sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
2557bbde75497ccf3164fc1d0f3a2380dcd10c964e8f09cdd8108548002851e7 | Shell | 4,231 | 110 | # ====== About run.pl, queue.pl, slurm.pl, and ssh.pl ======
# Usage: <cmd>.pl [options] JOB=1:<nj> <log> <command...>
# e.g.
# run.pl --mem 4G JOB=1:10 echo.JOB.log echo JOB
#
# Options:
# --time <time>: Limit the maximum time to execute.
# --mem <mem>: Limit the maximum memory usage.
# -–max-jobs-run <njob>: ... |
26973ffb2c57b6cf693d09481eeea83d0916dad227613b6bd2c004575e099e1b | Shell | 4,299 | 104 | #!/bin/bash
# download data
wget -O data.tar \
'http://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE45719&format=file'
mkdir data
tar -C data -xvf data.tar
gunzip data/*
## raw reads
paste data/GSM111*_zy* | \
awk '{for (i = 4; i <= NF; i += 6) printf ("%s%c", $i, i + 6 <= NF ? "\t" : "\n");}' > \
reads_zy.txt
sed -i '1... |
71e5672cb11777130ccf3ed130d91970b3535550edde848c5b6b87d55a8d5c0f | Shell | 4,590 | 112 | #!/bin/bash
### File management
chmod +x ${APPLI_DIR}/cgi-bin/*.{cgi,pl}
mkdir -p ${DATA_DIR}/{exploratory_data,gels,go/goa,go/obo,go/results,logs,peptide_data,quantification_data,spectrum_data,swath_lib,tmp,validation,pathway_data}
if [ ! -e ${APPLI_DIR}/html/data ]; then
ln -s ${DATA_DIR} ${APPLI_DIR}/html/data
... |
1ee2c3cdc7a59dd4531a5339b669f6491553a0a128eaef6266bf1e3a76a2e843 | Shell | 4,658 | 113 | #!/bin/bash
#===============
# author:
# Li Tang
# Central South University
# tangli_csu@csu.edu.cn
#===============
# function description
# Accuracy calculation
# bedtools need to be installed
#===============
input_loop=$1
gold_dir=$2
false_dir=$3
prefix=$4
golden_sig=${gold_dir}/${prefix}"_gold.bedpe"
false1=${fa... |
2274b7f20a1981a20eac242a5900dfdee2e38ce68405c1e09bdce2c5b8b4e79e | Shell | 4,662 | 95 | #download the sra file from SRA database: SRP282056
cd /data2/deng/Aging/Ex/Lau_GSE157827/rawData
#
cat SraAccList.txt | while read id;do; /Softwares/deng/sratoolkit.2.10.0-centos_linux64/bin/prefetch ${id}; done
#convert from sra file to fastq file
export PATH=/Softwares/deng/sratoolkit.2.10.0-centos_linux64/bin
#ht... |
8a48d734209fbab307d375b8a4fdc424768116d639e44510b91d10c8555072a4 | Shell | 4,730 | 128 | #!/usr/bin/env bash
# check-secrets.sh — pre-push gate for accidental secret commits.
#
# Run manually: bash scripts/check-secrets.sh
# As pre-push hook:
# cp scripts/check-secrets.sh .git/hooks/pre-push && chmod +x .git/hooks/pre-push
#
# Scans the diff staged for push (or the working tree if no remote set) for
# ... |
55ce2b8895fcd4787862b1ca33cdb6fc1991723fb53d50110bce552a12df0f04 | Shell | 4,744 | 77 | #!/usr/bin/env bash
entries=20
outfld="files2/"
mkdir -p ${outfld}
ext="assembly_report.txt" #,protein.faa.gz"
db="refseq,genbank"
og="archaea,fungi"
og="default,${og}"
for d in ${db//,/ }
do
for o in ${og//,/ }
do
if [[ ${o} == "default" ]]; then
mkdir -p "${outfld}genomes/${d}/"
... |
1d6f3942ebbb4303a8e834b6ffb7f5e48a0c56f53d73ab1f7fb344861e4bb4c1 | Shell | 5,006 | 84 | #!/bin/bash
set -e
set -x
###STEP 1
#load conda environment that contains bedtools installation
#for example the one described in https://github.com/biomonika/HPP/blob/main/palindromes/environment.yml
source /opt/miniconda/etc/profile.d/conda.sh
conda activate alignment #uses bedtools v2.30.0
###STEP 2
#using coordin... |
9e6778acf3be704bbddcc0de8bc18f66c05c981cfbd3b78778652dcaf292f3de | Shell | 5,046 | 151 | #!/bin/bash
#
# Copyright (C): 2020-2021 - Gert Hulselmans
#
# Purpose: Filter BAM file for usage with popscle dsc-pileup by keeping reads:
# - which overlap with SNPs in the VCF file
# - and which have a cell barcode (default: "CB" tag) contained in the cell barcode list
# Keeping only rele... |
67dff960377f0de1ce943f72db5cf9f83e17b6f0879f304799d10f4b0e3e20ca | Shell | 5,067 | 64 | #!/bin/bash
set -e
set -x
#At the start, we have the following files:
#merged.chrX.repeats.species.bed => merged coordinates of the continous stretches of repeat sequences
#ampliconic.bed => merged coordinates of the regions with high intrachromosomal similarity
#PARs.bed => coordinates of pseudoautozomal regions fro... |
28d59043db0658fc1e5b2ade55311ddd9700348ae0da0d7fea992fce3f35fa40 | Shell | 5,195 | 162 | #!/bin/bash
# Orchestrates a full inference-timing sweep: repeatedly calls
# benchmark_single_config.py, once per (model panel x variant x decoder)
# combination, each as its own fresh process, then calls plot_results.py at
# the end.
#
# Each combination runs in its own `python3` process (not a Python-level
# loop ins... |
14ba0d3d5d52007790a846faf4fb43ad4a50de77821d31f49fb0182ec27c587f | Shell | 5,779 | 200 | #!/bin/bash
QTVERS=`qmake --version|sed -n 2,2p|awk '{print $4}'`
echo "Make All for Qt Version ${QTVERS} ..."
QTMAJV=`echo ${QTVERS}|cut -d. -f1`
if [ `echo "56"|grep -ci "${QTMAJV}"` -eq 0 ]; then
echo "Wrong qmake, check environment"
echo " QT Major version must be 4 or 5; is ${QTMAJV}"
qmake --version
exit... |
10ebf618583af97f9c94acd0a87a3fc45ecbdbd681c21ae504e602b682dd7651 | Shell | 5,944 | 117 | #! /bin/bash
# Specify data directories
DATA_DIR=/.../.../KeywordReading
NORM_DIR=/.../.../SyllableRepetition
LIVE_DIR=/.../.../KeywordReading/online_sessions
TEMP_DIR=/tmp/ReplicateDelayedSynthesis
settings=config/debug_settings.ini
contamination_package_path=".../Contamination Analysis Package/Toolbox"
stage=1
sto... |
8700b4a1ec887eb4d607d84a5c7f296379e4d98690f79ea2614fb51fa18ab82f | Shell | 5,954 | 199 | #!/bin/bash
echo How do you connect to GitHub? If you enter your username and password when you pull a private git repository, then answer https, otherwise answer ssh.
echo \(ssh or https\)
read CONN
if [ ! $CONN == "ssh" ] && [ ! $CONN == "https" ]; then
echo Please specify either ssh or https
else
module lo... |
db633b04883670f226051296864ccad125a0b5a962eed19a543fecfcb4206e51 | Shell | 6,155 | 260 | #!/bin/sh
# copypkg-lnx.sh - copy ultrascan3 directories to us3pkg/PKGNAME
SRCDIR=$us3
HOMEQ=`cd $SRCDIR/../;pwd`
DSTDIR=$HOMEQ/us3pkg
SOMOBASE=$HOMEQ/ultrascan3/us_somo
SOMORHDR=${SOMOBASE}/develop/include/us_revision.h
ME=`whoami`
SYSTYPE=`uname -s`
if [ "${SYSTYPE}" != "Linux" ]; then
echo "$0 requires a SYSTYP... |
1face100662543a96287501f504dcf179c54037b602c25526786e378bbc502c7 | Shell | 6,238 | 180 | #!/usr/bin/env bash
# Builds the macOS or Linux vcpkg binary cache used by application builds.
#
# USAGE
# scripts/build-toolchain.sh --cache-dir DIR [--qt6] [--profiles "APP HPC"]
#
# OPTIONS
# --cache-dir DIR Required. vcpkg binary cache to populate.
# --qt6 Qt6 toolchain [default].
# --qt5 ... |
7a6db7c9cb49bbbad74274be23948fc9d5e3ca81e2e8716f7f9d35de702fe391 | Shell | 6,412 | 131 | #!/usr/bin/env bash
# lr_benchmark.sh: Run a benchmark for vg long read mapping
# Meant to be run on UCSC Courtyard/Plaza
set -ex
set -o pipefail
# Here we use : and := to set variables to default values if not present in the environment.
# You can set these in the environment to override them and I don't have to wri... |
8dc56a2aa03454daa88b72d53d6da4584071ddaa934695353dcf72f8a1200d49 | Shell | 7,185 | 206 | #!/bin/bash
#
# Copyright (C): 2020-2021 - Gert Hulselmans
#
# Purpose: Sort VCF file in the same order as the BAM file, so it can be used with popscle.
# Function to check if any of the programs in a pipe failed.
check_exit_codes () {
local GET_PIPESTATUS="${PIPESTATUS[@]}";
local exit_code;
for exit_c... |
ab78ecea885629c0b3129a4820eff85e463cad93cb45dacfd454292f999f9e53 | Shell | 7,211 | 152 | #!/bin/bash
#===============
# author:
# Li Tang
# Central South University
# tangli_csu@csu.edu.cn
#===============
# function description
# calculate E-P percentage
# calculate AR
#===============
inputDir=$1
ccres=$2
tss=$3
active_peakDir=$4
inactive_peakDir=$5
prefix=$6
outDir=$7
if [ -f "$outDir/${prefix}_resul... |
c1a677ace0cdf026599891587dbafd41d9ca6fae121e8b703ca3e660bce8a6c0 | Shell | 7,234 | 132 | # for i in $( ls *.dat ); do echo $i; done | sed 's/world//g' | awk '{ print "mv world"$1,"World"$1 }' | bash
# for i in $( ls *.dat ); do echo $i; done | sed 's/configuration//g' | awk '{ print "mv configuration"$1,"World"$1 }' | bash
# Lista de arquivos
# list_name_file=('configuratio... |
e412d3b9f22bc6dc17189737549d1813e29feaa916f3d01d6b178634ad5a2cfe | Shell | 7,308 | 90 | #!/bin/bash
set -e
#set -x
#At the start, we have the following files:
#merged.repeats.species.bed => merged coordinates of the continous stretches of repeat sequences
#ampliconic.bed => merged coordinates of the regions with high intrachromosomal similarity
#PARs.bed => coordinates of pseudoautozomal regions from Bo... |
afddbf3045e8187c777ff239823641ca9e83a1e8fca5913c4ea419d4a0069517 | Shell | 7,373 | 112 | #!/bin/bash
while getopts c:g:a:n: flag
do
case "${flag}" in
c) cellProbs=${OPTARG};;
g) geneProbs=${OPTARG};;
a) atlas=${OPTARG};;
n) nissl=${OPTARG};;
esac
done
cd /cis/home/kstouff4/Documents/MeshRegistration/
newV="True" # set to True if using rescaleUnits() function from ... |
f78310dda9165fd10356942710cb7ed326fd77ffcf0d0b5f6dc46b1f3529aeca | Shell | 7,602 | 177 | #!/usr/bin/env bash
# publish-docs.sh: Entrypoint for Travis to build and publish Doxygen documentation for vg
# Based on the method of https://gist.github.com/domenic/ec8b0fc8ab45f39403dd
set -e
# Configuration
# What branch do the docs go on?
DEST_BRANCH="gh-pages"
# What repo do they go in? Must be an SSH repo spe... |
a71b3cbbabcc72a4e6acf668ec6ee81780adbd3fa579b9057a9ef02ef1a275dc | Shell | 8,016 | 219 | #!/usr/bin/env bash
# Resolves the pinned vcpkg binary cache for the current host.
#
# USAGE
# eval "$(scripts/fetch-toolchain.sh --export)" # sets US3_VCPKG_CACHE
# scripts/fetch-toolchain.sh # prints the path
#
# OPTIONS
# --export Emit shell assignments instead of a bare path.
# ... |
bfe823a0dac31ab9cd7e163d6d87e59f6fb2c5f428c3a98375a1544aed688bc1 | Shell | 8,134 | 165 | #!/usr/bin/env bash
# Script to run Giraffe in long read mode on a set of simulated reads and evaluate its speed and accuracy.
set -ex
: "${DATA_DIR:="/private/groups/patenlab/anovak/projects/hprc/lr-giraffe"}"
: "${GRAPH_BASE:="${DATA_DIR}/graphs/hprc-v1.1-mc-chm13.d9"}"
: "${MINPARAMS:="k31.w50.W"}"
: "${CONDITION... |
f30de8d2afb0ebe854ffc641c73c6720116a41772d3597424cd50d7b5e79d15f | Shell | 9,765 | 304 | #!/bin/bash
start=`date +%s`
QUAL=1
ZIP_TRIM=1
BLACKLIST=1
PREP_INPUT=1
PROC_SAMPLE=1
RUN_CORR=1
RUN_MACS=0
RUN_MACS2=1
RUN_EPIC2=1
REM_OUTPUT=1
GENOME=GENOMEGOESHERE
ODINISTHEBESTDOGEVER
if [ "$ZIP_TRIM" = "1" ]; then
gunzip *.gz
trim_galore *.fastq
fi
cd ..
############################### EXTENSION SETUP ... |
dd9007c3bfbb2a57cb201bf4810fc7c48653e570d6054d71054d1077c4c2cf53 | Shell | 9,778 | 264 | #!/bin/bash
## DEFAULT DIRECTORIES
# Scratch directory
scratch_dir="/cluster/scratch/ftamara"
# Intel wind directory
IW_dir="$scratch_dir/intel_wind"
# Wind prediction directory
WP_dir="$IW_dir/wind_prediction"
# initialization folder
IN_dir="$IW_dir/data_generation/openfoam_batch/initialization"
# Dataset
data... |
231db62b8dae4f41620d8b6af4364e00d75d5ff642758213caca0c872ac77c9b | Shell | 10,022 | 296 | #!/usr/bin/env bash
# giraffe-wrangler.sh: Run and profile vg giraffe and analyze the results.
set -e
usage() {
# Print usage to stderr
exec 1>&2
printf "Usage: $0 [Options] FASTA XG_INDEX GCSA_INDEX GBWT_INDEX MINIMIZER_INDEX DISTANCE_INDEX SIM_GAM REAL_FASTQ\n"
printf "\n"
printf "Inputs may be... |
dffd72b660ad1c1bac78226bb8a36039733246b5a59cac8df2cdb212645d52db | Shell | 10,250 | 129 | #!/bin/bash
#SBATCH --job-name=repeatmask.20230627
#SBATCH --partition=main
#SBATCH --mail-user=mcechova@ucsc.edu
#SBATCH --nodes=1
#SBATCH --mem=500gb
#SBATCH --ntasks=128
#SBATCH --cpus-per-task=1
#SBATCH --output=repeatmask.20230627.%j.log
#SBATCH --time=168:00:00
set -e
set -x
pwd; hostname; date
source /opt/mini... |
b888cce99ac99cd7ebb08de0ccbd488312ab7e6f2247c2fc0b56cbcf04b1548c | Shell | 11,085 | 254 | #!/usr/bin/env bash
# make_pbsim_reads.sh: script to simulate reads with pbsim2.
# Intended to run on UCSC behind-the-firewall systems
# You may also need to CFLAGS=-fPIC pip3 install --user bioconvert
set -ex
# Here we use : and := to set variables to default values if not present in the environment.
# You can set t... |
03e4cde058f8150a6c60084495eb3547fcd1e5418b597b37654073e0288be103 | Shell | 11,086 | 324 | #!/bin/bash
DIR=$(cd "$(dirname "$0")"; pwd)
S3_TEMPLATES_MOUNTPOINT=${S3_TEMPLATES_MOUNTPOINT:-"/s3_alignment_templates"}
templates_s3bucket_name=
inputs_s3bucket_name=
outputs_s3bucket_name=
searchId=
input_filepath=
output_dir=
templates_dir_param=
other_args=()
use_iam_role=
skipCopyInputIfExists=false
remove_in... |
5d4707ee2cf2782929eb720917e509e18e2da155b41fe050776a289fee1b92ab | Shell | 11,469 | 287 | #!/bin/bash
# =============================================================================
# uninstall.sh — UltraScan3 safe uninstaller for macOS
#
# Usage:
# sudo ./uninstall.sh [--dry-run] [--yes]
#
# Options:
# --dry-run Print every action that would be taken; make no changes.
# --yes Skip the interac... |
32fd853a09e706dc1469cebcd03288426a955ddd90cfad44fddfa6b18f243da9 | Shell | 11,789 | 336 | #!/bin/bash
DIR=$(cd "$(dirname "$0")"; pwd)
S3_MIP_TEMPLATES_MOUNTPOINT=${S3_MIP_TEMPLATES_MOUNTPOINT:-"/s3_mip_templates"}
S3_VNC_TEMPLATES_MOUNTPOINT=${S3_VNC_TEMPLATES_MOUNTPOINT:-"/s3_vnc_alignment_templates"}
templates_s3bucket_name=
inputs_s3bucket_name=
outputs_s3bucket_name=
searchId=
input_filepath=
output... |
9ea115f4f545a860153153c75fe988156b5abbc8180791c18fbadce4ce1cdbb3 | Shell | 12,609 | 386 | #!/bin/bash
# Copyright 2023 Image Analysis Lab, German Center for Neurodegenerative Diseases (DZNE), Bonn
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licen... |
e013c65602eba5753867f5afb7e8e4e96c867f05c7443bc7fa19eec766134f2c | Shell | 14,190 | 185 | #This script uses GATK to call SNPs.
#To speed up the process, mpileup was run for each chromosome separately
module load bioinfo-tools
module load bwa/0.7.17
module load picard/2.23.4
module load GATK/4.2.0.0
module load FastQC/0.11.9
module load trimmomatic/0.36
module load samtools/1.14
module load plink... |
ccd458aefd2baf4fcafec6bf093f9e5a4c7b3e7845cfad69bcf3cb61ebf7bc57 | Shell | 16,085 | 350 | #!/bin/bash
usage() {
cat <<-EOF
RNAC_for_diploid.sh
Usage: `basename $0`
Options:
-g: genome.fa
-f: R1.fq
-r: R2.fq
-t: N, threads
-v: SNP FILE
-s: GENOME ASSEMBLY
-h: help information
Action:
-A: Reads mapping
-P: Contacts parsing, haplotype imputati... |
51e042880d693607ccebed8fc26be3d3eb1a2b653f654038671d86673e8cedbf | Shell | 16,264 | 449 | #!/bin/bash
#
# 20x 40x brain aligner by Hideo Otsuna
#
InputFilePath=$1
NSLOTS=$2
# Resolutions in microns
RESX=$3
RESZ=$4
# true or false, forcefully use the user input or the size from confocal file
ForceUseVxSize=$5
# Reference channel can be one of: {ch1, ch2, ch3, ch4, Signal_amount}
# If the value is ch<number... |
e8ac80c79c199bdde9ec9bfae8341c6b3821b99bc50a5d8ecea6a1a653875fec | Shell | 16,399 | 432 | #!/bin/bash
# Save the current LC_NUMERIC setting
original_lc_numeric=$LC_NUMERIC
# Set LC_NUMERIC to en_US to use US American number format
export LC_NUMERIC=en_US.UTF-8
echo "-----------------------------------------------------------------------------"
echo "T1T2 Processing Script by Hartung, Komnenic, Cooper, J... |
f244fa0c3d34288f80b8f6a9c1e320d25fb1b6e39779a3fe80fc86eb973b1f17 | Shell | 16,444 | 299 | #!/bin/bash
usage() {
cat <<-EOF
RNAC_for_olfactory.sh
Usage: `basename $0`
Options:
-g: genome.fa
-f: R1.fq
-r: R2.fq
-t: N, threads
-s: GENOME ASSEMBLY
-v: SNP FILE
-h: help information
Action:
-A: Reads mapping
-P: Contacts parsing, haplotype imput... |
cb0bdd6d5542da4fa73579a9620ecbcc8ecf8f71901b9ae828c3c8b01f4d508d | Shell | 18,225 | 515 | #!/bin/bash
#
# 20x 40x VNC aligner by Hideo Otsuna
#
InputFilePath=$1
NSLOTS=$2
#nc82decision (reference channel) can be one of: "Signal_amount","ch1","ch2","ch3","ch4"
nc82decision=$3
FINALOUTPUT=$4
returnedErrorFilename=$5
InputFileName=$(basename $InputFilePath)
# final output name is the filename without extensi... |
b0ff22ee872e942123af776e64852e213d63dd930c7fbf2fb374bdbcbfc68f0a | Shell | 18,970 | 580 | #!/usr/bin/env bash
# Script to build a test Docker and run tests on it.
# Tests are run using toil-vg: https://github.com/BD2KGenomics/toil-vg
# Drops test-report.xml with the test results in the current directory.
# This script is hooked into http://vgci.cgcloud.info
# Note: we assume we run this in vg/ ie inside th... |
918393b5809f4a73b883705dd4b79da72508f5dd04425561fec018f5e3682c14 | Shell | 19,852 | 573 | #!/usr/bin/env bash
# =============================================================================
# bootstrap-macos.sh -- UltraScan3 macOS OS-level prerequisite installer
#
# PURPOSE
# -------
# Installs the Homebrew packages and CLT components that must exist on a
# macOS machine BEFORE build.sh is run. This script... |
70ff76f0ed20cd2a2ec01e22acf64d7bdeedbe06cd2d0781cfa79371823b2782 | Shell | 20,060 | 299 | #!/bin/bash
# Usage: ./runQP.sh -a True -c True -g False -n False -d True -t allen -r allen
while getopts c:g:a:n:d:t:r: flag
do
case "${flag}" in
c) cellProbs=${OPTARG};; # compute cell type probs
g) geneProbs=${OPTARG};; # compute gene type probs
a) atlas=${OPTARG};; # compute atlas to a... |
7d88407fec90dd871a09b8e67c051a4b5ff7a4f2c67b7512f15b899ac5661736 | Shell | 27,563 | 775 | #!/bin/bash
set -euo pipefail
# Colors for output
RED='\033[0;31m'
GREEN='\033[0;32m'
YELLOW='\033[1;33m'
BLUE='\033[0;34m'
CYAN='\033[0;36m'
MAGENTA='\033[0;35m'
NC='\033[0m' # No Color
# Function to print colored output
print_status() { echo -e "${BLUE}[INFO]${NC} $1"; }
print_success() { echo -e "${GREEN}[SUCCESS]... |
2e0f7e97f4321ce2fe758c5eed2b886c138b09fbf7729faae4799cfc2b7a17e0 | Shell | 34,071 | 868 | #!/usr/bin/env bash
# =============================================================================
# bootstrap-linux.sh -- UltraScan3 Linux OS-level prerequisite installer
#
# PURPOSE
# -------
# Installs the system packages and tools that must exist on a machine BEFORE
# build.sh is run. This script does NOT build U... |
35ad4595c235346ff890b741dea004555837bd78119789fc5904c517589d5a01 | Shell | 47,243 | 1,183 | #!/usr/bin/env bash
set -euo pipefail
echo "=========================================="
echo "UltraScan3 Build Setup"
echo "=========================================="
echo "NOTE: First build takes 30-45 minutes."
echo " Dependencies are cached after that."
echo ""
# Detect if running in CI
if [ "${CI:-false}" =... |
36520af518b714fc329271fa7d7e8f0e6481953aa8833bfd049b025644d0e828 | Shell | 81,848 | 1,885 | #!/usr/bin/env bash
set -euo pipefail
IFS=$' '
# The MIT License (MIT)
# Copyright (c) 2026 - Vitor C. Piro - pirovc.github.io
# All rights reserved.
# 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... |
4c775517276eae17c06fdf8b7b577fbc2674a1e0fbce15981e1d313f2dcfdecb | Shell | 115,429 | 1,019 | #!/bin/bash
#SBATCH --mail-type=ALL
#SBATCH --mail-user=jfisher7@uab.edu
#SBATCH --job-name=rec_1
#SBATCH -n 1
#SBATCH --mem-per-cpu=60000
#SBATCH --nodes=1
#SBATCH --time=0-12:00:00
#SBATCH --share
#SBATCH --partition=short
#SBATCH --error=%j.%N.gbm_gene_url_1.err.txt
#SBATCH --output=%j.%N.gbm_gene_url_1.out.t... |
66852eee902051eab1f0b905cb801e50668bbd902a4c44f46baa8caf3663fda4 | Shell | 115,429 | 1,019 | #!/bin/bash
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6af8726f63297a57c2faac91122d1973e5e5e324212396eff68425b1e7f09b5d | Shell | 115,429 | 1,019 | #!/bin/bash
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7feca6125f0a48f694dbb8f11972b4241c888b1cc2e5cd58192b9f6cc145d4f5 | Shell | 115,429 | 1,019 | #!/bin/bash
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9ca0a3b34c3f9edbef30ed49e6558942e300f6654a7a4a79de2cef3778407e61 | Shell | 115,429 | 1,019 | #!/bin/bash
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ae2b866f35ad147b38cbc355bbd057e5423c6c2efd70a42111b62af2e7bde5ca | Shell | 115,429 | 1,019 | #!/bin/bash
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f13942f47d1dc704bb7c93ac1df14fff4b2b165b4e588096517fed34f4f72131 | Shell | 200,000 | 1,756 | #!/bin/bash
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5e545e34ae1d6907907411b0e9f57ac85f4c74674da1d5d0cf99f74cb7cbc521 | Stan | 824 | 34 | // This model was adapted from the NASC-seq pipeline
// https://github.com/sandberg-lab/NASC-seq/blob/master/data/NASCseqModel.stan
data {
int<lower=0> N;
int<lower=0> contents[N];
int<lower=0> conversions[N];
int<lower=0> counts[N];
real<lower=0, upper=1> p_c;
real<lower=0, upper=1> p_e;
}
parameters {
... |
8268bf76a65768065651e850a46014dde5d5e347088ef08315bf0e79d12e554b | Stata | 271 | 4 | ** PLot the analysis of mixed intention model
twoway lfit Pcomp_expert Pcoop_expert ||scatter Pcomp_expert Pcoop_expert , by(Subject)
twoway scatter abs_Vcomp_expert abs_Vcoop_expert
twoway lfit Comp_component Coop_component ||scatter Comp_component Coop_component
|
31e6abf1c5ae7c45864aa0de8a27179ad3ee00d3f5eaf2f57cdc0118a93d5244 | Stata | 933 | 29 | xtset Subject Trial
**Behavioral logistic reg
xtlogit Switch Victoiret1 Victoiret2 Victoiret3 Switcht1 Switcht2 Switcht3 WsLsaa WsLsaat2 WsLsaat3, vce(cluster Subject)
margins, dydx(*)
marginsplot
**Switch and PE t-1
xtlogit Switch c.PE_t1##subj_comp , vce(cluster Subject )
margins, over(subj_comp ) a... |
557c1985dc2f43e4affcda1a724c991f6931f98735473556a9b06c6a5cd3ae3a | Stata | 1,029 | 18 | ** Proportion of stay in 320 simulated dataset for Influence Competitive and Cooperative
xtlogit Stay if mode == 7 , vce(cluster Subject)
margins, dydx(*)
xtlogit Stay if mode == 8, vce(cluster Subject)
margins, dydx(*)
**Behavioral logistic reg for the 320 simulated dataset with Influence Competitive (mode = 7), Coop... |
6d4008f1d7e183938a1ad057de5bd1390c83ea24dbb3d7d9f9cf45612cbeaf58 | Stata | 4,738 | 151 | % To modified run :
import excel "C:\tDCS_Panel_Regression_analysis\data_test_confidence.xlsx", firstrow clear
import excel "C:\tDCS_Panel_Regression_analysis\Yulong_Test_confidence.xlsx", firstrow clear
% To run :
% xtset means set the data to panel data
xtset Subject Trial
% ACC - Training and T... |
14f9655e90cf375c1169f75873b60e174af34f888cfeccfa0b581a1bf3bee587 | Text | 9 | 1 | # bluishO |
09a478811ac23bbaaaf588676380fef94fc275bd9a281884114c5535a479348f | Text | 12 | 1 | Version 1.0
|
9e102ff6626756c65754d4f468b238b84863c707d3bd1fe6bc8a032b328c52c2 | Text | 15 | 1 | # 2.5DAttention |
88ebf39f19f729d1580bf3b6db3861eb7fb84e810322b1318daeb9eb2a05369c | Text | 21 | 1 | Walle_2024_NatCommun
|
d444c15262c3d5f1680b4991b43bf881dd4e92268d4c6cfe3f4ac2555973adc1 | Text | 21 | 1 | # Publication-Scripts |
dc92c0bdedb2031d02b75d1208540c3db7c19e207bc75b8cc2ba2b9d0f87be08 | Text | 21 | 1 | # ERNA-Abstract-Model |
75bd03ab86a9e749118fd5acfbcd10e8457dd4303a9857618b4cc6acffba8145 | Text | 33 | 1 | # Cai_Multiple_Demand_System_2023 |
a3790d9ca5d86c2c21de52bd1e9734e50fc84e2718020ee35775c62bfe0d48bf | Text | 36 | 1 | # Szczepanska_2024_accompanying_data |
54a25c6d688b5509026e710203b06f9a7b6f533c94b1ae3aa2291f33d86d6e15 | Text | 47 | 2 | # EEG-CRS_learning
Pre-processing and analysis
|
65a199ac4a6f86cd0d685810e0666fa351b18a38fd3dc07481c4cf1d2da9000a | Text | 51 | 2 | # ONBCEncoding
Share code resources for a research
|
729c848e21d0d16020ee00880b048dfbc555000dc183c7abee6fa0ef77500a4c | Text | 53 | 1 | https://sherlab.shinyapps.io/IPSC-derived-Microglia/
|
b8cb299786700c5a80ff419ddd2b03250388fa39be7efb2a9b325f7e180809d7 | Text | 55 | 2 | # DeepCys
Machine learning of cysteine ligandabilities
|
f078e6798abc8c4aff5a89677b387a87647d2b454be0a3b1855bc10fce6864f2 | Text | 60 | 2 | # VG3_2023
Code relevant to the analysis of the VG3 dataset
|
8f011453c83dc3bf4ceeec1fa3f1c92fab4c5294d2fb517799531ce3842596cf | Text | 62 | 2 | # BVCDevPublic
Code used for Muessig et al, 2024, Nat Comms.
|
dd99f2b83ff6c502f01093d7209e143a89cbcb76174b6fa5106c5ee75fe40ea6 | Text | 70 | 2 | # Ising-like-model-neuronal-networks
Codes of Analysis of the project
|
9992a848e99a27b3e406eeb9363f93be578f4e2e83a735cdda7683c025f41810 | Text | 83 | 2 | # Farinella_2024
Raw and processed data along with code for Farinella et al., 2024
|
c3954e5092426bdfe564839b2d59e5b0bc68c36837553ed6c616111570e94c44 | Text | 87 | 1 | Script used in R to process data and generate figures for Tsartsalis et al publication
|
8e18cca55bee98fe99a63bd8a2256d19f24b667815392237935ba7db3a3e96ac | Text | 92 | 4 | # BAMs-Cell-Reports
2024-03-05:
- This paper is now accepted in principle at Cell Reports
|
2c90e5b3498a563acb9e160464da680cdcc63560d97c46c1e01d356e39b45128 | Text | 99 | 1 | Secretin Signaling in the Ventromedial Hypothalamus Regulate Energy Metabolism and Bone Homeostasis |
80c19e5fac92c9075214dac80923a77769287e1eb148acfd3d636a0baff8e2b1 | Text | 99 | 2 | # manuscripts repository
meant for distribution of code, CAD, etc., that was part of a manuscript.
|
234e623c79024ca4b053aa65dbe518051f3a987e30f3b6453da254cbde38c1d1 | Text | 110 | 3 | # SourceSpaceDecoding_SDvsLD
Scripts for decoding in source space - Semantic Decision vs Lexical Decision
|
f6954ffba8de94542cc43bdc73725a1bccf08c9dc4642a328d5428430f3b0197 | Text | 110 | 3 | # ERNA GUI
GUI for extracting ERNA field evoked potential amplitudes from high frequency stimulation trains.
|
eb96d4dcd60413b82276cd811bdfab56ef16b3678a870af8fb6dd815f40f4424 | Text | 113 | 2 | # Data_Environmental_Enrichment
Data of Impact of enriched environment on motor performance and learning in mice
|
2521a807d73da9966d1c6168f3f8d46ba1cac3f69f002ee872f9ccd85f836239 | Text | 121 | 1 | ### Repository containing code for the analysis and the [web-app](http://giorgilab.unibo.it/Agc1/) of Agc1 mouse dataset
|
abe7bb80ae0e15a04028c68962b11e10747b4f2aaaa3e3ed64757668db1e63fb | Text | 121 | 2 | # iGluSnFR-Analysis
Analysis of excitatory transmission via fluorescent traces obtained from optical imaging of iGluSnFR
|
0a7b0787d7c5218ed06614cde9a8fa646f5d5e052f3fa9e4b3c8d18e4804161a | Text | 128 | 2 | # YangEtAlPNAS2024
Experimental data and analysis code for Yang, et al., PNAS, 2024, "Eye blinks as a visual processing stage".
|
9d5aa925624ce549eb49b5b60202598141cf6d8ddb397ca932677d07ac534421 | Text | 130 | 4 | # saffire_sv
Draft pipeline for calling large structural variants from paf. Additionally will automate SafFire output creation.
|
20b92cd3e538b5f60a67a47459d7d4a691565f7f7b674e3bb835ee979d6397cf | Text | 132 | 4 | # iatriage
Improving Patient's Triage
Data Source : https://www.kaggle.com/datasets/hossamahmedaly/patient-priority-classification
|
a96b0f577710ef20eddd501952e8b715f095e3b526be467395c6ff2435db16e0 | Text | 132 | 5 | # julearn_paper
Examples for julearn paper
Check the `README.md` files in the directory of each example for further instructions.
|
cacd6b3e0b1a1283bf601cca7214f664750c3e931da69f630966d247873612b0 | Text | 134 | 4 | # artic-ncov2019
Initial implementation of an ARTIC bioinformatics platform for nanopore sequencing of nCoV2019 novel coronavirus.
|
d2d43174688babf54158891d938b7e4797bff601f505263bebae660e8b308834 | Text | 134 | 2 | # SCC_DBS_EP
Code used to describe and characterize Evoked Potentials from Deep Brain Stimulation of the Subcallosal Cingulate region
|
63e6f6f891c8ec879d2815b7ca5f98249814b3662b1ba2d0117cbf1f42bb7848 | Text | 141 | 5 | # BoeckerCommunicationsBiology2024
Analysis code for investigating the participants' behavioral performance.
# Contact
lukas.kunz@ukbonn.de
|
0ed76368dfbb2b96832c187faa1f3bc09d8ad2e9b93dd37ee66d30aa448b161e | Text | 142 | 4 | # KCNE1_DMS
Deep Mutational Scan of KCNE1
This is accompanying code for a manuscript describing a Deep Mutational Scan of KCNE1. Stay tuned!
|
90fe230b79ff55072fcb46c761ee883e85ed87445c065bcb1f50664464ca0a7b | Text | 146 | 5 | These scripts accompany the Alais et al., 2023 paper.
(https://doi.org/10.7554/eLife.91019.2).
Raw data are available at https://osf.io/nzp9v/
|
e8f05c44fd5066563d9d43797b630cf68224a4421e4df65db489bfcca35c599a | Text | 151 | 5 | # q2-taxa
This is a QIIME 2 plugin. For details on QIIME 2, see https://qiime2.org. |
84beadc50859f7b7419b93f5fcc9c353bd75470c8b6b4eae312be7f6525ae3a1 | Text | 152 | 3 | Data used by https://neuroquery.org
Technical details and extensive validation are provided in [this paper](https://elifesciences.org/articles/53385).
|
331e49e744efd7cd2712dce6cf3d9e7e15ad845cc7d9930a84975bdbd7cb986b | Text | 155 | 9 | # Data from Auditory Parametric Working Memory Task and scripts used to analyze it.
### Run
Select relevant analysis in main.py:
```
python main.py
```
|
41ed5dfce1cbfc832b836502f9b83cff2142fa10bf472cb09b232e27f4edc53c | Text | 156 | 2 | # txci-atac
Code for txci-atac manuscript mouse brain and human cortex processing. Code presented here is in a markdown file following the entire pipeline.
|
be0fa7c3c40424708a7bb826201d8419cdfb23b8dfe4cb269081cb2d971174bb | Text | 159 | 3 | #STAR Protocol paper
Wang, Samantzis, Balbi (2024)
Protocol for the functional synaptic connection analysis using cell-pair cross-correlogram of spike events
|
0c7feb7f93ab802e020b17b018193007fdceb8d26a0331354cc4f80067f0b082 | Text | 174 | 2 | # Bioresorb_MATLAB
Fully Bioresorbable Hybrid Opto-Electronic Neural Implant System for Simultaneous Electrophysiological Recording and Optogenetic Stimulation - MATLAB code
|
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