc.
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or with... |
490095d34605d817bf03ad7f519274f8b2e3936b72dc5e360e93f26095029782 | R | 30,748 | 1,040 | ---
title: "Targeted ASD Stool Metabolomics Analysis"
author: "Kevin Liu"
date: "`r Sys.Date()`"
output:
pdf_document:
toc: true
keep_tex: true
---
```{r setup, include=FALSE, message=FALSE}
knitr::opts_chunk$set(echo = TRUE)
options(scipen = 999)
library(tidyverse)
library(egg)
library(rstatix)
library(t... |
66f7f011873913913f560df709e22611416ee36efae0e86eb110cb97fb4eb146 | R | 30,815 | 785 | #!/usr/bin/env Rscript
# --- Progress logging helpers + perf CSV -------------------------------------
assign(".start_time", proc.time(), envir = .GlobalEnv)
# Event counter
assign(".__event_idx", 0L, envir = .GlobalEnv)
# In-memory performance log (data.frame)
assign(".__perf_log", data.frame(
event_id = int... |
fc4e70f87472af2178a32aa60f3748b15b0577447927deac869182d1161a2ea9 | R | 30,886 | 876 | ---
title: "R Notebook"
output: html_notebook
---
<!--
# Lag cross-correlation: blebbistatin-treated Arp3 KO neurite-tip velocity vs soma actin
## What this file does
Reads per-cell kymograph CSVs (`list.files(...)` at lines 71, 104, 138 for
the 170515 + 170522 imaging batches) for DIV-1 Arp3 KO neurons treated with... |
e12e0849f5fa0bf4278d6655dc41807f5a2565953d7d41189b75fab65187a441 | R | 32,295 | 556 | ################################################################################
### Import packages:
library(Seurat)
library(Signac)
library(cowplot)
library(GenomicRanges)
library(TFBSTools)
library(JASPAR2024)
library(BSgenome.Mmusculus.UCSC.mm10)
library(tidyverse)
library(TxDb.Mmusculus.UCSC.mm10.kno... |
0edf1f7045b71c206bbe4fe92d5d493366653ecbe3fb040f72e9aeea68f7e97d | R | 32,615 | 817 | #' @title Visualize Gene Expression Dynamics Along Differentiation Trajectories
#' @description This function set provides tools to visualize smoothed gene expression trends along developmental trajectories derived from pseudotime analyses. GeneTrendCurve.Palantir() uses pseudotime results from Palantir, while GeneTren... |
664a2794d10462704cfd3d431e3be550d0e9a8038cbdc23ce7559de2052cb1cb | R | 33,105 | 875 | ---
title: "Canonical template: Fig 4o brightfield CCF (Lyn-live) for one genotype"
output: html_notebook
---
<!--
================================================================================
CANONICAL TEMPLATE - DO NOT RENDER DIRECTLY
=============================================================================... |
82b696c8dd143a750688a0f979dabfa88b1929dd5ca7f415e52dacee5afd1620 | R | 33,277 | 685 | usermodel <- function (covstruc, estimation = "DWLS", model = "", CFIcalc=TRUE,
std.lv = FALSE, imp_cov = FALSE, fix_resid = TRUE, toler = NULL,Q_Factor=FALSE)
{
time <- proc.time()
test <- c(str_detect(model, "~"), str_detect(model, "="),
str_detect(model, "\\+"))
if (any(tes... |
7e518e5ed98fc87a40e979d9a2cda217650b13e83098e53cd6d2cf81d6915011 | R | 33,552 | 851 | s_ldsc <- function(traits,sample.prev=NULL,population.prev=NULL,ld,wld,frq,trait.names=NULL,n.blocks=200,ldsc.log=NULL,exclude_cont=TRUE){
if(is.null(ldsc.log)){
logtraits<-gsub(".*/","",traits)
log2<-paste(logtraits,collapse="_")
if(object.size(log2) > 200){
log2<-substr(log2,1,80)
}
log... |
241117dcbe5f69a5d41f1ce5200ebe768d9dbd7777b82466a40c9c651b93ad01 | R | 33,685 | 765 | ---
title: "Emergency diagnoses - basic frequency and analyses"
author: "Emma Whitfield"
date: "`r Sys.Date()`"
output: word_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
library(tidyverse)
library(flextable)
library(gtsummary)
library(lubridate)
library(RMySQL)
library(glue... |
d277bee323079f246de04584229054e678ed7814f986b278ac1b03cbaa9b1d7e | R | 33,771 | 950 | ---
title: "R Notebook"
output: html_notebook
---
<!--
# Lag cross-correlation: DMSO-control Arp3 KO neurite-tip velocity vs soma actin
## What this file does
Reads per-cell kymograph CSVs (`list.files(...)` at lines 70, 103, 138 for
the 170515 + 170522 imaging batches) for DIV-1 Arp3 KO neurons treated with
DMSO ve... |
0d26f0597b7e801132c4739920f72e66cb7d03f9caa39c9bbee773d8285b0b64 | R | 33,777 | 637 | #========================================================================================#
# Author: James M Roe, Ph.D.
# Center for Lifespan Changes in Brain and Cognition, University of Oslo
#
# Purpose: run spatial correlation between effect size maps at each cutoff
# and 3 AB deposition maps
#===========... |
f8ad54a6ab30c5664757e3c71f651e8a8dce7f295f64590989fc42e65c5bba30 | R | 33,802 | 713 | #### ==================================================================== ####
#### 1. LIBRARIES & SETUP ####
#### ==================================================================== ####
library(patchwork)
library(RColorBrewer)
library(car)
library(mult... |
37c0513824af02b0447448de52919937df87f28fc2dcec033e8e7562596c8a82 | R | 33,890 | 436 |
---
title: "Comparison analysis of multiple datasets using CellChat"
author: "Suoqin Jin"
date: "`r format(Sys.time(), '%d %B, %Y')`"
output:
html_document:
toc: true
theme: united
mainfont: Arial
vignette: >
%\VignetteIndexEntry{Comparison analysis of multiple datasets using CellChat}
%\VignetteEngine{k... |
e2cc7fba7c841aaa3ca971891ab382d09420f46cdc3685cea06240497a50c402 | R | 33,930 | 431 |
---
title: "Inference and analysis of cell-cell communication using CellChat"
author: "Suoqin Jin"
date: "`r format(Sys.time(), '%d %B, %Y')`"
output:
html_document:
toc: true
theme: united
mainfont: Arial
vignette: >
%\VignetteIndexEntry{Inference and analysis of cell-cell communication using CellChat}
... |
3f7d2edb6b342f7bc728f42aa88fdea4dc983059be13299fda8fff33aee1173c | R | 34,429 | 1,005 | library('SingleCellExperiment')
library('here')
library('jaffelab')
library('scater')
library('scran')
library('pheatmap')
library('readxl')
library('Polychrome')
library('cluster')
library('limma')
library('sessioninfo')
library('ggplot2')
library('viridisLite')
load("rda/sce_layer.Rdata", verbose = TRUE)
source("lay... |
ef994a98b2b8df05d3470d137a65ea6c01549305b7eca1ca3b2607edd3e57b84 | R | 34,521 | 1,024 | ---
title: "R Notebook"
output: html_notebook
---
<!--
# Lag cross-correlation of neurite-tip velocity vs soma intensity (brightfield, WT vs Arp3 KO)
## What this file does
Reads per-cell brightfield-derived neurite-tip velocity and soma-intensity
tables (data pasted as in-line tibbles in this Rmd) for WT and Arp3 K... |
f7236e4b7b70b5385d208fe9e10f9120c7070d0ae6c3f87cfcd8a260382839e3 | R | 34,585 | 1,074 | ---
title: "R Notebook"
output: html_notebook
---
<!--
# Lag cross-correlation of neurite-tip velocity vs actin (Lifeact) and membrane (LynTM) intensities
## What this file does
Reads per-neurite kymograph tip-intensity CSVs (`Actin_tip*.csv`, `Lyn_tip*.csv`
and `Neurite_*` tip-velocity CSVs; loaded from per-cell su... |
c29eaf49cb886727ed678d80c20610e5df4c2dd26542b5eb88261e4d02ce7e3d | R | 35,349 | 992 | #' @title Create an Enhanced Dimensional Reduction Plot
#' @description This function creates a dimension reduction plot that can handle both discrete and continuous variables seamlessly. It incorporates additional customization options for visual representation and automatically recognizes input variable types to opti... |
1457c5535197a5f0e6939a93af09de04d430a453213aa3172fa0fce91c4a708a | R | 35,431 | 910 | ---
title: "Fig2"
author: "Sayeh Kazem"
output: github_document
---
## Fig. 2: Tissue-specific associations of CNVs with complex traits
#### -- Figure legend -- ####
**Legend:** (A) The heatmap displays association effect sizes between five categories of traits (x-axis) and tissue-specific gene sets (y-axis) for dele... |
1f91dfec5a1104f16628af3a4fa8591fa9468bc726413498344877502168c224 | R | 35,798 | 1,121 | ---
title: "R Notebook"
output: html_notebook
---
<!--
# Lag cross-correlation of somatic actin intensity change vs binarized actin-wave occurrence
## What this file does
Reads per-cell somatic actin-intensity CSVs (`soma_actin*.csv`) and per-wave
occurrence CSVs (`wave*.csv`) from per-cell subfolders (lines 58, 63,... |
f9d05b248d3e9d727aa6c4ef49fe80a7bc0b96d305c50db68e0971533d7ae7da | R | 35,803 | 1,113 | ---
title: "R Notebook"
output: html_notebook
---
<!--
# Polarized-neuron extension / retraction duration + velocity (with side-output neurite-tip CCF)
## What this file does
Reads per-cell soma-actin and per-wave occurrence CSVs (`soma_actin*.csv`,
`wave*.csv` from per-cell subfolders; lines 58, 63, 74, 82) for DIV... |
039c18f2f76b884502afc24c1713044441b5c6745a24df4ad836c61140161783 | R | 35,837 | 1,117 | ---
title: "R Notebook"
output: html_notebook
---
<!--
# Soma actin / wave-occurrence CCF (alternative-cohort variant)
## What this file does
Alternative-cohort variant sourced from `D:\DVElite`. Reads per-cell
somatic actin-intensity CSVs (`soma_actin*.csv`) and per-wave occurrence
CSVs (`wave*.csv`) from per-cell ... |
451e2bb2a7b763ba5e88bb1bbdde063565e3e3684ec4c5ce486f770ccb17414d | R | 36,008 | 760 | # R script for generating figures in updated BioRxiv submission:
#Setup ----
#set library paths and load libraries:
.libPaths(c("/lisc/data/scratch/molevo/agcole/R/libs/seurat4/","/lisc/data/scratch/molevo/agcole/R/libs/course24/"))
setwd("/lisc/data/scratch/molevo/agcole/R/Aurelia_51k/Ac_manuscript_revision_ACOE")
l... |
f46bb570e6a62d9d3069bd39b55e715f5381cab4a2d940be7d6c66c692bef0de | R | 36,287 | 729 | ################################################################################
### Modifier Interval Candidate Gene Pipeline Part 9:
### Final Model: Which are the top candidate genes based on all methodologies?
### Generate Summary figure with one axis being the candidate genes and the
### other being the method... |
e77266b5b56a3f31fa4b043edc31277e05b276ceb585c9b8c43a052a16068848 | R | 36,604 | 891 |
#' The CellChat Class
#'
#' The CellChat object is created from a single-cell transcriptomic data matrix, Seurat V3 or SingleCellExperiment object.
#' When inputting an data matrix, it takes a digital data matrices as input. Genes should be in rows and cells in columns. rownames and colnames should be included.
#' The... |
6a5a29e112745e8472bc40ae2dbbeaf0a42eb01cba7bb5d5f932ff9d3798d058 | R | 36,743 | 1,140 | ---
title: "R Notebook"
output: html_notebook
---
<!--
# Lag cross-correlation between neurite-tip velocity and soma actin / neurite-tip actin
## What this file does
Reads per-neurite tip-intensity CSVs (`Result*.csv` from per-cell subfolders,
lines 52, 57, 87, 123) for DIV-1 and DIV-2 unpolarized neurons. For each
... |
4ddc4b5d661f7c5283f318282df1b9c692d9aa4da8de0138610cb63d2d5c5ab7 | R | 36,745 | 1,334 |
local({
# the requested version of renv
version <- "1.1.5"
attr(version, "sha") <- NULL
# the project directory
project <- Sys.getenv("RENV_PROJECT")
if (!nzchar(project))
project <- getwd()
# use start-up diagnostics if enabled
diagnostics <- Sys.getenv("RENV_STARTUP_DIAGNOSTICS", unset = "FALS... |
24d1a10a892913affa1e451b621c2b55f32134b0035938a91f007fb6a1b1c38b | R | 37,339 | 738 | #' Run the QTrait function to test trait-specific heterogeneity in genetic correlation models
#'
#' \code{QTrait} tests whether the genetic association between a latent factor (defined by a set of indicator traits) and an external trait can be fully explained by the common factor, or whether specific indicator traits... |
c3bc7a44f02018f0fdd16e8d5abb414823fe8e0ad568b6c0ff03b7a2b0aea862 | R | 37,637 | 995 | # Auto-correlation script
library(readr)
library(dplyr)
library(pracma)
library(lmtest)
library(signal)
env_hopp_music <- read_csv("C:/Users/User/OneDrive - Fondazione Istituto Italiano Tecnologia/IIT_Postdoc/WP4/Deeplabcut/TinyDancer_PM/AcousticStim/env_hopp_music.csv",
col_names = FALSE)... |
e80bb2901fdc29267b353ebbec07378a87bd482af91dad110bd18a81b192fa3a | R | 38,599 | 1,178 | ---
title: "R Notebook"
output: html_notebook
---
<!--
# Lag cross-correlation of neurite-tip velocity vs KIF5C1-560 and actin intensity
## What this file does
Reads paired per-neurite kymograph tip-intensity CSVs (`Actin_tip*.csv`,
`Kif5C_tip*.csv`, `Kif5C_neurite*.csv` from per-cell subfolders; lines 64, 94,
123) ... |
0fa6f54a78d32ec60ee6bfaf74309d303cb7a0a9f7d8792a199f588430d0474c | R | 38,692 | 1,169 | ---
title: "R Notebook"
output: html_notebook
---
<!--
# Lag cross-correlation between neurite-tip growth velocity and actin / LynTM intensity in polarized neurons
## What this file does
Reads per-neurite axon-wave and minor-wave CSVs (`axon_wave*.csv`,
`minor_wave*.csv`; lines 69-74, 105-106) plus paired actin and ... |
4913941762b46f1dcb47af7069327200b221a62124db0f5baa7542a2b766833b | R | 38,988 | 968 | ---
title: "Species-level amacrine cell analysis"
output:
BiocStyle::html_document:
toc: true
date: "2023-06-01"
params:
species: Chicken_reclustered
initial: TRUE
batch_int: TRUE
integrate_by: "animal"
harmony: TRUE
contamination_threshold: 6
contamination:
nFeature_threshold: -2.5
doublet_fi... |
ca4305efb76d74871eb8d7f0b6c835feaabafd0011ec705040a5ced2ce975e57 | R | 39,203 | 842 | ####################################################################################
## 'Package' that holds in house R functions for automatic cleaning pipeline ##
## ##
## Author: Dennis C.Y. Chan ... |
344df7cce255f27068b0e173614d867b48ee0f6be9968ef85079e7cdbad8c0ed | R | 39,523 | 915 | ---
title: "Emergency diagnoses - plots and tables"
author: "Emma Whitfield"
date: "`r Sys.Date()`"
output: word_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
library(tidyverse)
library(flextable)
library(lubridate)
library(glue)
library(ggrepel)
library(ggstance)
library(p... |
27a6dab3e9042e010010886937b1a47bab063510fc9a5a07e1f00050164ff194 | R | 40,102 | 1,114 | #========================================================================================#
# Author: James M Roe, Ph.D.
# Center for Lifespan Changes in Brain and Cognition, University of Oslo
#
# Purpose: Compute the rank order of thickness changes across all converter MRIs and correlate with the rank order of regiona... |
66e2702209bcffca5f24fe810646f41c06ec2fc1395be61845529db0f243c0ac | R | 40,296 | 1,009 | #' Normalize data using a scaling factor
#'
#' @param data.raw input raw data
#' @param scale.factor the scaling factor used for each cell
#' @param do.log whether do log transformation with pseudocount 1
#' @export
#'
normalizeData <- function(data.raw, scale.factor = 10000, do.log = TRUE) {
# Scale counts within a ... |
33ababbf566bd5dfaa1234eb7ca926eaeb05f619ea4730e6e8c9fa4fcaf6c257 | R | 40,585 | 924 | #' Compare gene expression between two groups
#'
#' @param x A list that provides model parameters and optionally meta data; use output of vst function
#' @param umi A matrix of UMI counts with genes as rows and cells as columns
#' @param group A vector indicating the groups
#' @param val1 A vector indicating the value... |
d7c3cadb80cd8612e5e7ba8168cb5a72c78eb6e08327ce20555477a09c628f3e | R | 40,854 | 965 |
#' The CellChat Class
#'
#' The CellChat object is created from a single-cell transcriptomic data matrix, Seurat V3 or SingleCellExperiment object.
#' When inputting an data matrix, it takes a digital data matrices as input. Genes should be in rows and cells in columns. rownames and colnames should be included.
#' The... |
61e540d5cecd6226c538eaefec7e1d9a15a7e5a5dd7db047ef3661c6fd2f1309 | R | 40,957 | 1,146 | # This is a copy of the file 'io.R' downloaded from https://github.com/cmap/cmapR GitHub repository on Oct 1, 2019.
# BSD 3-Clause License
#
# Copyright (c) 2017, Connectivity Map (CMap) at the Broad Institute, Inc.
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modi... |
7beeb746af3c2e3105ad7ae929529eb64b3ff6fdfda85eac4a973111281cbda5 | R | 41,687 | 862 | ### MNT application of snRNA-seq pilot workflow to Visium DLPFC data
### Initiated MNT 29May2020
### Original SCE file in:
### /dcs04/lieber/lcolladotor/with10x_LIBD001/HumanPilot/Analysis/Human_DLPFC_Visium_processedData_sce_scran.Rdata
### Working in
### /dcs04/lieber/lcolladotor/with10x_LIBD001/HumanPilot/An... |
4331511be4f77a89ee29a01523fa2ebf987e7ac9984059c81ceb3dae2eb381d0 | R | 41,845 | 1,189 | ---
title: "WT_KO_Blebbistatin_brightfield"
output: html_notebook
---
<!--
# Master kymograph consolidator: length-vs-time per neurite class (Fig 5l upstream)
## What this file does
Per-neurite kymograph batch consolidator (a misnomer-name file: original
`Growth_profiling.Rmd` is actually a kymograph batch consolida... |
260ec873ef4a3226ba0a6f27d2f2b6441733d73f1625bfdff498a972f8c3fe57 | R | 43,876 | 548 |
---
title: "Inference and analysis of cell-cell communication using CellChat"
author: "Suoqin Jin"
date: "`r format(Sys.time(), '%d %B, %Y')`"
output:
html_document:
toc: true
theme: united
mainfont: Arial
vignette: >
%\VignetteIndexEntry{Inference and analysis of cell-cell communication using CellChat}
... |
f29eb2eb4d399a343bf3de98d9d6374ab4a6cfc747a1ae7ca1f977b73add4511 | R | 44,229 | 1,453 | ---
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... |
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