sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
23648ad83dbacb3201f590d2353d578d881c6966ce6e1336313ff1930df2004c | R | 66,484 | 1,162 | ---
title: "Whole-brain comparison of rodent and human brains using spatial transcriptomics"
subtitle: "Results 2, Figure 2"
author: "Antoine Beauchamp"
date: 'March 14th, 2022'
output: html_document
---
# Initialization
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE,
include = F... |
81a73a0fc827cbe30f1fdd327b105155781a48f1b98448dc904ddc19b96a49b1 | R | 67,987 | 1,204 | ---
title: "Whole-brain comparison of rodent and human brains using spatial transcriptomics"
subtitle: "Results 2, Figure 2"
author: "Antoine Beauchamp"
date: 'March 14th, 2022'
output: html_document
---
# Initialization
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE,
include = F... |
aef416908e211328f51cddf2abb965e4166cff792d0b28f542b1e14509eb1073 | R | 69,916 | 1,652 | data(EPSatlas, envir=environment())
data(SAGITTALatlas, envir=environment())
data(atlasIndex, envir=environment())
#data(atlasOntology, envir=environment())
data(ontology, envir=environment())
#' Get atlas binary image
#'
#'
#' @param coordinate matching coordinates in the main plane to be registered to (in millime... |
19bf0eb99b189c8e80b6f823a977ac5dc72674df92fa6c0a31c065296a13dcf5 | R | 73,218 | 427 | ---
output:
pdf_document:
includes:
in_header: TranscriptomicSimilarity_biorxiv_header.tex
before_body: TranscriptomicSimilarity_biorxiv_front_matter.tex
bibliography: TranscriptomicSimilarity.bib
csl: science-advances.csl
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE,
... |
4cb81f7183ce5a468a1a806ed808dd13a952f866c3e96e1299da3f2d989e75f3 | R | 88,686 | 1,646 | library(CellChat)
library(shiny)
library(Seurat)
library(ggplot2)
library(dplyr)
library(tibble)
library(shinydashboard)
library(stringr)
library(tableHTML)
library(waiter)
library(shinyjs)
library(markdown)
library(DT)
library(slingshot)
library(viridis)
library(shinycssloaders)
waiting_screen <- tagList(
spin_lo... |
af8023943073b718e624ddec2df5373cf409fbf7a43c48c207faa85b6ace14c2 | R | 90,814 | 582 | ---
output:
pdf_document:
includes:
in_header: TranscriptomicSimilarity_elife_header.tex
before_body: TranscriptomicSimilarity_elife_front_matter.tex
bibliography: TranscriptomicSimilarity.bib
csl: elife.csl
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE,
in... |
fc7ad1589d9dbcb235281b4623feacee34e3eda4670918224dd3ab8eea3c933d | R | 91,616 | 604 | ---
output:
word_document:
reference_docx: "template_word_elife.docx"
bibliography: TranscriptomicSimilarity.bib
csl: elife.csl
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE,
include = FALSE,
cache.lazy = FALSE)
```
```{r libraries}
library(tidyv... |
0952e33ab8a32fa5cc4e92d97d4bc8d93db846482fcfd783e7bffbdcba5d1c08 | R | 103,988 | 1,930 | EEGData <- read.csÅv("R_Data_Demo_EEG_72p.csv")
library(lmerTest)
library(tidyverse)
library(dplyr)
library(psych)
library(plyr) # packageVersion("plyr") 1.8.4
library(lmSupport)
# Change WD
setwd("/Users/joshuaupshaw/Documents/A_Projects/First Year Project/Data/R project")
# Remove blank rows 64-79
# EEGData <- EEGD... |
6a2c8b42e554ae84d859a79142c73331f032844457b8a54f8cc3e5182654d075 | R | 105,550 | 2,294 | library(limma)
library(edgeR)
library(RColorBrewer)
library(dplyr)
library(ggplot2)
library(VennDiagram)
library(mixOmics)
library(devtools)
library(dplyr)
library(RSkittleBrewer)
library(genefilter)
library(ballgown)
library(tidyverse)
library(ggrepel)
library(variancePartition)
library(doParallel)
library(stringr)
li... |
4a3f8850478de18586f52fb3f12986872cc7b96ea7af90f4b3ec76b76a0b0e5b | R | 135,773 | 2,121 | # Packages
library(lmerTest) # packageVersion("lmerTest") 3.1.1
library(psych) # packageVersion("psych") 1.8.4
library(plyr) # packageVersion("plyr") 1.8.4
library(ICC) # packageVersion("ICC") 2.3.0
library(lmSupport) # packageVersion("lmSupport") 2.9.13
library(moments) # packageVersion("moments") .14
library(Performa... |
ea8f58a3e1f39ee46a3889655069e519dbcaa81534cb1c913a5534d04207bde3 | R | 142,294 | 3,099 | # title: "decidua MDS plots"
# author: "Kimberly Olney"
# date: "02/14/2020"
# output:
# pdf_document: default
# html_document:
# df_print: paged
library(limma)
library(edgeR)
library(RColorBrewer)
library(dplyr)
library(ggplot2)
library(VennDiagram)
library(mixOmics)
library(devtools)
library(dplyr)
library(str... |
6325bb4a2958b5cfc2e1d38a823f944a10ef316e5d396ab4001aa2ac3b62761c | R | 200,000 | 3,156 | ---
title: "Akeret et al. 2021_Anatomical phenotyping and staging of brain tumors"
subtitle: "Statistical code"
author: "Kevin Akeret"
---
# Setup
```{r Setup, message = FALSE, warning = FALSE}
knitr::opts_chunk$set(message = FALSE, warning = FALSE)
library(openxlsx)
library(readxl)
library(biostatUZH)
library(tidy... |
31cb3086871495243ef94b06a6fc05ddb4c5b38ebbe0c1603dc3a5b1f683decb | Rust | 444 | 15 | //! Native numerical kernels for the BSB.
//!
//! The algorithm core (`geom`, `bvh`, `poisson`) is pure Rust with no Python
//! dependency, so it can be unit-tested with `cargo test`. The `py` module
//! holds the PyO3 bindings and only compiles under the `python` feature, which
//! maturin enables when building the ex... |
33a6494d55decde303e158e887ef527fd084ebda09fccd873e88b65e26995c45 | Rust | 1,406 | 48 | //! A small seeded PRNG (SplitMix64-seeded xoshiro256**), so kernels that need
//! randomness (Poisson sampling, affinity subsampling) are reproducible from a
//! seed regardless of thread or platform, without an external crate.
pub struct Rng {
s: [u64; 4],
}
impl Rng {
pub fn seeded(seed: u64) -> Self {
... |
92cc7cb53eb1784948f55dab8e146275fdf433c96330dae3511946e9e3bd46b7 | Rust | 6,664 | 238 | //! Geometric primitives: 3D vectors, axis-aligned bounding boxes, and the exact
//! segment-to-segment (capsule) distance test that is the connectivity criterion.
pub type Vec3 = [f64; 3];
#[inline]
pub fn sub(a: Vec3, b: Vec3) -> Vec3 {
[a[0] - b[0], a[1] - b[1], a[2] - b[2]]
}
#[inline]
pub fn add(a: Vec3, b: ... |
fb4350b8e2501d2e13772a095eadfb441728f7869cf483bc716a69cc9841c2fe | Rust | 7,058 | 204 | //! PyO3 bindings exposing the pure-Rust kernels to Python. Compiled only under
//! the `python` feature (enabled by maturin); the algorithm core stays free of
//! any Python dependency so it can be unit-tested with `cargo test`.
use numpy::ndarray::Array2;
use numpy::{
IntoPyArray, PyArray2, PyReadonlyArray1, PyR... |
7b8f539a3d2fcbb44fe6547e7bed3b8a86cfd6cda60e1743a907b0787cfe8e04 | Rust | 8,502 | 273 | //! Bridson Poisson-disk sampling in a 3D box, with optional fixed points.
//!
//! `fixed` points are treated as already-placed neighbours (e.g. somas from
//! adjacent chunks read in as a halo): new samples respect `min_distance` to
//! them, but they are not themselves emitted. This is what lets per-chunk
//! samplin... |
ebe4b946e8d2c0f1d6408c258744487f013d4e5f929fdd1b8b6223531b40070b | Rust | 13,074 | 415 | //! A bounding-volume hierarchy over line segments, used as the per-morphology
//! acceleration structure (the "BLAS"). Build once over one morphology's
//! segments in its local frame; query it with another cell's segments,
//! transformed into this frame, to find segment pairs within contact distance.
//!
//! The bro... |
76c50e4942e9d40bad7e925b9b84a235a2274dd435d590d681488af7684a7d2b | Rust | 14,528 | 475 | // Copyright (c) 2020 10X Genomics, Inc. All rights reserved.
extern crate clap;
extern crate csv;
extern crate data_encoding;
extern crate failure;
extern crate rayon;
extern crate ring;
extern crate rust_htslib;
extern crate simplelog;
extern crate tempfile;
extern crate terminal_size;
#[macro_use]
extern crate log;... |
3c124ed81d4b185b76d92284412a8f455ea2af7929b066126c8e5aa74d1abb74 | Rust | 14,641 | 399 | //! Whole-connection kernel: given a morphology library and the two cell
//! populations as instances (morphology index + rotation + position), find every
//! pair of cells whose morphology segments come within a contact distance, and
//! return the `[cell, branch, point]` location triples.
//!
//! This is the full two... |
da6d88980bbe922cdf848609582b23cb52d4409f0a5d642aef35f4fd74faaef8 | Rust | 17,184 | 358 | extern crate fnv;
use fnv::FnvHashMap;
use std::env;
use std::io::BufReader;
use std::io::BufRead;
use std::fs::File;
static DEBUG: bool = false;
static DEBUG_CELL: &str = "ACGGGTCGTTCCACGG-1";
fn main() {
let args: Vec<String> = env::args().collect();
let calls_file = &args[1];
let cluster_file = &args[2... |
b5333b122e327c9a3e99c1307505323f8713facf8018794eca6b018add950fa1 | Rust | 26,095 | 516 | extern crate fnv;
#[macro_use]
extern crate clap;
extern crate hashbrown;
extern crate statrs;
use std::io::BufReader;
use std::io::BufRead;
use std::fs::File;
use hashbrown::{HashMap,HashSet};
use fnv::FnvHasher;
use std::hash::BuildHasherDefault;
type FnvHashMap<T,V> = HashMap<T,V, BuildHasherDefault<FnvHasher>>;
ty... |
803741f40b3c027b55fedcfcb0b5731f9b9613486f108b0f728d3514ab67e36c | Rust | 37,484 | 861 | #[macro_use]
extern crate clap;
extern crate hashbrown;
extern crate rand;
extern crate statrs;
extern crate itertools;
extern crate rayon;
extern crate vcf;
extern crate flate2;
use flate2::read::MultiGzDecoder;
use vcf::*;
use rayon::prelude::*;
use rand::Rng;
use rand::rngs::StdRng;
use rand::SeedableRng;
use cl... |
36f1c858163493be97edbefe5f14e1ea043c19c5c6b77ef9c9ca318b0efa066b | Scala | 968 | 26 | # -*- mode: dockerfile -*-
#
# Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (th... |
5385ee1cce9ea750e79af82dc4a3c010a1a2f55ae8c1c91ec76509cb9288bca1 | Shell | 45 | 3 | #!/bin/bash
./run_jawclench.sh
./run_p300.sh
|
b2e9f77764ba9d67801535d883220f8b425b8a9ac1411d977753a33617b38c02 | Shell | 55 | 1 | gmx rmsf -s chainA.tpr -f all_combined.xtc -o rmsf.xvg
|
48f832d923ef41dff028523255ca762c455996e6b8f99ad5621b377607605931 | Shell | 59 | 6 | #!/bin/sh
rm -rf docs
mkdir docs
doxygen
cd docs
git add .
|
a3733792abb663b62505235d2eb8fec62bb6df7d538d97498b2b344e87f53501 | Shell | 75 | 3 | #!/usr/bin/bash
module load miniconda/3
source activate ~/.conda/envs/meld
|
f800d7bafc87d05a28243aadc25e5ac35784add960e5753db186b4f743e69422 | Shell | 75 | 4 | for f in $1
do
perl Stockholm2Fasta.pl $f > ${f%.stockholm}.fasta
done
|
67378452bf04a5dea986fe2c56dc8532a105050cfe509a29110011bb2a2fc8b2 | Shell | 79 | 7 | for entry in "examples"/*
do
for f in $entry/*
do
python $f
done
done |
a2b50ed6cc7a4587f66b3b1eff97f1a0bac78b410b39a32035ec087189b3f2fc | Shell | 81 | 1 | METEOR_PACKAGE_DIRS="../Packages" meteor --settings ../config/medkenOrthanc.json
|
739d98a75146c13f16db329abcd1b39cecae90b4fe2a7d8450e43c4ae36b7cb8 | Shell | 82 | 3 | #!/bin/bash -p
$1 --no-main-window --python-script "$2" "$3" "$4" "$5" "$6" "$7"
|
974591a25d8f4995a078496560ac6c769ddb6be06d82ec05af09e7a4f0739941 | Shell | 83 | 3 | # rmf 4.22.2020
python ../../scripts/writeFIMOresults.py fileList.fimoGFF6000.txt
|
f25961d216227f484f2016c621e56860273596c5455145bd00ed07cd82e82e46 | Shell | 87 | 3 | # rmf 9.24.2021
for f in *_cleaned.txt; do echo $f >> fileList.cleanedGroups.txt; done |
fc35f3e1f968e138263df5350e293bd79161a9389450ec756ab4ff8f65b27ba8 | Shell | 90 | 9 | #!/bin/sh
rm -rf docs
mkdir docs
doxygen
cd docs
git add .
cd pdf
make
git add refman.pdf
|
bf80f3a3cd23dcb8962248b1a93fb73c9efa24567cad0b545bf53973982d871d | Shell | 93 | 3 | #!/bin/bash
rm -rf hallway_policy_checkpoints hallway_data.db
clear; python solve_hallway.py
|
ff7b5ba1f83fcb3c02adea35cd449dbfb0b7b8e68cb498a2f53a58162d598042 | Shell | 94 | 3 | # rmf 12.4.2020
python ../scripts/writeSecondaryIDsFile.py fbgn_annotation_ID_fb_2020_05.tsv
|
1a3759a87b498e29068d3e0401a87478c9b2fc94889531582ab611a3f9f0b467 | Shell | 95 | 5 | #!/bin/bash
`bedtools getfasta -fi $1 -bed $2 -fo $3.fa -s`
`sed '1d; n; d' $3.fa > $3.txt `
|
5be1808b1c45a5d203e6a01f9de6d7088485346bab0a930dbb20f5e942fa9369 | Shell | 98 | 5 | #!/bin/bash
set -e
rm -rf dataset-gen/datasets
rm -rf simulations/__*
rm -rf simulations/acc_*.txt |
c2f316d1681722dac8ca75d094b3cd4c218a6af52dae6db191d25e9c90815216 | Shell | 98 | 3 | # rmf 12.22.2020
python ../../../../scripts/getDAVIDenrichmentScores.py fileList.DAVIDparsed.txt
|
fdfaece5d28a3fee37f0e5eba3d44ef34d596a23f02248ed7a5d8e0f1ac03569 | Shell | 109 | 3 | # rmf 4.14.2021
awk -F '\t' 'NR > 1 {print $1}' ../fimoSummaryFile_FPKM1.0_p5e-05.txt | sort | uniq | wc -l
|
0703cec8331d881b3992ff78845b1e98e7624c346b4519f3eb6ec76902162bc8 | Shell | 114 | 6 | #!/bin/bash -p
source $FREESURFER_HOME/SetUpFreeSurfer.sh
$FREESURFER_HOME/bin/mkheadsurf -s $1 -srcvol T1.mgz
|
da131575c2410dc627cef164db75f6e31c8a4cbe0f0d72bbde2e33107745187c | Shell | 114 | 4 | iteration=$1
cd /home/despo/adesai/Desktop/1803/Scripts
matlab -nodisplay -r '''diceScript('$iteration');exit'''
|
f8cff7940b110fc9824d3348cd9adebfda1522a6a1177ce775c40332d8731ac0 | Shell | 115 | 2 | echo "Starting Meteor server..."
METEOR_PACKAGE_DIRS="../Packages" meteor --settings ../config/orthancDICOMWeb.json |
f3fb335821dc78cd52ff21fc0a5ba9cd40b4a898a847d904164feec2131a2448 | Shell | 117 | 3 | # rmf 5.6.2021
awk 'NR > 1 {print $1}' transcripts_significantSites_LLCs_phase2to6.txt > LLCsPhase2to6_Xrp1site.txt
|
fc0fd3803fcd1174ed93a1f6ad59eeea7f01009055fcf64d9a33d707c88ff457 | Shell | 117 | 6 | #!/bin/bash -p
source $FREESURFER_HOME/SetUpFreeSurfer.sh
$FREESURFER_HOME/bin/recon-all -s $1 -i $2 -all -qcache
|
4bed16a2ed60e9993bbe132df5481b42ab49e0997bb37564148114194dad323d | Shell | 119 | 3 | # rmf 9.24.2021
for f in *InOld.txt; do outbase=${f%%.txt}; perl scripts/mac2unix.pl $f > ${outbase}_cleaned.txt; done |
ac79cde5f853b9ff679eca97d236c7f5486f42bb8fc24a6918418c67cd66fc2c | Shell | 122 | 2 | echo "Starting Meteor server..."
METEOR_PACKAGE_DIRS="../Packages" meteor --settings ../config/publicOrthancDICOMWeb.json
|
b6cb996d3134ead70f0971a58a68b227d583bd8dbbaaf2609639b12c07e788b3 | Shell | 133 | 4 | for model in ACOARIMA ACOLSTM DecisionNN SemiDirect GRAF UAHS CAHS Narya HASCO RecSim CES SciNet
do
python3 main.py -m $model
done |
c6ad91664ac5f1cdc627bca22ceec49f6beaac6b6b5c092cd3d7cdd15484ec6c | Shell | 134 | 6 | #!/bin/bash
# rmf 4.30.2021, last modified 5.17.2021
for f in *LCs_*Phase*to*.txt; do echo $f >> fileList.maxPhaseGroups.txt; done
|
168f66d1371dc450cd44c071d74486d5610a2ed389e9605b4f1f0582fae4faa0 | Shell | 136 | 5 | #!/bin/bash
# rmf 12.21.2020, last modified 9.20.2021
for f in DAVID*.parse.cleaned.txt; do echo $f >> fileList.DAVIDparsed.txt; done
|
bde46fe6d362cef5610b7cd56b640161c928714ac0610c8ba3444104c7b6380c | Shell | 137 | 5 | #!/bin/bash
# rmf 3.27.2018; last modified 4.2.2019
for f in ERR*fasta; do python ../scripts/runMemeChip.py $f '-meme-mod zoops'; done
|
09ea1cb5d5d15b193c360b0a8c99b067d2170991088439f78a96f0ff81c4a661 | Shell | 138 | 4 | #! /bin/bash
DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
cat $DIR/DISCLAIMER.txt
$DIR/jre/bin/java -jar $DIR/sources.jar $DIR
|
0b0c44b1fc16bd86451db4519828c71da88bcef89e867dda12e760c8d345e23d | Shell | 139 | 5 | #!/bin/bash
# rmf 4.6.2018; last modified 4.2.2019
for f in ERR*.fastq; do base=${f%.*}; fastq2fasta.pl -i $f -o ${base##*/}.fasta; done
|
4329dc5848287da14af865508f2410929064651f289649a6087251790aa493c6 | Shell | 143 | 5 | # rmf 5.14.2020, last modified 10.8.2020
# cleaned up 3.2.2022
# files in order: ELC, RLC, LLC
python plotHistRP24.py R2A.txt R2R.txt A2R.txt
|
df8faa682dd3d708070c0d23fd672c40234ab2b7a6a63233745184eaa5ed518f | Shell | 148 | 3 | # rmf 12.17.2019
python ../../scripts/plotEnhancerTargetDistances.py /nfs0/BB/Hendrix_Lab/Drosophila/Annotations/flybase_r6.06.gtf batch.txt 10000
|
bbd8ef8198598cf3063694107fbbcaab78f13b4dd3b6116361e8b176cf38e39d | Shell | 151 | 5 | #!/bin/bash
# rmf 3.2.2022
python scripts/plotHorizontalHeatmapAndBarplot_sigOnly.py motifEnrichmentSummary_DAVIDgroups_eScore1.3_5FPKM_N10.txt 0.05
|
6f012a6cbcdfe6c0eb4a97a04d37550dcc649e73bb9967d6997e97483ba5417f | Shell | 153 | 9 | for iteration in {1..10000}; do
echo $iteration
qsub -o DiceQCall$iteration.o.txt -e DiceQCall$iteration.e.txt DiceQCall.sh $iteration
#sleep 6
done
|
0d9ed36828a66f3caaa58925214db45310f4f590dc5cd3392d7ab5f2ae6f70d2 | Shell | 155 | 6 | #!/bin/bash
# rmf 1.31.2020, last modified 6.17.2020
# get gene expression files
for f in geneFPKMtable_*.txt; do echo $f >> fileList.geneExpr.txt; done
|
f40c30f4df80a7bcb42447f96f1fc1d26de9bd2eaa186777b7f00f0b00ce7758 | Shell | 155 | 5 | #!/bin/bash
# Usage: ./optimize_qed_scrape_log.sh <slurm-file>
# Writes a new file "<slurm-file>.top_hits"
grep "GraphGymEnv: 0.9[2-9]" $1 > $1.top_hits
|
d901bd4ac7598a819c652a6ba154ec1a3e0b804d7d531f413719347488a37669 | Shell | 159 | 6 | #!/bin/bash
# rmf 1.31.2020, 2.11.2020
# get transcript expression files
for f in transcriptFPKMtable_*.txt; do echo $f >> fileList.transcriptExpr.txt; done
|
6da66c4b0b55b435ad7a02eee88a5761250cc8cdf47267a879dd004b93ecbdc0 | Shell | 162 | 8 | #!/bin/bash
clear
python optimize_qed_evaluate.py \
--restore-dir $1 \
--checkpoint $2 \
--min-atoms 6 \
--max-atoms 25 \
--max-num-bonds 100
|
2cfa27f6796570fe75b541dfb6af6c948d54ca935ae37cfcddb57605e5567fdf | Shell | 167 | 6 | #!/bin/bash
module purge
conda activate /home/dbiagion/conda-envs/rlmol
export PYTHONPATH=$PYTHONPATH:$PWD/command_line_tools
unset LD_PRELOAD
module load cudnn/8.1.1
|
a4635aed6eb5fa658230ed770a17f6414bbca74604db20b0957f009af56527d5 | Shell | 168 | 3 | # rmf 4.30.2019, last modified 4.21.2020
python ../scripts/getLocationsPromotersAndFirstIntrons.py /nfs0/BB/Hendrix_Lab/Drosophila/Annotations/dmel-all-r6.21.gtf 6000
|
f3868d01fe30075acab234bdc53d01738b94504c1ccc10a71774e0f3a38e8621 | Shell | 170 | 6 | #!/bin/bash
# rmf 9.20.2021
# cleaned up 3.1.2022
for f in DAVID*parse.txt; do outbase=${f%%.txt}; perl ../../../../scripts/mac2unix.pl $f > $outbase.cleaned.txt; done
|
ae008e58df467f581f2d7a441dca61349d52bdb6a7b6e87cdc6c2fa246f6264a | Shell | 171 | 4 | #prepare human and mouse tables (Table S2) and Figs 2/S3
Rscript Fig2abc_S3.R #human results
Rscript Fig2de.R #mouse results
Rscript Fig2f.R #mouse vs human 1-1 orthologs
|
f04030fb6b2754f3d1236b6a184a36b5630aef7104f796ded61b8daabf5fd116 | Shell | 171 | 3 | # rmf 5.4.2020, last modified 5.16.2020
SGE_Batch -c 'python ../../scripts/getGlobalMotifCounts.py fimoSummaryFile_FPKM1.0_p5e-05.txt' -r globalMotifCounts -q nucleotide
|
7ea096930233b9dbd37e58eb191438b23f2614c125fbb49b00331acca64ade70 | Shell | 174 | 6 | cellranger aggr --id=DP_OC2_3_Merged_NoNorm \
--csv=/d2/studies/scanPy/ACWS_DP/RawData/OC_AggrIndex.csv \
--normalize=none \
--localcores=12 \
--localmem=128 \
--nosecondary
|
1ef5f4c8a6c8c139d3793c52c51caad58d2359e6186bc75295db77637e7c6163 | Shell | 178 | 5 | # rmf 9.20.2021
# need to convert LLC to LLCs etc.
awk -F '\t' 'BEGIN {OFS="\t"}; $1 = $1"s" {print}' enrichmentScoresTableDAVID.txt > enrichmentScoresTableDAVID_formatted.txt
|
5c9c90405e4b7079a173ec027414ee949b95c0c5baf31fe85c78a5c0bd659ce8 | Shell | 183 | 13 |
fslmerge -t grey s*c1*
ls s*c1* > images_grey.txt
fslmaths grey -Tmin -thr 0.2 -bin grey_mask
fslmaths grey -Tmean grey_mean
mkdir data
mv s*.nii data
mkdir tests
|
907b16a6bd713b19059a02cc1acf5d9d3e61668a7f15f712e5ad2bed83e4a4b1 | Shell | 185 | 5 | #!/bin/bash
# rmf 6.18.2021
for f in significanceTestingResults_OR/correctedPvals/*lightActivated*BHFDR*txt; do echo $f >> fileList.hypergeomCorrectedResults.lightActivated.txt; done
|
4dfe1ec904fbe7fe38b3e8699a12534af0b24c0847e2fb88dfd8f216d121e9e4 | Shell | 186 | 3 | mamba create -n learnMSA -c conda-forge -c bioconda python==3.10 pip cudatoolkit ipykernel cudnn tensorflow==2.10.* mmseqs2 pytorch::pytorch
conda activate learnMSA
pip install learnMSA
|
53006808587dd8b3cb21d6d1fe37c6d3d97a2c714591ef22468f82106af1a1c3 | Shell | 188 | 3 | source /home/travis/nest-$NEST_VERSION/bin/nest_vars.sh
export NEST_MODULE_PATH=${NEST_INSTALL_DIR}/lib/nest:$NEST_MODULE_PATH
export SLI_PATH=${NEST_INSTALL_DIR}/share/nest/sli:$SLI_PATH
|
d279bebb8d6f5f71f07b6411efe3646732b97a637fd29dd92bac1e35d8cc3f75 | Shell | 188 | 4 | # rmf 4.3.2020
python ../scripts/renameMemeMotifs.py ERR649813_cnc_memeChip/meme_out/meme.txt cnc13_
python ../scripts/renameMemeMotifs.py ERR649814_cnc_memeChip/meme_out/meme.txt cnc14_
|
f1972b17a88373952ac8eb7f4e2d2029a73de96ac8a702bf9ff860b50aa07d34 | Shell | 191 | 7 | #!/bin/bash
# rmf 3.2.2022
# RP24
python scripts/graphBoxPlot_compareSiteSignificance.py results_RP24Ttest_FBgn0003460_2_oldLLCs_Cluster6_calcium_ion_transmembrane_transport.txt 0.05 RP24
|
a17eecbaa267c70330e96bb5432adf5046c147593a025f79c2865016ca25035c | Shell | 194 | 7 | #!/bin/bash
# rmf 12.4.2020
# cleaned up 3.1.2022
for f in ../significanceTestingResults/correctedPvals/*_BHFDRcorrected.txt; do echo $f >> fileList.motifEnrichmentCorrectedResults.txt; done
|
ad7bb60b2f06f7a1458683d6ee11340b1963ac946a17796d32fd9555c7c8f659 | Shell | 195 | 9 | #!/bin/bash
clear
python optimize_rad.py \
--min-atoms 4 \
--max-atoms 12 \
--max-num-bonds 30 \
--num-gpus 1 \
--num-cpus 34 \
--local-dir /scratch/$USER/ray_results/qed
|
b3b3032ecb7d72acc5acd1ba57f25a026bb823b9c8844a9b5b82525a467fa134 | Shell | 197 | 4 | # rmf 4.22.2020
# usage: <all promoters fasta file> <outfile name>
python ../../scripts/writeAllGenesList.py ../../promoters/allTranscriptPromoters6000bpAndFirstIntron.fasta allTranscriptList.txt
|
bf95f02b26cf249c8c8031ccc38d0f9f255e77f19b80a25121e0d9e43d3c193c | Shell | 198 | 4 | last_FIELDS_line=$(cat out.STATE | grep -n FIELDS | cut -f1 -d: | tail -n 1)
total_length=$(cat out.STATE | wc -l )
tail -n $(echo $(($last_FIELDS_line - $total_length-1))) out.STATE > snap.STATE
|
4e3fb821874e0a6b334d7ee988bd537efa3e9f09e53b3518b9264cafe2188a93 | Shell | 199 | 9 | #!/bin/bash
clear
python optimize_qed.py \
--min-atoms 6 \
--max-atoms 25 \
--max-num-bonds 100 \
--num-gpus 1 \
--num-cpus 34 \
--local-dir /scratch/dbiagion/ray_results/qed
|
5abb2a512bfeef95f1f6a92bc1f50ec45b01e706c3ca0dcf10885619eaac9311 | Shell | 199 | 5 | #!/bin/bash
# Usage: optimize_qed_get_results.sh <slurm-file>
# Writes a csv results file, <slurm-file>.top_hits.csv
./optimize_qed_scrape_log.sh $1
python optimize_qed_parse_tophits.py $1.top_hits
|
02a78b3755f26d7f828ce579290b5a1849acfe0ca98317749f99bd6e95f53ab1 | Shell | 204 | 4 | set -eu
pdfcrop fig1-tikz.pdf fig1-tikz.pdf
convert -flatten -density 300 fig1-tikz.pdf fig1-tikz.png
convert -flatten -density 600 -compress lzw -units pixelsperinch -depth 8 fig1-tikz.pdf fig1-tikz.tif
|
7780bd048d3ef801262664a7b208d90bc856c412090cdde7cc74e8405269acc6 | Shell | 205 | 10 | #!/bin/bash
set -e
source venv/bin/activate
export PYTHONPATH=$(pwd):$(pwd)/chemcpupy
for sz in 8 12 16 28
do
python simulation/acidbase_writer_acc.py bin ${sz} 2 > acc_bin_2class_${sz}.txt &
done
wait |
d9938cb666c0d575ac4cde7817dc09e124027e0c7d27698b3dd1063ababd23eb | Shell | 205 | 10 | #!/bin/bash
set -e
source venv/bin/activate
export PYTHONPATH=$(pwd):$(pwd)/chemcpupy
for sz in 8 12 16 28
do
python simulation/acidbase_writer_acc.py bin ${sz} 3 > acc_bin_3class_${sz}.txt &
done
wait |
e87c9c173598d0a4fb63431fb2e6a1f6fab7664ec0493167647232c6c121653a | Shell | 205 | 6 | #!/bin/bash
# rmf 12.4.2019, last modified 12.17.2020
# gets all fimo.gff files from fimo output
for f in allTranscriptsOutput6000/allTranscripts*.out/fimo.gff; do echo $f >> fileList.fimoGFFs.txt; done
|
03bbcdd653f3a38b2e52146185437c701d8cdf91124ba11244614f88a99b9ff1 | Shell | 208 | 8 | #!/bin/bash
while IFS= read -r line
do
SUBJ=$(echo "$line" | awk -F, '{print $1}')
SESS=$(echo "$line" | awk -F, '{print $2}')
echo "Subject is $SUBJ and session is $SESS"
done < "34_preterm.csv" |
24a1c5fb52a0f21ac8ee8a0b652522b5a0c49f612136110a024a276aca1f613e | Shell | 209 | 11 | # (Re-)initialize repository
git init
# make sure the submodules are initialized
git submodule init
# update
git submodule update
# Get latest submodule version
git submodule foreach 'git pull origin main'
|
05bb4d2d217b742cf97b8dee307b83395a51eb74379144c33b9657f6f32c31c3 | Shell | 210 | 3 | #usage bash plumed_scripts/make_ref_file.sh ref_struct md_start_struct
vmd -dispdev text $1 -f $2 -e ./plumed_scripts/mark_reference_atoms.tcl
cat marked.pdb | grep -E "^.{62}1\.00\s" > reference_struct.pdb
|
b6c1626600d3714de4d38e4733e54633fccc0c455f49fd5aee82be5a25b89bd0 | Shell | 211 | 7 | # rmf 12.4.2020
# need this file to map secondary IDs
wget "http://ftp.flybase.org/releases/FB2020_05/precomputed_files/genes/fbgn_annotation_ID_fb_2020_05.tsv.gz"
gunzip fbgn_annotation_ID_fb_2020_05.tsv.gz
|
9a457873828f2c94b910b8ee7c0688c49281371a81fb4bc17745508f720816b3 | Shell | 214 | 9 | #!/bin/sh
# copyright: GeoDS Lab, University of Wisconsin-Madison
# authors: Yuhao Kang, Song Gao, Jinmeng Rao
START=$2
END=$3
for i in $(seq $START $END);
do python POI_visits_daily.py --month $1 --day $i;
done |
0bf000fa39fe16de1b311f58a03c8a1c7c5a8ab09dc4c2dd39e61f5527547d2c | Shell | 216 | 9 | file="metis-5.1.0"
wget https://cloud.tsinghua.edu.cn/f/fd30d629a08645bbbdb8/?dl=1 -O "${file}.tar.gz"
gunzip "${file}.tar.gz"
tar -xvf "${file}.tar"
cd ${file}
make config shared=1 prefix="~/.local/"
make install
|
7923f4bf2ce3a325c0e4defa023acce7a2ce06c3defcddb77b98677869a13432 | Shell | 218 | 4 | # rmf 4.22.2020, last modified 4.29.2020
python ../../scripts/calculateMedianExpr.py dmel-all-r6.21.gtf fileList.transcriptExpr.txt
python ../../scripts/calculateMedianExpr.py dmel-all-r6.21.gtf fileList.geneExpr.txt
|
a41e13ebfa7a7c4e64c761ddc63a84d97993b5a1a907f5a671558edcfffebe79 | Shell | 219 | 11 | #!/bin/bash
set -e
source venv/bin/activate
export PYTHONPATH=$(pwd):$(pwd)/chemcpupy
for sz in 8 12 16 28
do
python simulation/acidbase_writer_acc.py 3bit ${sz} 2 > acc_3bit_2class_${sz}.txt &
done
wait
echo "Done" |
786ae50719b21dd14e2d30d79ebcec87108d36d67b1b9ebe83fddaebdf31102a | Shell | 221 | 8 | FILE=$1
URL=https://people.eecs.berkeley.edu/~tinghuiz/projects/pix2pix/datasets/$FILE.tar.gz
TAR_FILE=./$FILE.tar.gz
TARGET_DIR=./$FILE/
wget -N $URL -O $TAR_FILE
mkdir $TARGET_DIR
tar -zxvf $TAR_FILE -C ./
rm $TAR_FILE
|
9037dd951c2022aeee93db9af7873c6dff944b9d3d9df22c00195483cfb957f7 | Shell | 223 | 7 | #!/bin/bash
# rmf 9.2.2020, last modified 4.19.2021
# cleaned up 3.1.2022
for f in ../bindingSitePlots/bindingSiteInfo*.txt; do python3 ../../../../scripts/getTranscriptIDsFor2Dplots.py ../../dmel-all-r6.21.gtf $f; done
|
d64a7e264401d4815653e4b77e91c105d684e453743a7851d21af79a50931db3 | Shell | 224 | 6 | #!/bin/bash -p
source $FREESURFER_HOME/SetUpFreeSurfer.sh
$FASTSURFER_HOME/run_fastsurfer.sh --sid $1 --t1 $2 --py $FASTSURFER_PYTHON_PATH --sd $SUBJECTS_DIR --fs_license $FREESURFER_LICENSE_PATH --threads 1 --device cpu
|
2ec338b801e2676444d2526b5b19a37cf313406c0d51299532f937cbda2fc221 | Shell | 227 | 5 | #!/bin/bash
# rmf 5.4.2021
for f in ../transcripts_*DAVID*txt; do b1=${f##../transcripts_significantSites_}; b2=${b1%%.txt}; python ../../../../../scripts/getNotSignificantTranscriptIDs.py $f ../${b2}_transcriptIDs.txt; done
|
72182f76baa45ed3ddddbfe16bb5b383c5e185f8fb2d07771d006fc3fb2d6556 | Shell | 228 | 5 | #!/bin/bash
savepath=$1;
python main.py --mode=train --dataset="midair" --seq_len=4 --db_seq_len=8 --arch_depth=6 --ckpt_dir="$savepath" --log_dir="$savepath/summaries" --records=data/midair/train_data/ --enable_validation $2
|
890dc1e36ea05055c2ddca6f7f69a84f6dfda40d89081de0f1f1c6092f4a33d2 | Shell | 228 | 6 | # rmf 9.24.2021, last modified 10.23.2021
# cleaned up 3.2.2022
# usage: <fileList of cleaned up/down groups> <DEGs file> <escore thresh>'
python scripts/plotScatterUpDownTranscripts.py fileList.cleanedGroups.txt DEGs.txt 1.3
|
321085291d5641af9a144aa208441ddb24a896330780f71441c7fab2526c4a20 | Shell | 233 | 5 | #!/bin/bash
# rmf 4.13.2021
for f in transcripts_significantSites_DAVID_*.txt; do f1=${f##*Sites_}; f2=${f1%%.txt}; file=../../../../promoters/DAVID_processedFiles/${f2}_transcriptIDs.txt; ln -s $file ${f2}_transcriptIDs.txt; done
|
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