sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 17k | content stringlengths 1 200k |
|---|---|---|---|---|
3c5a11229079aba2d309cfb276065456b92dba5f3894ed2f8d1a77286e8b4cf2 | R | 44,457 | 1,291 | ---
title: "cellposeSAM_CNER_Calcium-liveCell_v3"
output: html_document
date: "2025-07-17"
chunk_output_type: console
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
# I. Load packackes
```{r}
library(devtools)
# Core data manipulation & visualization
library(tidyverse) # ggplot2, dpl... |
12b31ad1bc30ce9eaa1f8c021e092093c3ec7e99bb877f8064ccdb5cd7797052 | R | 44,619 | 1,162 | ---
title: "03 Analysis"
output: html_document
---
```{r setup, include=FALSE}
# If running interactively from within /scripts, move up to project root
# If running interactively from within /scripts, move up to project root
if (basename(getwd()) == "scripts") setwd("..")
# Now we are in the project root
knitr::opts... |
0e95f637eadb54507ecea74d35e61b7a21baf91e1ca6480ecca708d85b17dae4 | R | 44,742 | 986 | #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') #check that it switched!
li... |
cd53c81e3918d9e9096ed62e303622a4d19d17436dcd79fc2f5b045187448bcd | R | 44,787 | 985 |
#' Compute the communication probability/strength between any interacting cell groups
#'
#' To further speed up on large-scale datasets, USER can downsample the data using the function 'subset' from Seurat package (e.g., pbmc.small <- subset(pbmc, downsample = 500)), or using the function `sketchData` from CellChat, i... |
448eb6a0aae2dfa7cf432b0cb4343401458864bc6833eb87b1a6be7fb16ce505 | R | 44,813 | 958 | #' @useDynLib sctransform
NULL
#' Variance stabilizing transformation for UMI count data
#'
#' Apply variance stabilizing transformation to UMI count data using a regularized Negative Binomial regression model.
#' This will remove unwanted effects from UMI data and return Pearson residuals.
#' Uses future_lapply; you... |
7881a0e3a37ba198ff45a0d4383db18fdc7b68db69e0147a977f08d43f7c2443 | R | 44,951 | 1,214 | # ==============================================================================
# Script: 6_hyperbolic_LPR_error.R
# Manuscript relevance: 3.3.ii, Fig. 4, Table S2, Table S5
# ==============================================================================
# PURPOSE:
# Quantify and visualize how the observed lactate/p... |
17c633811116501f1ea95d3c250645df3e01266b06a8764827a0527acf2a6bae | R | 46,119 | 1,201 | #========================================================================================#
# Author: James M Roe, Ph.D.
# Center for Lifespan Changes in Brain and Cognition, University of Oslo
#
# Purpose: Compute longitudinal cortical thickness trajectories with GAMMs using MRIs at a given distance from Aβ+ combined w... |
3aaa123d1d1263ddc1ed22fedc398b7f343f670914c3a8e51be1dbdcf4118877 | R | 46,163 | 1,386 | ---
title: "neuroLSD_CalciumMaster"
output: html_document
date: "2025-07-21"
chunk_output_type: console
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
# Aim
Create master file that loops through all calcium imaging evals and combines results in master file for stats, plotting and saving.
# ... |
9fbe3e50e8d4c8b8ee512e8405e1f8c7d20e2e3febb401fa30119ea625388b3e | R | 47,884 | 1,187 |
ORTHOTYPES = c(
"oAC1 [A2]", "oAC2 [VG3]", "oAC3", "oAC4", "oAC5", "oAC6 [A8]",
"oAC7 [SEG]", "oAC8 [nGnG-gl]", "oAC9", "oAC10", "oAC11",
"oAC12", "oAC13 [A17]", "oAC14 [A17]", "oAC15", "oAC16*", "oAC17*",
"oAC18 [nNOS]", "oAC19 [CA2]", "oAC20 [NPY]", "oAC21*", "oAC22*",
"oAC23*", "oAC24", "oAC25", "oAC26",... |
0a7d6ea705f3127b70c64ea86829cab2ee2ac7ddb1c9f87c29318b4aa88e846a | R | 48,713 | 1,034 | library(data.table)
library(ggplot2)
library(pals)
library(stringr)
library(gridExtra)
library(grid)
library(ggstance)
library(viridis)
library(ggpointdensity)
library(ggh4x)
library(forcats)
# set model paths
aamod <- '$dbdir/AA_Whole_Blood.db'
allmod <- '$dbdir/All_Whole_Blood.db'
mamod <- '$dbdir/MX_Whole_Blood.d... |
061637afb28232ef3169ef249a5b06147ed049742daeaf5406a29f8dcd43e9fd | R | 49,063 | 1,239 | ---
title: "Enhanced Visualization"
author: "Yichao Hua"
date: "`r Sys.Date()`"
output: rmarkdown::html_vignette
vignette: >
%\VignetteIndexEntry{Enhanced Visualization}
%\VignetteEngine{knitr::rmarkdown}
\usepackage[utf8]{inputenc}
---
## Table of Contents
1. [Create an Enhanced Dimensional Reduction Plot](#cr... |
f62474de1b87b9779a65bf3c24f1e8e64c64def460af76f60303e41698107a12 | R | 49,179 | 1,340 | # DESCRIPTION:
# This script analyzes the alternative splicing in relation to
# different polyadenylation (PolyA) sites and cell differentiation timepoints
# (t00, t04 and t30). It uses a quasi-binomial regression model to assess the
# log-odds of exon inclusion and visualizes the results.
library(readr)
... |
c5dbcf9e990e343c0d260cc8bf35f4796230072dc5d7d202c4bdf389a2cd9f63 | R | 49,359 | 1,094 | ################################################################################
### Sox10Dom Aganglionosis GWAS: Plotting Manhattan plots, top GWAS hits,
### candidate genes closest to top hits, resolving strandedness, plotting
### phenotypes across peak SNPs, PCA of populations
##################################... |
8368572a7fa6034791421674ddd40fb031d3044f25a316ecdc05191130a31d76 | R | 49,363 | 1,505 | # screen -S scran
# qrsh -l mem_free=60G,h_vmem=60G,h_fsize=100G -pe local 4
# module load conda_R/3.6.x
library('SingleCellExperiment')
library('scran')
library('scater')
library('BiocParallel')
library('PCAtools')
library('igraph')
library('ggplot2')
library('cowplot')
library('jaffelab') ## for ss(), splitit(), mypl... |
4e9a29bd047822f9b5771cf5d7af9305518498d59299dd69e74def0c09999ff7 | R | 50,033 | 1,131 | # ==============================================================================
# Script: 5_linear_LP_models.R
# Manuscript relevance: 3.2, 3.3.i, Fig. 3
# ==============================================================================
# PURPOSE:
# Analyze lactate–pyruvate segmentation output to understand how segmen... |
bd60a31224a20f00249a3799d5805f32a02bcdac48ea340be12cd77829e94d24 | R | 50,034 | 1,409 | ---
title: "R Notebook"
output: html_notebook
---
<!--
# Lag cross-correlation of neurite-tip growth velocity vs Arp3 / MRLC intensities (LSM980 cohort)
## What this file does
Reads paired per-neurite Arp3 + MRLC + actin kymograph and tip-intensity CSVs
from LSM980 Airyscan triple-channel movies (`list.files` patter... |
b826573f8cda001949ebd14dd33e2164451932f95fdda3a61df8069a5d636464 | R | 50,696 | 1,282 | #========================================================================================#
# Author: James M Roe, Ph.D.
# Center for Lifespan Changes in Brain and Cognition, University of Oslo
#
# Purpose: Simulate longitudinal cortical thickness trajectories with GAMMs
# using MRIs at a given distance from AB... |
874030bd5515a21280ed84c7d49ef8f1106893ec16382760be57857bf3d18fac | R | 51,672 | 1,650 | ---
title: "R Notebook"
output: html_notebook
---
<!--
# KIF5C1-560 vs neurite-tip velocity CCF in Arp3 KO neurons (alternative-cohort variant)
## What this file does
Alternative-cohort variant sourced from `D:\DVElite`. Reads per-neurite
tip-intensity CSVs (`Actin_tip_*.csv`, `Kif5C_tip*.csv` from per-cell
subfolde... |
f6d359f8b724caefe55ef8324eb813a6a1ae47f6a14ff22afca9ef7d36dab100 | R | 51,965 | 1,529 | ---
title: "Code for manuscript"
output: html_notebook
---
# Loading packages
Stage packages needed
```{r}
library(tidyverse)
library(h2o)
library(terra)
library(zoo)
library(ncdf4)
library(CFtime)
library(corrplot)
library(readxl)
library(ggpmisc)
library(mgcv)
library(gridExtra)
library(lubrid... |
0f049a97a27a10ff0883ce5515f0545ac74185879a2bebe290d933397fe72a81 | R | 51,990 | 1,063 | #' Estimate a model-implied genetic covariance matrix
#'
#' `rgmodel` uses LDSC-derived output from Genomic SEM's multivariable LD Score regression (`ldsc()`)
#' to specify and estimate a saturated genetic correlation matrix using the usermodel function.
#' The function takes an object from `ldsc()` and returns an ... |
70b418f1f3986cddc6237ab7839ec224113112340ab348b83ea27ea8a3950f1c | R | 52,031 | 1,232 | #!/usr/bin/env Rscript
# Complete post-segmentation analysis for Frontiers manuscript 1904810.
#
# The primary PCA and Bayesian models preserve the variable order, preprocessing,
# response definitions, and unmodified PCA signs used in the original analysis.
# Editorially requested additions (KINARM bootstrap, paralle... |
7fb8fc743376fe2c4fb37db2e72af238f98f5b9b4e0e70ebabc5844d60df8a2d | R | 52,460 | 1,316 | ---
title: "SpatialDE clustering"
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 clustering
This script contains code for several ve... |
b3773c101ec53105582ffd01f74b088c6bad340465e7839b859151d2e6c8a6df | R | 52,768 | 1,519 | ---
title: "R Notebook"
output: html_notebook
---
<!--
# Extension / retraction duration and velocity in polarized neurons
## What this file does
Reads per-neurite tip-velocity CSVs (`Tip_actin_*.csv`, `Actin_neurite*.csv`
from per-cell subfolders, lines 98 onward) for DIV-3 polarized neurons, then
classifies each g... |
f7d2f1daed80a10a857f939b84dfc34ed391f860b748b164d2589ad601a85f5c | R | 52,963 | 1,314 | ---
title: "diff118_iNiDA_d23"
output: html_document
date: "2024-10-10"
editor_options:
chunk_output_type: console
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
# load packackes & set project directory
```{r}
# --- Load Required Libraries ---
# --- Core Tidyverse ---
library(tidyverse) ... |
14004ec269befc3c6f1b294640f20f4b06d226d2e0ce0018536112409ce3a6e7 | R | 53,295 | 1,375 | ---
title: "Sub-cluster SACs"
output:
html_document:
keep_md: true
toc: true
date: "2023-07-28"
params:
OT: FALSE
manual_annotation: list(Mouse = 2, Rat = 0, Peromyscus = c(2,3), Squirrel = 1, Rhabdomys = 1, TreeShrew = 1, Cow = 0, Sheep = 0, Opossum = 1, Chicken = 0, Lizard = 1, Zebrafish = 0, Killifish ... |
a35af895a0ad508f8ff1bb5b4758bd908307c76301f161567359668b0ffea98d | R | 54,172 | 1,642 | ---
title: "R Notebook"
output: html_notebook
---
<!--
# Polarized-neuron extension / retraction duration + velocity (alternative-cohort variant)
## What this file does
Alternative-cohort variant of `edfig02jk_polarized_neurons_duration_velocity.Rmd`
sourced from `D:\DVElite\Polarized_neurons` rather than the publis... |
de92d798aa94efda58c1165cb68c2f3349910c4fb9e02668bbbbd9651295f720 | R | 55,242 | 1,697 | ---
title: "R Notebook"
output: html_notebook
---
<!--
# KIF5C1-560 Z-score intensity at extending / pausing / retracting neurite tips
## What this file does
Reads paired per-neurite tip-intensity CSVs (`Tip_actin*.csv`, `Tip_Kif5*.csv`
from per-cell subfolders; lines 68, 103, 128) for DIV-2 neurons co-expressing
Li... |
c003c2669067bc19ec6cff00e812145c82c0d4c9a15aa49fd6b334748c78f4f8 | R | 55,287 | 1,701 | ---
title: "R Notebook"
output: html_notebook
---
<!--
# KIF5C1-560 vs neurite-tip velocity CCF in WT neurons (alternative-cohort variant)
## What this file does
Alternative-cohort variant sourced from `D:\DVElite`. Reads per-neurite
tip-intensity CSVs (`Tip_actin_*.csv`, `Tip_Kif5*.csv` from per-cell
subfolders; li... |
6af663f5103108e8f6054e73dd321698a4137a9b28143689f3838a0a9ca8e413 | R | 55,441 | 1,582 | # ATSS-AS COORDINATION
library(readr)
library(dplyr)
library(stringr)
library(tibble)
library(tidyr)
library(forcats)
library(ggplot2)
library(cowplot)
library(patchwork)
library(purrr)
library(arrow)
library(emmeans)
library(scales)
library(ggtext)
library(GenomicR... |
1bfcd396fce8453b87420a7b69d87618ca6b7e4b9c40bcf27b7ede979b3270c8 | R | 55,920 | 1,092 | ################################################################################
### Modifier Interval Candidate Gene Pipeline Part 7:
### How many differentially accessible loci in WT 16.5dpc ENS nuclei (by
### cell group: Neuronal Branches, Neuroblast, Progenitor) are within modifier
### intervals? Which TF bind... |
061f90e679279382d96d6ccae09a825c6ad53571513df4dc4fb4ac8b9ba38895 | R | 57,169 | 1,328 | #' 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 to do log transformation with pseudocount 1
#' @param do.sparse whether to use sparse format
#' @export
#'
normalizeData <- function(data.raw, scale.factor ... |
27ac8afb9f47c2753a4254c6590080d634b52b54fbf9b8af03496b99f0e81ce5 | R | 57,238 | 1,289 | ## #######################################################################################################
## 20161013 modified by Karsten Krug
## adapt the ssGSEA code to:
## 1) work with site specific signature sets
## 2) take directionality of regulation into account
## 3) multi-threaded using 'doParallel'
## ... |
53b1a430270ab0193e28b56cd1c9dfa71d5fc6665fab807df4bc05544b688490 | R | 57,253 | 1,297 | #OMA
.libPaths(c("/lisc/data/scratch/molevo/agcole/R/libs/seurat4/","/lisc/data/scratch/molevo/agcole/R/libs/course24/","/lisc/opt/sw/software/R/4.5.0/lib64/R/library"))
setwd("/lisc/data/scratch/molevo/agcole/R/Aurelia_51k/ac.kostyaPlus/ACOE_revisions/")
library(easypackages)
libraries("readxl","RColorBrewer",'ggplot... |
573116c0e871929100ee15c98795367513cebad2b6ab52b2f33e1b72b74915d9 | R | 59,419 | 1,356 | ################################################################################
### Import and process snATAC-seq data generated from Phox2b H2B-CFP+ bright
### and dim whole gut nuclei separately from 2020/2021: ENS progenitors and
### neuronal cells
#############################################################... |
01519184727d3b8a83ed486bdf33a5ad1a2b3666e091e86047c50a92eb7a4670 | R | 60,122 | 1,794 | ######EDITING code from IsoformSwitchAnalyzeR TO COLOUR FOR AGO UTRs
evalSig <- function (pValue, alphas) {
sapply(pValue, function(x) {
if (is.na(x)) {
return("NA")
}
else if (x == -1) {
sigLevel <- "*"
}
else if (x < min(alphas)) {
sigLevel <- "***"
}
else i... |
e56a843a8eac11f5ae496c60f0c64d6705281c6b8cdedc859d8d1130147d8681 | R | 61,991 | 1,828 | library('SingleCellExperiment')
library('here')
library('jaffelab')
library('scater')
library('scran')
library('pheatmap')
library('readxl')
library('Polychrome')
library('cluster')
library('limma')
library('sessioninfo')
dir.create('pdf', showWarnings = FALSE)
dir.create('rda', showWarnings = FALSE)
## Load data
loa... |
e6e9a5fc0e7fed65faef8f363714413d3f5126128eb458653e9e931deab2fbdd | R | 62,351 | 1,819 | ---
title: "Canonical template: pooled-replicate neurite-actin CCF"
output: html_notebook
---
<!--
================================================================================
CANONICAL TEMPLATE - DO NOT RENDER DIRECTLY
================================================================================
This Rmd i... |
a1fd279a14dffad206a313a62a483e5f4a0f30c70b8e6f1e65bd83f5d69024af | R | 63,430 | 1,732 | #========================================================================================#
# Author: James M Roe, Ph.D.
# Center for Lifespan Changes in Brain and Cognition, University of Oslo
#
# Purpose: Load simulated GAMM random slopes and intercepts and test
# cortex-wide models comparing thickness effect... |
edf75f668a1527207c0d1a89316416becbbf7977a28f7226621d661366bd2cfe | R | 66,940 | 1,297 |
#' Compute the communication probability/strength between any interacting cell groups
#'
#' To further speed up on large-scale datasets, USER can downsample the data using the function 'subset' from Seurat package (e.g., pbmc.small <- subset(pbmc, downsample = 500)), or using the function `sketchData` from CellChat, i... |
1ac6a1e2acb9abe8d5f9761b062bef054b911f23729fe89e958a26cef765ad6a | R | 67,126 | 1,788 | #========================================================================================#
# Author: James M Roe, Ph.D.
# Center for Lifespan Changes in Brain and Cognition, University of Oslo
#
# Purpose: Load GAMM random slopes and intercepts and test cortex-wide models comparing thickness effects
# between... |
cee46ecdd3e433f3838a6a82f66165cc46ee2cc57d696a882945cde1548e247b | R | 69,710 | 1,625 | # MIT License
#
# Copyright 2018 Broad Institute
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, ... |
dff2e78be59b2b682eb6051f2b9ebea4ac8022bd506be1f3e56127154876e08c | R | 71,061 | 1,637 | ---
title: "HeLaLysoIpASAH1"
output: html_document
date: "2024-12-03"
editor_options:
chunk_output_type: console
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
## load packages
```{r}
# --- Core tidyverse packages
library(plyr)
library(stringr)
library(tidyverse)
library(dplyr)
library(tibb... |
912e0e4a4ce79b457273afd570a2ad92918962887a756a97013a1e82eb7c41cd | R | 71,458 | 1,982 | #' Generate a Shiny App for interactive exploration of CellChat's outputs
#'
#' @param object CellChat object
#' @param ... Other parameters of `shinyApp` function from shiny R package
#' @return A Shiny app object on the basis of one CellChat object
#' @export
#' @importFrom stringr str_split_1
# #' @importFrom plotly... |
7df54d7e830e95fa45bedb774a6f807c8157c9f9decbe70e3abe71ee7c7dd599 | R | 74,977 | 2,138 | ---
title: "TF tree analysis"
output:
BiocStyle::html_document:
toc: true
params:
nIter: 10
metadata: TRUE
save: TRUE
---
Load necessary libraries for analysis
```{r setup}
knitr::opts_chunk$set(dev = 'png', dpi = 300, fig.height = 10, fig.width = 10,
root.dir = '/clusterfs/kslab/E... |
8dc01c33d16db1b4c10c72325689b713069a2ab496213b6438a9c70373568921 | R | 86,892 | 1,878 | ################################################################################
### Modifier Interval Candidate Gene Pipeline Part 2,3:
### How many genes are expressed within each modifier interval set?
### Zhao et al., 2022 Developmental Cell scRNA-seq data: Mouse Intestinal Atlas
### by Age. Which modifier inte... |
46afb0cddc5671543d66ffae78311b169c2b6481fcc00e0e5d63541c11f6d2c5 | R | 97,615 | 3,004 | ####Isoform Switch Functions ###
switchPlotTranscript <- function(
### Core arguments
switchAnalyzeRlist,
gene = NULL,
isoform_id = NULL,
### Advanced arguments
rescaleTranscripts = TRUE,
rescaleRoot = 3,
plotXaxis = !rescaleTranscripts,
reverseMinus = TRUE,
ifMultipleIdenticalAnnot... |
4b8d3c386fbeda3e26944e2305c238d9091026995cc1148076938a325ce0eda9 | R | 99,079 | 2,187 | # MODIFIED FUNCTIONS FROM ISOFORMSWITCH ANALYZER PACKAGE
### For analyzing consequences
analyzeSwitchConsequences_new <- function(
switchAnalyzeRlist,
consequencesToAnalyze = c(
'intron_retention',
'coding_potential',
'ORF_seq_similarity',
'NMD_status',
'domains_identifie... |
fbb5e12b231a9658bdbd8dd7e06d76e0a2c9cb148fa1ba4e8713730a47819b8d | R | 100,624 | 2,816 | ---
title: "R Notebook"
output: html_notebook
---
<!--
# Polarization-transition neurite dynamics (duration / velocity) - alternative-cohort variant
## What this file does
Alternative-cohort variant sourced from `D:\DVElite\S2S3_transition`. Reads
per-neurite tip-actin and neurite-actin CSVs (`TipActin*.csv`,
`Neuri... |
1931366a73e3bb7787298bed34f3681921cd1fae8880c84dc07a670d657b0da4 | R | 101,480 | 2,822 | ---
title: "R Notebook"
output: html_notebook
---
<!--
# Lag cross-correlation between neurite-tip velocity and tip actin at polarization transition
## What this file does
Reads per-neurite tip-actin and neurite-actin CSVs (`TipActin*.csv`,
`NeuriteActin*.csv` from per-cell subfolders; lines 65, 97, 130) for neurons... |
f17679352a5f29f30597be37b2f3be05951bf1fe97449ac5eae20ad14b9977dc | R | 103,149 | 2,408 |
############### Script generated by Jonathan Gallego Rudolf ####################
##### Progression to MCI analysis
##### 1) Cox regression models
### Survival analysis based on Cox regression proportional hazard models
### to estimate the risk of progression to MCI and the added value of incorporating ... |
b822bbed44dda05a2d0a70e3070907e9a00bb4bc838b084dc2286267c5820f0f | R | 113,540 | 2,077 | ---
title: "Analysis of IfAdo EEG data"
author: "Douglas J Angus"
date: "created 2025-09-23; updated 2026-05-12"
output:
html_document: default
word_document: default
pdf_document: default
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
```{r packages_data, include=FALSE}
library(tidyvers... |
babacf6961a9a1901fec6638e57c52b086635f342cea2653c8929d74ddec3205 | R | 123,983 | 2,987 | ---
title: "diff136_iNd35_ctrl_asah1e1_axonalproteome"
output: html_document
date: "`r Sys.Date()`"
chunk_output_type: console
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
# =================================================
# Module 0: Setup & Configuration & Experimental Background
# ====... |
e296a0d1ddf745996ff9448f24bd107dff194652e4a8306bf53fd1cc8565e6a3 | R | 139,475 | 3,306 | ### MAKING FIGURES ###
library(ggplot2)
library(ggalluvial)
library(dplyr)
library(tidyr)
library(data.table)
library(stringr)
library(readxl)
library(ggpubr)
library(cowplot)
library(ggrepel)
library(arrow)
library(gprofiler2)
setwd("")
# FIGURE 3A ----------------------------------------------... |
c1010a42a4899ebcf8189cf967221a441dc362302d40a36a3ec720339ed29217 | R | 140,083 | 3,077 |
#' Compute and visualize the contribution of each ligand-receptor pair in the overall signaling pathways
#'
#' @param object CellChat object
#' @param signaling a signaling pathway name
#' @param signaling.name alternative signaling pathway name to show on the plot
#' @param sources.use a vector giving the index or th... |
ac3a875f7bc9bdb61837c92403608cb8da25bb4afc710c08445a0feffaeb2262 | R | 141,900 | 3,731 | ---
title: "PGC_multi_ancestry_analysis"
author: "Xavier Bledsoe"
date: "4/30/2025"
output:
html_document:
code_folding: show
toc: true
toc_float: true
number_sections: true
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE, collapse = TRUE)
library(data.table)
library(stringr)
librar... |
575f9582b0b222e286283a45d8ed56df26295903516aef7abb44388788e800c4 | R | 145,109 | 3,148 |
#' Compute and visualize the contribution of each ligand-receptor pair in the overall signaling pathways
#'
#' @param object CellChat object
#' @param signaling a signaling pathway name
#' @param signaling.name alternative signaling pathway name to show on the plot
#' @param sources.use a vector giving the index or th... |
b21f1cf6628ca6bd7599feba87bff77fab4ccd3bbaeaf57155a8c3c906ac28fd | R | 169,293 | 3,339 | ---
# Written by Gisela Gabernet, Stefan Czemmel, Silvia Morini, Oskar Wacker, QBiC and released under the MIT License
output:
html_document:
toc: true # table of contents
toc_float: true # float the table of contents to the left of the main document content
toc_depth: 3 # header levels 1,2,... |
a046ff32c4318eac519cc616b922d8f3f62729ee6442d816689cf350df58f1ae | R | 176,428 | 4,284 | ---
title: "Vetere_2026_AllPlotsAndStats_V2"
output: word_document
date: "2026-05-03"
---
```{r setup, echo=FALSE, warning=FALSE}
# load libraries and set up color palettes and general functions
library(readxl)
library(data.table)
library(dplyr)
library(tidyverse)
library(plyr)
library(plotrix)
library(car)
library(... |
4bf8d06989ea050f9f0187c878cbbec1456a449ed522407d6788df0af7c3b392 | R | 180,268 | 3,949 | # Wrappers for functions
TrainTestModels_wrapper = function(object,
assay = 'RNA',
plot = FALSE,
expressed.genes = NULL,
proportion = 0.6,
... |
13571b119efb76b18d570feae80a0679f7ddf5ef82c928037977b30fed231b8f | R | 200,000 | 4,859 | ---
title: "Amacrine OrthoType analysis"
output:
html_document:
toc: true
keep_md: true
params:
biomart: FALSE
prep_ortho: FALSE
batch_int: FALSE
harmony: FALSE
save: FALSE
bigmatrix: FALSE
shuffling: FALSE
StopCheckPoint1: FALSE
StopCheckPoint2: TRUE
StopCheckPoint3: TRUE
expr_corr: FA... |
a4989b2bce7c34cfc30e5fef6ce0ff6f68976e9f6dc96b3727dbe0b4555b7204 | R | 200,000 | 4,412 | ---
title: "Amacrine cell manuscript figures"
output:
BiocStyle::html_document:
toc: true
---
Load necessary libraries for analysis
```{r setup}
source("../../utils/dario_functions.R")
LoadLibraries(load.lisi = FALSE)
SourceFiles()
JS.THRESHOLD = 0.10
```
Add new orthotype labels
```{r}
ac.ortho = LoadACOrt... |
7dd18697ae69a2659e92f8ee98a17adb1d8da15386a45bd71f82d710f49e7c54 | R | 200,001 | 2,776 | ## R script for analyses on rhizosphere microbiomes and their link with root phenotypes, yield and bulk soil physiochemical properties ##
## Please note that Microsoft Copilot was used to obtain suggestions about code building and analyses implementation
## Digging for meaningful connections: associations between ro... |
91beb689a30424d8fccf3d0c71d460d72bc556196c5c86dfbaef07c6220f2010 | R | 200,001 | 2,925 | ## R script for analyses on plant performance, root phenotypes and bulk soil physiochemical properties ##
## Please note that Microsoft Copilot was used to obtain suggestions about code building and analyses implementation
## Digging for meaningful connections: associations between root phenotypes and rhizosphere mi... |
847c12156e8a507ab3d361da5ab0041a7d9e65d93c0cff33c3fb20fb55fdf85d | R | 200,009 | 5,677 | # Dario's functions!
compare_frequency = function(object){
# 1. Pre-calculate totals to avoid repeated subsetting
total_sc <- sum(object$species == "scRNA-seq")
total_xen <- sum(object$species == "Xenium")
# 2. Build the dataframe
count.df <- data.frame(
type = as.numeric(ExtractString(names(... |
9f00fa053e1af3782e0684eaa7923943c9960c8cdf35742547b80f0d1bbe0a43 | R | 200,054 | 4,896 | ---
title: "diff132_d50_nDIA"
output: html_document
date: "`r Sys.Date()`"
chunk_output_type: console
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
# =================================================
# Module 0: Setup & Configuration & Experimental Background
# =============================... |
576ebc73d42b4f8e6146ab6515340e90480a299bac2645b838ef73a059985893 | R | 200,160 | 3,744 | #' ggplot theme in CellChat
#'
#' @return
#' @export
#'
#' @examples
#' @importFrom ggplot2 theme_classic element_rect theme element_blank element_line element_text
CellChat_theme_opts <- function() {
theme(strip.background = element_rect(colour = "white", fill = "white")) +
theme_classic() +
theme(panel.bord... |
332fdda46b2601ea81fcab5fcf84c187a9809c87453cab185f565a8a7e8d5a40 | R | 200,176 | 3,721 | #' ggplot theme in CellChat
#'
#' @return
#' @export
#'
#' @examples
#' @importFrom ggplot2 theme_classic element_rect theme element_blank element_line element_text
CellChat_theme_opts <- function() {
theme(strip.background = element_rect(colour = "white", fill = "white")) +
theme_classic() +
theme(panel.bord... |
9da91234d7685e67346bbb0257fe873f68e45f2a3af8da932e169de41230a63d | Rust | 255 | 16 | pub mod adapter;
pub mod alignment;
pub mod bam;
pub mod cli;
pub mod clump;
pub mod demux;
pub mod fastq;
pub mod fastqc;
pub mod filters;
pub mod format;
pub mod io;
pub mod parallel;
pub mod quality;
pub mod report;
pub mod specialty;
pub mod trimmer;
|
8d4cf626a35b36d02b3c177ce984146deca973d8f94918b8266c61cda27ab9a9 | Rust | 2,911 | 76 | use std::env;
use std::process::Command;
use std::time::{SystemTime, UNIX_EPOCH};
fn git_short_hash() -> String {
Command::new("git")
.args(["rev-parse", "--short", "HEAD"])
.output()
.ok()
.filter(|o| o.status.success())
.and_then(|o| String::from_utf8(o.stdout).ok())
... |
91fea7ebe3ef57a77b19c197b73740699a2d22b963dd279b796bdcbe8569f8c4 | Rust | 3,140 | 109 | use std::ptr;
use std::alloc::{alloc, dealloc, Layout};
use std::slice;
use jxl_oxide::{FrameBuffer, JxlImage, PixelFormat};
#[no_mangle]
pub fn malloc(size: usize) -> *mut u8 {
let layout = Layout::from_size_align(size, std::mem::align_of::<u8>()).unwrap();
unsafe {
let ptr = alloc(layout);
i... |
0bd8f9e54f6661a2ea3fcdd084f613a68cad990bcb86cf8c43643c3e16231d07 | Rust | 4,100 | 107 | //! Reference sketch — paired-uBAM streaming de-interleaver with bounded-buffer
//! adversarial-input detection.
//!
//! NOT compiled or wired into the crate. Carry the algorithm into `src/bam.rs`
//! when implementing the plan.
//!
//! Strategy:
//! * Strictly-interleaved happy path (`R1, R2, R1, R2, …`) → drains in... |
231c541fc3fdcbc7f3a4cd38b9c39952971a9e78b612c00ecece9f3ab1d542a3 | Rust | 6,091 | 172 | //! FastQC integration via the bundled `fastqc-rust` library.
//!
//! Replaces the v0.6.x-style shell-out to an external `fastqc` binary
//! with an in-process call. Targets byte-equivalent output to Java
//! FastQC 0.12.1 — the same version we previously bundled in the Docker
//! image — see <https://github.com/ewels/... |
1315ed4763563d82de9db92b3fc0ff0f9e2b52c84b243bdc19d666941f070d08 | Rust | 7,220 | 205 | //! Binary-driven integration tests for `--passthrough`.
//!
//! These tests close the §7 coverage gap (`--cores 1` dispatcher integration)
//! from the plan v2 validation matrix — exercising
//! `main.rs::run_paired` end-to-end via the built binary rather than the
//! library entry points. That covers wiring the lib t... |
9ed6c8730a2308cc4c395ee69673bb59f2b7833fb7737daddb4abbeb8cf28b15 | Rust | 7,624 | 206 | //! Input-format detection for FASTQ vs uBAM.
//!
//! Two-stage check (PLAN §3.1 / §5 step 2):
//!
//! 1. **Cheap byte peek.** First byte `@` → plain FASTQ. First three bytes
//! `1F 8B 08` → gzip family; fall through.
//! 2. **Decompress first block + payload check.** For the gzip family,
//! decompress and read... |
fa9b8ac70da2b7fb909baf8c1a3ef57e30f9b148c3b764daca36594eb00fa898 | Rust | 8,075 | 253 | //! Read filtering by length, N-content, and max-length.
use crate::fastq::FastqRecord;
/// Filter result for a single read.
#[derive(Debug, PartialEq)]
pub enum FilterResult {
/// Read passes all filters
Pass,
/// Read is too short (below length_cutoff)
TooShort,
/// Read is too long (above max_l... |
0687f92729888ba9e82d53a8c700afd4fc9e9059b95fab91e65606184a85181b | Rust | 9,821 | 258 | //! Binary-driven integration tests for uBAM input support (#316).
//!
//! These tests exercise `main.rs::run_single_file` / `run_paired_ubam_single_file`
//! end-to-end via the built `trim_galore` binary, covering wiring the lib
//! tests can't reach:
//! * format detection → reader factory dispatch
//! * output-p... |
d7981fc68fc99748a61d1d8d8da2b519ad2941ff7f23983e2a70f1e40699ed9b | Rust | 11,626 | 323 | //! Spike 1 — RecordSource dispatch overhead.
//!
//! Question: does `Box<dyn RecordSource>`-style dynamic dispatch in the inner
//! record-read loop measurably regress wall-clock vs a concrete-type baseline
//! or an `enum { Fastq(...), Bam(...) }` static-dispatch shim?
//!
//! Compares three loop bodies over the same... |
5ab138f5bdb6c28698a9a50e812529963f66b06387fcba356fc7d4e2a244c890 | Rust | 14,773 | 404 | //! Post-trimming demultiplexing based on 3' inline barcodes.
//!
//! After adapter/quality trimming, reads are split into per-sample files
//! based on barcode sequences at the 3' end of each read. The barcode is
//! removed from the sequence and appended to the read ID as `_BC:<barcode>`.
//! Reads that don't match a... |
058d0d06c4e55290706f8cf1f18e3491ea613217213e21dd63495c3f37db161c | Rust | 16,697 | 507 | //! Quality trimming using the BWA algorithm.
//!
//! This implements the same quality trimming algorithm used by Cutadapt,
//! which is based on the algorithm from BWA (Li & Durbin, 2009).
//!
//! The algorithm finds the longest suffix of the read where the average
//! quality is below the cutoff, using a running sum ... |
96d0ee1f2dd48acd8dcf8022a3705efd521d9beeb7741135d1339b525be45769 | Rust | 19,981 | 536 | //! Binary-driven integration tests for uBAM **output** support
//! (PLAN v2.1 §5 step 5).
//!
//! Tests exercise the built `trim_galore` binary with `--output-format ubam`
//! end-to-end, covering wiring the lib-tests can't reach:
//! * `main.rs::run_ubam_output` dispatch (SE / PE-two-FASTQ / PE-one-uBAM-interleaved... |
358f6b1a3a5189340850459ac2194b41d405625c868e7b8d93fff94dd621a6ba | Rust | 20,176 | 549 | //! Output file naming conventions and I/O utilities.
//!
//! Implements TrimGalore-compatible output naming:
//! - Single-end: *_trimmed.fq(.gz)
//! - Paired-end: *_val_1.fq(.gz) / *_val_2.fq(.gz)
//! - Unpaired: *_unpaired_1.fq(.gz) / *_unpaired_2.fq(.gz)
//! - Reports: *_trimming_report.txt
use anyhow::{Context, Re... |
23c2288d36a3f3cdf692fff9426d6891b4d1b7b79ae95670651b636c1899ddce | Rust | 22,552 | 567 | //! Optional read reordering for tighter gzip compression (`--clumpify`).
//!
//! When `--clumpify` is enabled, the reader thread routes reads to N in-memory
//! bin buffers keyed by a canonical k-mer minimizer. When a bin's accumulated
//! raw bytes exceed the per-bin byte budget, the bin is sorted by minimizer
//! ke... |
477dcfa31a759a09126bc8c890c7903bc517515cef55572f6d724d6ed1aefa88 | Rust | 25,456 | 787 | //! Specialty trimming modes that bypass the normal trimming pipeline.
//!
//! These modes (--hardtrim5, --hardtrim3, --clock, --implicon) process
//! input files with simple fixed operations and exit immediately.
use anyhow::{Result, bail};
use std::path::{Path, PathBuf};
use crate::bam::{BamWriter, peek_header};
us... |
7b2be82155634bc7fe08ac728e9eeadad34001cc537aaa96856b1bc7e493200a | Rust | 29,380 | 704 | //! Semi-global adapter alignment engine.
//!
//! Reimplements Cutadapt's core adapter matching algorithm using
//! unit-cost semi-global dynamic programming alignment.
//!
//! Per @an-altosian's #248 audit, ~62% of reads in real-world
//! Buckberry-scale data carry no adapter at all, and for those reads
//! the entire... |
4d8ac4dcba021425f865a4a9fa4a43c2837744cee6ef9eb808c4a33072b0ef84 | Rust | 32,271 | 895 | //! FASTQ record type and streaming I/O.
//!
//! Provides gzip-aware reading and writing of FASTQ records with 64KB buffers
//! for efficient I/O throughput.
use anyhow::{Context, Result, bail};
use flate2::Compression;
use flate2::read::MultiGzDecoder;
use flate2::write::GzEncoder;
use gzp::deflate::Gzip;
use gzp::pa... |
5046d3ea0cac0c0cfb56087a1249bcd630e247ccc144d89c21ec827585c02f45 | Rust | 32,452 | 911 | //! Adapter definitions, presets, and auto-detection.
//!
//! Provides built-in adapter sequences for common sequencing platforms
//! and auto-detection by scanning the first 1M reads.
use anyhow::{Context, Result};
use std::io::BufRead;
use std::path::Path;
/// Built-in adapter presets.
#[derive(Debug, Clone)]
pub s... |
3681f3920b4a6ec53314e28e7885e778d11030bed7827b9ec60c551427493176 | Rust | 48,548 | 1,172 | //! Trimming orchestrator for single-end and paired-end pipelines.
//!
//! This module wires together quality trimming, adapter trimming, clipping,
//! filtering, and report generation into complete processing pipelines.
use crate::alignment;
use crate::fastq::{FastqRecord, FastqWriter};
use crate::filters::{self, Fil... |
963377fa1b3874ee318919cd6be5d90fcd57638eca257880160e13698e9415f9 | Rust | 63,408 | 1,667 | //! Command-line argument parsing and validation.
use clap::Parser;
use std::path::PathBuf;
/// Output container format. FASTQ is the default and preserves byte-identity
/// with Perl Trim Galore 0.6.11. uBAM is opt-in and carries the input BAM's
/// aux tags through (via `--preserve-tags`).
///
/// See `plans/062520... |
06bae91095c2afa022a7010dff1cb4c25060345112a9ed5f11c9f16a7f86fa80 | Rust | 64,597 | 1,764 | //! Trimming report generation.
//!
//! Generates TrimGalore-compatible trimming reports that can be parsed by MultiQC.
use std::io::Write;
/// Statistics collected during trimming.
#[derive(Debug, Default, PartialEq)]
pub struct TrimStats {
/// Total sequences processed
pub total_reads: usize,
/// Reads ... |
3d66cb733f32e31bdb34d128fed9f8e9fba08d9ef6b6c7c66bd872bdc2cc4ada | Rust | 67,317 | 1,672 | //! uBAM (unaligned BAM) input reader.
//!
//! Converts a `noodles::bam` record stream into the `FastqRecord` shape the
//! rest of the trimming pipeline expects. See `plans/06252026_ubam-input-support/PLAN.md`
//! §3.2 for the record-conversion contract.
use anyhow::{Context, Result, bail};
use noodles::bam;
use nood... |
4a6f412e4bc41c43735685e5056d4b7ba4ab0f6d901387362390613c56dfa8ed | Rust | 75,969 | 2,029 | use anyhow::{Context, Result};
use clap::Parser;
use std::fs::File;
use std::io::{BufWriter, Write};
use std::path::Path;
use trim_galore::adapter;
use trim_galore::bam::BamReader;
use trim_galore::cli::{Cli, rewrite_perl_short_flags};
use trim_galore::clump;
use trim_galore::demux;
use trim_galore::fastq::{FastqReade... |
aed94fdac4132e085b3cde4b2dfd6dc1afea3c1dddf3d607aa70f8ede5b18bc9 | Rust | 90,845 | 2,350 | //! Worker-pool parallelism for trimming pipelines.
//!
//! When `--cores N` is specified (N > 1), reads are distributed across N
//! worker threads. Each worker handles trimming **and** gzip compression,
//! producing independently-compressed gzip blocks. The blocks are written
//! to output files in sequence order, p... |
0e63cf88b505a1a04327bb666af3a985c5e11835c0c00aed4058c0dcc315d60e | SAS | 1,847 | 68 | # SMakefile for zlib
# Modified from the standard UNIX Makefile Copyright Jean-loup Gailly
# Osma Ahvenlampi <Osma.Ahvenlampi@hut.fi>
# Amiga, SAS/C 6.56 & Smake
CC=sc
CFLAGS=OPT
#CFLAGS=OPT CPU=68030
#CFLAGS=DEBUG=LINE
LDFLAGS=LIB z.lib
SCOPTIONS=OPTSCHED OPTINLINE OPTALIAS OPTTIME OPTINLOCAL STRMERGE \
NOICO... |
72a76b832dcb4cd2784652620c244a85a173de7009d48ebd03e3a107553439bf | SAS | 17,179 | 381 | /*===========================================================================*
| es_identify.sas
|
| Forensic helper: given an effect size that does not match its F and
| degrees of freedom, work out which statistic it actually is and how it
| was computed.
|
| Companion file: mixed_effectsize.sas -- comp... |
b8b034cdf699f363cdc5c9d38d410bf2de83be0724dc5ec1a0db34f9d27cf405 | SAS | 51,092 | 1,000 | /*===========================================================================*
| mixed_effectsize.sas
|
| Effect sizes for fixed effects in models fitted with PROC MIXED --
| MARGINAL models (REPEATED statement, population-average) and true
| MIXED models (RANDOM statement, subject-specific) alike.
|
| THE ... |
f39c887c8dc970b0f4f874c82023f9edbc0002ad193566b907c6c9c82faaaea3 | SPSS | 1,911 | 68 | * Encoding: UTF-8.
*Multilayer Perceptron Network.
MLP status (MLEVEL=N) BY exposure
/PARTITION TRAINING=7 TESTING=3 HOLDOUT=0
/ARCHITECTURE AUTOMATIC=YES (MINUNITS=1 MAXUNITS=50)
/CRITERIA TRAINING=BATCH OPTIMIZATION=SCALEDCONJUGATE LAMBDAINITIAL=0.0000005
SIGMAINITIAL=0.00005 INTERVALCENTER=0 INTER... |
fa5480e159dba97b85ab6ae888758d42709ac4c75ddf1b3cbb52cc42f4aa835a | SPSS | 2,228 | 86 | * Encoding: UTF-8.
Classification from Predictive Models
RECODE tree (4=1) (2=1) (3=0) (1=0) INTO tree.cat.
EXECUTE.
RECODE lr (4=1) (2=1) (3=0) (1=0) INTO lr.cat.
EXECUTE.
RECODE ann (4=1) (2=1) (3=0) (1=0) INTO ann.cat.
EXECUTE.
RECODE random (4=1) (2=1) (3=0) (1=0) INTO random.cat.
EXECUTE.
RECODE svm (4=1) (2... |
cb6ae4074ba38b146d12d495156a64e2e86fb1e59c2a2c7acee3082a979e6844 | SPSS | 2,888 | 139 | * Encoding: UTF-8.
SORT CASES BY final.
SPLIT FILE LAYERED BY final.
FREQUENCIES VARIABLES=hcho pm2.5 tvoc pm0.3 pm0.5 pm5 metsec temp rh co2 co airflow
/FORMAT=NOTABLE
/STATISTICS=STDDEV SEMEAN MEAN MEDIAN
/ORDER=ANALYSIS.
SPLIT FILE OFF.
EXAMINE VARIABLES=hcho pm2.5 tvoc pm0.3 pm0.5 pm5 metsec temp rh co2 ... |
b6e618216676b967f16fae2e3e6246841d2f054c0b5a5e2e2dd6ff390c530fda | SPSS | 3,288 | 147 | * Encoding: UTF-8.
Algorithm for Predictive Analytics Pattern Recognition
// High areas
1) Ventilation problem
2) external exposure to particulate + aldehyde
3) health link chemical related complaints
Moderate
1) ventilation maintainance/ indoor activities
2) health symptoms
3) particulate and aldehyde
Low
1) poor ... |
0e0532382f7971c0a0f348707438d899bd84235bc21bdab7db979ac8876c4794 | SPSS | 55,599 | 1,733 | * Encoding: UTF-8.
DATASET ACTIVATE DataSet1.
New Score SBS
--[Coding the SS Final 0-3]--based on the fact of the because of the indoor elements
COMPUTE sss1=s1+ss1.n.
EXECUTE.
COMPUTE sss2=s2+ss2.n.
EXECUTE.
COMPUTE sss3=s3+ss3.n.
EXECUTE.
COMPUTE sss4=s4+ss4.n.
EXECUTE.
COMPUTE sss5=s5+ss5.n.
EXECUTE.
COMPUTE sss... |
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