sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
3b69ac22773500e06723dc54beccdf1d5987381d33b42c9a9b22c44036f8a1b2 | Shell | 2,855 | 73 | #!/bin/bash
# 00_charm.sh - build the 5-tissue head model from T1+T2 with SimNIBS charm (standard defaults).
# Produces a tetrahedral FEM mesh in m2m_<SUBJECT_ID>/.
#
# Usage: bash pipeline/00_charm.sh <SUBJECT_ID> <T1.nii> <T2.nii> <output_dir> [settings.ini]
# Example: bash pipeline/00_charm.sh "$SUBJECT" "$WORK_DI... |
164ad8656144cdeede46f950670798deda87b6f8e228ca3b69b5b004a75b739c | Shell | 2,865 | 27 | # rmf 4.23.2021
# F24
# young RLCs
python ../../../../scripts/applyTtestF24.py F24_young.txt transcripts_significantSites_DAVID_RLCs_transcriptGroups0.05_Cluster7_locomotor_rhythm.txt DAVID_RLCs_transcriptGroups0.05_Cluster7_locomotor_rhythm_transcriptIDs.txt youngRLCs
python ../../../../scripts/applyTtestF24.py F24_... |
882cabc037521bf6c6e50ce435a08316c9d4515d54eda0ab5e46203fefba7be1 | Shell | 2,871 | 84 | #!/bin/bash
#script de comprobacion si la imagen DICOM esta comprimida
#y la devuelve en raw
#Uso
#
#bash descompresionDICOM.sh
#_log="/home/cafetero/logs/registro_descom_VVD17RABIOBANCO03_$(date +"%m_%d_%Y__%H-%M").log"
#PATH_RECOLECTOR="/home/cafetero/ceibanon/data_ra600/VVD17RABIOBANCO03"
function testYdescSobreS... |
cd438d4f0fefaae6ede4e364a1f458ffa615e9dce3bde7f7e412227dc91627e8 | Shell | 2,916 | 91 | #!/usr/bin/env bash
# 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 (the
# "Lic... |
1eaf7e374995446cc218bce29340696f1bd10b84c6d183672cca8ed621c398aa | Shell | 3,078 | 65 | #!/bin/bash
RESFOLDER=res_01_FWHMx
TASK=hrf
DS=TR600
mkdir -p ${RESFOLDER}
for sdx in {01..17}
do
for rdx in {01..06}
do
INFILE=fmriflows/preproc_func/sub-${sdx}/sub-${sdx}_task-${TASK}_run-${rdx}_tFilter_5.0.100.0_sFilter_LP_0.0mm.nii.gz
OUTFILE=${RESFOLDER}/sub-${sdx}_run-${rdx}_fmriflows_5.... |
02c665d8d34515a6b455f6937d264d84d836e257b528f47d3616edcb1181b7f5 | Shell | 3,082 | 65 | #!/bin/bash
RESFOLDER=res_01_FWHMx
TASK=memory
DS=TR2000
mkdir -p ${RESFOLDER}
for sdx in {01..12}
do
for rdx in {01..04}
do
INFILE=fmriflows/preproc_func/sub-${sdx}/sub-${sdx}_task-${TASK}_run-${rdx}_tFilter_5.0.100.0_sFilter_LP_0.0mm.nii.gz
OUTFILE=${RESFOLDER}/sub-${sdx}_run-${rdx}_fmriflow... |
3a6ebae6319dfaa9d1e558d109a7dc297d5f5eb7d2bb9863731f5c2cb17a6d4d | Shell | 3,083 | 73 | #!/bin/bash
# Regenerates the frozen read fixtures in tests/data from data/*.fa.
#
# The reads are committed rather than simulated at test time because
# data/simulator.pl walks a Perl hash to pick references, and Perl hash
# order varies between runs and Perl versions. Pinning the hash seed makes
# this script reprod... |
1fc417cd384665f3ce42b987fb559e12860d87dd07c4174b9385248acb700065 | Shell | 3,122 | 101 | #!/bin/bash
WAIT_PERIOD=60
PROCESS_ID_FILE=
LOG_FILE=
function where_am_i() {
local source="${BASH_SOURCE[0]}"
while [ -h "$source" ]; do
local dir="$( cd -P "$( dirname "$source" )" && pwd )"
source="$(readlink "$source")"
[[ $source != /* ]] && source="$dir/$source"
done
local dir... |
b4fb481014e0da8a06bf7329232da07937aa7b0bb401e840caa50f291795f0c5 | Shell | 3,123 | 98 | #!/usr/bin/env bash
# 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 (the
# "Lic... |
23939b34a6b0ff668cbe6aeab617d768e03e730cd0b788c6762644c6d74504ef | Shell | 3,149 | 65 | #!/bin/bash
RESFOLDER=res_01_FWHMx
TASK=MGT
DS=TR1000
mkdir -p ${RESFOLDER}
for sdx in 001 002 003 004 005 006 008 009 010 011 013 014 015 016 017 018 019 020 021 022
do
for rdx in {01..04}
do
INFILE=fmriflows/preproc_func/sub-${sdx}/sub-${sdx}_task-${TASK}_run-${rdx}_tFilter_5.0.100.0_sFilter_LP_0.0m... |
28dbd879908dc20ac496f5d7fa1d37f9253f879205ae0090900d75c43657b40f | Shell | 3,200 | 83 | #!/bin/bash
#=============================================================================
#SBATCH --account=bd1179
#SBATCH --partition=compute # Specify partition name
#SBATCH --time=08:00:00 # Set a limit on the total run time
#SBATCH --nodes=1 # I think one could try more than one node
#SB... |
468ad7a54a19ef7283932de7a4a1b24516633b3c73cac8f1a3e232bc3aaf02cc | Shell | 3,208 | 31 | # rmf 9.21.2020, last modified 4.14.2021
# cleaned up 3.2.2022
# RP24
# young RLCs
python ../../../../scripts/applyTtestRP24.py geneGroupFile_young.txt transcripts_significantSites_DAVID_RLCs_transcriptGroups0.05_Cluster7_locomotor_rhythm.txt DAVID_RLCs_transcriptGroups0.05_Cluster7_locomotor_rhythm_transcriptIDs.txt ... |
ea601ca1b7869d4d51af969c3dc5b480d0fc9abbc39efaabf113d4aa22af708b | Shell | 3,218 | 63 | #!/usr/bin/env bash
# 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 (the
# "Lic... |
f158fb5334cb08b0df9f1f6ab2e508c4c545b69bc53031e9c8621182c95fbd1d | Shell | 3,271 | 109 | # Wrapper script to set the run_id and
# copy the config file to the output directory for a given experiment
# run_id is the first parameter, config is the second
run_id="$1"
config_file="$2"
if [ "$1" == "" ]; then
echo "Need to pass <run_id> as first argument"
exit
fi
if [ "$2" == "" ]; then
echo "Need... |
d37b7a34d10037af836c9e40cae77d22b532b7b3662a8a49500185c38e7937b8 | Shell | 3,279 | 116 | #!/bin/sh
# 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 (the
# "License"); yo... |
a0cea7cfc094767ced9cf0e32ed39f101f2358114fcbac6e44e836e65ba23736 | Shell | 3,352 | 32 | # rmf 4.14.2021, last modified 4.19.2021
# cleaned up 3.2.2022
# mean expression
# young RLCs
python ../../../../scripts/applyTtestExpression_mean.py transcriptExprYoung.txt transcripts_significantSites_DAVID_RLCs_transcriptGroups0.05_Cluster7_locomotor_rhythm.txt DAVID_RLCs_transcriptGroups0.05_Cluster7_locomotor_rh... |
038c77610160fd054708c52fefc1a685539ff54f7def3b85a2e8d031edbe8e87 | Shell | 3,365 | 54 | #!/bin/bash
# 07_build_nuclei.sh - Group 2 deep stimulation-relevant nuclei ROIs from CIT168/Pauli, warped to subject
# space (L/R split). Basal ganglia (Pu, Ca, NAC, GPe, GPi) plus midbrain and subthalamic nuclei (SNc, SNr,
# VTA, RN, STN). Reuses the CIT168 atlas cache (2009c->NLin6 affine + pauli_prob) staged under
... |
d1c85968ae84a4b1a59feb802ae0fe3d62955a15b12cc6768b511d8310a3e547 | Shell | 3,378 | 32 | # rmf 4.14.2021, last modified 4.15.2021
# cleaned up 3.2.2022
# median expression
# young RLCs
python ../../../../scripts/applyTtestAllExpressionVals.py transcriptExprYoung.txt transcripts_significantSites_DAVID_RLCs_transcriptGroups0.05_Cluster7_locomotor_rhythm.txt DAVID_RLCs_transcriptGroups0.05_Cluster7_locomoto... |
dac385728887ad5da9b9ce44ea1eb3882175785555851c5bfa7fa771750a5417 | Shell | 3,378 | 32 | # rmf 4.14.2021, last modified 4.19.2021
# cleaned up 3.2.2022
# median expression
# young RLCs
python ../../../../scripts/applyTtestExpression_median.py transcriptExprYoung.txt transcripts_significantSites_DAVID_RLCs_transcriptGroups0.05_Cluster7_locomotor_rhythm.txt DAVID_RLCs_transcriptGroups0.05_Cluster7_locomoto... |
f511f8294fc50647def071a4cce7be1206e18da56bc513f731a8ac1ebdf2e68a | Shell | 3,400 | 106 | #!/bin/bash
# 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 (the
# "License"); y... |
02968ba885b5870bf4e942eaf8198b1c2dc3a84e9b70b4651bf1d9616663d068 | Shell | 3,462 | 69 | FREESURFER_HOME='/Applications/freesurfer/7.3.2'
source $FREESURFER_HOME/SetUpFreeSurfer.sh
workbenchdir='/Applications/workbench/bin_macosx64'
standard_mesh_atlases='/Users/lindenmp/Google-Drive-Penn/work/git/HCPpipelines/global/templates/standard_mesh_atlases'
indir='/Users/lindenmp/research_data/Glasser_et_al_2016_... |
ca36e73b08ede7ca1cb50597a87f96d0954e555dc2542228c72f3770bb8f9d90 | Shell | 3,480 | 83 | #!/bin/bash
# Check changed vignettes for SeuratWrappers
# Set global options to cause the script to fail upon failure of any one step
set -eo pipefail
# A simple function to get the extension of files
function extension() {
local fname="${1}" # Name of file to get extension of
echo "$(echo ${fname} | r... |
f70c7de14ec392d41713a25522f24984aa7851d62b7401a7f8f18863abd32ab9 | Shell | 3,526 | 69 | ###### Zhao et al 2014 dataset
cd cxcl2_Erle_testSet
#prepare table of variant effects
Rscript joint_table.R
#prepare fastUTR data
Rscript process_seqs_and_mpraVals.R
#FastUTR dataset
for x in {0..9}; do { for y in {0..4}; do { echo $x, $y; sbatch --mem 20000 -J $x$y -e fastUTR_predictions/f$x\_c$y.err -o fastUTR_pre... |
4877719613415bbb234f314363a7eeea343f02dd03cc716949e428b393660227 | Shell | 3,549 | 77 | #!/bin/bash
#SBATCH -A TSVETANOV-SL3-CPU
#! icelake ccalake
#SBATCH -p icelake
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --time=00:10:00
#SBATCH -J vba_analysis_slurm # Name of the job
#SBATCH -o vba_analysis_slurm.out
#SBATCH -e vba_analysis_slurm.err
#! set array number
#SBATCH --array=1-200 # Set to match nu... |
c0202dac3cd81907077066513a75acc46d52fd3b5a856851ad4eff54ae62c4be | Shell | 3,578 | 67 | #!/bin/bash
# 01_dwi2cond.sh -- DTI baseline conductivity tensor via standard SimNIBS dwi2cond.
#
# DTI model = the SEPARATE single-shell DTI scan (not the MUDI multi-shell), already
# eddy/topup-corrected upstream. Path: dtifit --save_tensor -> dwi2cond --all
# --regmthd=12dof <subjectID> <DTI_tensor>. Do NOT re-run d... |
e2f39f9d4450136109dad303473c3a7beab4be0ad4bcd5e04abe95028d47cc71 | Shell | 3,596 | 90 | #!/usr/bin/env bash
# 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 (the
# "Lic... |
fa73865af5943a5d44c05c792fcbc8c7d9f3291de6326ff666a6321c153c9f6e | Shell | 3,613 | 37 | #plot benchmarking results of neural net vs lasso regression for human/mouse
Rscript Fig5bc.R
Rscript Fig5c_S6c.R
#metagene plot of ISM analysis
Rscript Fig5d.R
#visualize a few examples of ISM results
python Fig5e.py
#ablation analysis
Rscript CV_predictions_ablations.R
Rscript FigS6b.R
#plot neural network model ... |
ed31ff1d981130995dc1ad42d333898f6368d9a86c5b3589c717aeeed9636ced | Shell | 3,642 | 115 | #!/bin/bash
# if you have multiple seed regions, and a computer with several cores,
# you can try the following to speed up the computations:
#
# (1) create a list called e.g. seeds.txt where for each line there is the
# complete path to the image. E.g. go to the folder containing all the
# seed masks and laun... |
6c4b8bd4e8e3e836ec0fc44b571535def9f72e4a1f7e0bc6c3d827382899f2b8 | Shell | 3,727 | 132 | # Wrapper script to set the run_id and
# copy the config file to the output directory for a given experiment
# run_id is the first parameter, config is the second
run_id="$1"
config_file="$2"
if [ "$1" == "" ]; then
echo "Need to pass <run_id> as first argument"
exit
fi
if [ "$2" == "" ]; then
echo "Need... |
99069570290da8420b34c06ff7c563c93652116a75e28e340c16cf1f0be3ae2a | Shell | 3,731 | 112 | #!/bin/bash
# ----------------------------------------------------------------------------
# build_AMBA_data
# Author: Antoine Beauchamp
#
# Pipeline to generate necessary data files from the Allen Mouse Brain Atlas
#
# Pipeline steps:
# 1. Resample DSURQE imaging files from its common space to CCFv3.
# 2. Download t... |
913eda1ffa85ab92abf4046a31223135b77f4e20ea5e4a008c15529d4f3d5414 | Shell | 3,852 | 18 | python ../scripts/filterDEtranscripts.py ELCs_q0.05_phase0-12.txt /nfs0/BB/Hendrix_Lab/Drosophila/CircadianRhythms/RNASeq/RP24Analysis/Hisat2AlignmentTranscripts/transcriptGroups_q0.05/upAndDownGenes/R2A_downInOld.txt
python ../scripts/filterDEtranscripts.py ELCs_q0.05_phase12-24.txt /nfs0/BB/Hendrix_Lab/Drosophila/Cir... |
966d8e372ee20682fe18a1e8c70d90549fef72765bf8167bf868b89324e8f1c8 | Shell | 4,182 | 41 | #!/usr/bin/env bash
rm *.pkl
rm logs/ -rf
echo "============================== EXAM =============================="
# rm -rf Prognostic
# python3 prepare_prognostic_test_data.py -w
# mv Prognostic/X4.pkl ../Xtest.pkl
# mv Prognostic/y4.pkl ../ytest.pkl
for tol in 2 5 10; do
for i in {0..9}; do python3 make_dataset.py ... |
e32a85435f64228eca67bef1d0638b93792bdc07b3cc1a84652951675bb878c0 | Shell | 4,191 | 107 | #!/bin/bash
# ----------------------------------------------------------------------------
# process_expression_data.sh
# Author: Antoine Beauchamp
#
# Pipeline to process mouse and human gene expression data sets.
#
# Pipeline steps:
# 1. Create a set of atlas labels at multiple levels of granularity using
# the n... |
e22d97b2b9f40ed62a0728067c052cff77ec1c91fb9f02aedf4b862bc3f2e26d | Shell | 4,231 | 80 | #!/bin/bash
# 05_register_mre_to_T1.sh - resample the MRE maps (stiffness + alpha) into charm/mesh T1 space so MRE,
# ROIs, and E-field share one space for the cross-modal comparison.
#
# MRE is delivered already in the FreeSurfer-conformed T1 (256^3, "_ToT1" = recon-all orig.mgz grid), so
# this applies the orig->char... |
2754f6b58e8aaa8c16844bbb5fab114c39f1acefabe295f3d4a13c2309ace51a | Shell | 4,570 | 70 | #!/bin/bash
# Calculates SNR for each subject, reslices them into a common space,
# and does a "soft mean" - for each voxel, averaging across all subjects for which that voxel was inside their brainmask
# Rhodri Cusack TCIN 04/2021, cusackrh@tcd.ie
FILES=`ls -1 /dhcp/dhcp_fmri_pipeline/*/*/func/*brainmask.nii.gz` # ... |
1d550a18488829e738e679255bcacbcba7ac1e8617dfa314e3879255c4ab668b | Shell | 4,719 | 71 | #!/usr/bin/env bash
## MNIST
./compare_hyperParams.py --seed=1 --experiment=splitMNIST --scenario=task
./compare_hyperParams.py --seed=1 --experiment=splitMNIST --scenario=domain
./compare_hyperParams.py --seed=1 --experiment=splitMNIST --scenario=class
./compare.py --seed=2 --n-seeds=20 --experiment=splitMNIST --s... |
51cdfd43d716459ef9f1bb2c205555803af981ff1db00d4175a5f3412e8f8b5c | Shell | 4,771 | 97 | #!/usr/bin/env bash
MANYLINUX_VERSION=$1 # This means that downloaded python version has been built in CentOS 7. See https://www.python.org/dev/peps/pep-0599/ for details.
PYTHON_VERSION=$2 # Three digits. Before build check the latest available versions on https://github.com/niess/python-appimage/tags
MA... |
733a0911a4f394f9279aa3d07110bd4e156812138ed3c1f7202450fd7aaf8e7f | Shell | 5,103 | 123 | workspace='./FACS/FACS/'
TAG='Aorta'
f1=$workspace$TAG\_rm.batch_dge.txt
python 1getAnno.py $workspace$TAG\-counts.csv
python 2compress.py $workspace$TAG\-counts.csv.anno.txt ./OUT/$TAG\_ref_mouse.txt
python mouse2human.py ./OUT/$TAG\_ref_mouse.txt ./OUT/$TAG\_ref_human.txt
TAG='Bladder'
f1=$workspace$TAG\_rm.batch_d... |
b43d369705315a82a035551b89a1af6eac05d86f7e9a8ff9a71605c1f6d2909a | Shell | 5,154 | 218 | #!/bin/bash
# Downloads and extracts the Kitti dataset
# First argument == path to desired dataset destination
echo "An account on www.cvlibs.net is required to download the KITTI dataset. By running this script, you acknowledge that you comply to the download policy of www.cvlibs.net (http://www.cvlibs.net/datasets/k... |
4983395b9df42461aaa0cbad270bf3efdd97587e84b8f90b0c7dd6caf76471d6 | Shell | 5,244 | 151 | #!/bin/bash -l
usage() {
echo ""
echo "Usage: $0 <OPTIONS>"
echo "Required Parameters:"
echo "-n <protein id> Name of target i.e. T1084A_T1084B"
echo "-p <monomer pdb file list> Path list of monomer pdb file, could be one file for the homodimer
... |
e51fc9316d84d243e8b9a9ade9d683dceacf9ece6dd3bc267e72ee8c936c248e | Shell | 5,394 | 166 | #!/bin/bash
######################################
#### SumstatsQC Dev version 2 ########
#### Data cleaning step ######
#### required parameters : #
#### sumstats #
#### pop #
#### prefix #
#### AF ... |
69cfcd624413b20e72d42e7f9d2d75cb6ff4aacf2869a2cd12e7fdb580835678 | Shell | 5,418 | 157 | #! /bin/bash
#Cortical Thickness - Michel Thiebaut de Schotten & Chris Foulon
[ $# -lt 3 ] && { echo "Usage : $0 T1Folder ResultDir SaveTmp [LesionsFolder]"; exit 1; }
#Those lines are the handling of the script's trace and errors
#Traces and errors will be stored in $2/logThickness.txt
export PS4='+(${LINENO})'
echo -... |
155822d13872b1793f297d1a9b3e81919f419cc2355fcea0ad4320c54cfc3683 | Shell | 5,466 | 92 | #!/usr/bin/env bash
########### ICLR 2025 Blogpost ###########
python3 ICLRblogpost/compare_FI.py --seed=1 --n-seeds=30 --experiment=splitMNIST --scenario=task
python3 ICLRblogpost/compare_FI.py --seed=1 --n-seeds=30 --experiment=CIFAR10 --scenario=task --reducedResNet --iters=2000 --lr=0.001
########### NeurI... |
38e4ba79a0b4161a3072f7e7ca0f37f04c91a79a76615280cbfb47eba72e9877 | Shell | 5,477 | 160 | #!/bin/bash
######################################
#### SumstatsQC Dev version 2 ########
#### Split Sumstats into chr ########
#### required parameters : #
#### sumstats #
#### pop #
#### prefix #
##################################... |
c5dd21ec6efed6cc7cb46ff51530b401c592c44e2896848ab6b0c8e30d786318 | Shell | 5,950 | 111 | #!/bin/bash
# 08b_matched_reg_control.sh - matched-registration control for the DTI-vs-<D> V1 orientation divergence.
#
# Baseline analysis/08_tensor_divergence.py carries the DTI and <D> tensors to T1 through two different
# registrations, so the reported V1 angle mixes the genuine tensor-estimate difference with a
# ... |
21df3a2691dee86e61ec7e6e5d96b83e4ad602faeb38a4f6137a6cb9621de9b0 | Shell | 6,026 | 155 | #!/usr/bin/env bash
set -euo pipefail
umask 077
usage() {
echo 'usage: nsys_snn.sh capture [OPTIONS] OUTPUT_PREFIX -- COMMAND [ARGS...]' >&2
echo ' nsys_snn.sh capture-graph [OPTIONS] OUTPUT_PREFIX -- COMMAND [ARGS...]' >&2
echo 'options: --control=api|manual (default: api), --session=NAME (manual on... |
010e1f2d87d673428fe2a092ef001232b8cc2d899eb83e3901bdd4e03b60778a | Shell | 6,037 | 140 | #!/bin/bash
# run_subject.sh -- run the per-subject pipeline (ISO + MD-dMRI, plus the DTI model when a DTI scan is wired
# in the config) for one subject, then check the outputs reproduce the recorded baseline. Also the unit the
# cohort scale-out calls per subject.
#
# Usage: PIPELINE_CONFIG=<subject config.sh> bash p... |
6d44cfb464345c4adc47b099f66932aaf909f400fe348b27349ef88ee34a3982 | Shell | 6,215 | 158 | #!/bin/bash
set -e
echo "=== Galaxy GCP Batch Job Execution ==="
echo "Job: ${job_id_tag}"
echo "Tool: ${tool_id}"
echo "Container: ${container_image}"
echo "Timestamp: $$(date)"
echo "Host: $$(hostname)"
echo ""
# Debug network and NFS connectivity
echo "=== Network and NFS Connectivity Debug ==="
echo "Testing NFS s... |
8001a7e2178caa1aa9455462d464f2dcae8498979f6d52356e21f98114fea9a5 | Shell | 6,411 | 119 | #!/bin/bash
# 02_register_dmri_to_T1.sh - carry the QTI mean-tensor maps from dMRI space to T1 (charm/mesh) space.
#
# Registration is an S0-driven 12-DOF affine (dMRI S0 -> charm T2, same T2-like contrast), applied to
# every map. Affine, not nonlinear: the dMRI is already Synb0+topup distortion-corrected, and in a
# ... |
5c568b48f0fb58ab37878fd63ddb490230644319be63baa6f007f4964a327655 | Shell | 6,511 | 191 | #!/bin/bash -l
usage() {
echo ""
echo "Usage: $0 <OPTIONS>"
echo "Required Parameters:"
echo "-n <protein id> Name of target"
echo "-p <monomer pdb file list> Path list of monomer pdb file, could be one file for the homodimer Use \"\" for the list input, i.e. -p... |
a759447c81acbba895e999d6c4573c9388fd5eede00a3f870d0a06c88d5d5f92 | Shell | 6,980 | 194 | #!/usr/bin/env bash
# Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (the
# "Lic... |
83336a3c7bb3a4ed9b8b4b54cba8fda348b2df93eaa8114faafc70fd5594b5a1 | Shell | 7,296 | 196 | #!/usr/bin/env bash
# Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (the
# "Lic... |
c51e81da8f68ece73061cd40d4ad889b6469afec02e24c6856621c17b31e08f9 | Shell | 7,482 | 183 | #!/bin/bash
######################################
#### SumstatsQC Dev version 2 ########
#### Processing of Ref Panels ########
#### Required parameters : #
#### pop #
#### sumstats #
#### prefix #
#### multicpu ... |
848f513f5b88b33e554d87eed1a986d89ae759e93bc0a88c2ac304eb0fb718a9 | Shell | 8,005 | 121 | #!/bin/sh
#######################################################################
#### This scripts perform the preprocessors for ProFitFUn-Meta ###
#### This script will require path to Stride, Naccess and CLASS.exe ###
#######################################################################
PTSFF=$(pwd)
JOB=$1
UP... |
861dbded74a2ad92c26483fb856ac3d8af5b676dee3131be16e073ef58d54553 | Shell | 8,005 | 121 | #!/bin/sh
#######################################################################
#### This scripts perform the preprocessors for ProFitFun ###
#### This script will require path to Stride, Naccess and CLASS.exe ###
#######################################################################
PTSFF=$(pwd)
JOB=$1
UP... |
c81aa86e5c8f168f0281b9d0db94ed9e4f1a8e1b6ea1267f1c356d0e594d5537 | Shell | 8,304 | 249 | #!/usr/bin/env bash
# Copyright 2009 The Go Authors. All rights reserved.
# Use of this source code is governed by a BSD-style
# license that can be found in the LICENSE file.
# This script runs or (given -n) prints suggested commands to generate files for
# the Architecture/OS specified by the GOARCH and GOOS environ... |
85f5f5e0f1a2d28c2139d7107472df2f8bf35b2320b5b586fe83c4754d604775 | Shell | 8,564 | 279 | #!/bin/bash
set -x
# Intro:
# - This script will cook a template for VBG specific to your population
# - This will ensure a better result from VBG
# - You only need to run this once for your study if you're using only 1 scanner
# - We use the whole head T1 WIs (any modality could work actually)
# of two patients wi... |
9344da5493607d00cf69e6d64275f451a0df8bb34a5bd79aa067248da3ec5894 | Shell | 8,765 | 149 | #!/bin/bash
# run_cohort.sh - scale-out over the cohort. Stages each subject from the mounted cohort share into the
# per-subject layout (symlinks; no copy), writes a per-subject config, and runs run_subject.sh
# (default charm, ISO+MD-dMRI, plus the DTI model when a matching ParkMRE_DTI scan is found on the share).
# ... |
6f29df870c716ad6c6268c20bb2680b4e330fccbf0b894efd69a73ad28f7ddea | Shell | 9,821 | 270 | #! /bin/bash
#Normalize Patients - Michel Thiebaut de Schotten & Chris Foulon
#$1 = T1Folder $2 LesionFolder $3 ResultFolder $4 templateFile $5 skull_strip
#$6 synParam $7keepTmp $8 lesionMaskingMethod $9 otherFilesFolder
#$10 otherResultFolder
[ $# -lt 8 ] && { echo "Usage : $0 T1Folder LesionFolder ResultFolder \
tem... |
2542cc2d21c4d405ac3c287bb147b4fdf865ddbc765a3e35dd0a81465d62400a | Shell | 10,853 | 292 | #! /bin/bash
#Normalize Patients - Michel Thiebaut de Schotten & Chris Foulon
#$1 = T1Folder $2 LesionFolder $3 ResultFolder $4 templateFile $5 skull_strip
#$6 synValue $7keepTmp $8 lesionMaskingMethod $9 otherFilesFolder
#$10 otherResultFolder
[ $# -lt 8 ] && { echo "Usage : $0 T1Folder LesionFolder ResultFolder \
tem... |
07e4d603c49c055ada408d92b5534169bd012c6d98a092d1836da228d3e1966c | Shell | 10,975 | 171 | #!/bin/bash
set -e
# Generate Dockerfile
generate_docker() {
docker run \
--rm repronim/neurodocker:0.7.0 generate docker \
--pkg-manager apt \
--base neurodebian:stretch-non-free \
--arg DEBIAN_FRONTEND=noninteractive \
--install gcc g++ make graphviz tree tree less swig netbase \
... |
6c6ffe28e1563967be16f2aa0be0ee8585a02e08267ba61e2884ca8b804ef687 | Shell | 11,658 | 240 | #!/bin/bash
######################################
#### SumstatsQC Dev version 2 ########
#### Extract QC info step ######
#### required parameters : #
#### sumstats #
#### pop #
#### prefix #
#### AF ... |
8f05191c41fd9e87bb19793e9d00c1e89e35b0cf602df045bada86a2f09c81a1 | Shell | 13,243 | 402 | #!/bin/bash
# script que lanza limpiador, descomprimir, obtener id y subir.
# este script incluye los paths que serán los que usen el resto.
# precaucion con el slash final de los paths
_path_lib="./lib/"
printHelpAndExit(){
echo "Usage: ./maestro.sh -m machine -p project [-d department]"
echo ""
echo "-m, --mac... |
7647b774d3d5ee5bf76b4e09d03cf2295ceb95a2c7ce9730f21911495d841e3a | Shell | 13,843 | 334 | #!/usr/bin/env bash
# =============================================================================
# tractotron_cli.sh — Tractotron: lesion–tract overlap analysis
# =============================================================================
#
# SYNOPSIS
# tractotron_cli.sh -l LESIONS_DIR -t TRACTS_DIR -o OUTPUT_DI... |
f7df68c9796aa41e4a1add3a402d186a1f82c36ea5bab659546cc8638667ef68 | Shell | 14,386 | 276 | #!/bin/bash
######################################
#### SumstatsQC Dev version 2 ########
#### Merge sumstats with ref by chr ##
#### required parameters : #
#### sumstats #
#### pop #
#### prefix #
#########################... |
79318ad323906fd55c0f14f89ea4e643446d12c81e9e21db5affec25ba03ac31 | Shell | 14,771 | 223 | #!/bin/bash
######################################
#### SumstatsQC Dev version 2 ########
#### Quality control parameters ######
#### required parameters : #
#### sumstats #
#### pop #
#### prefix #
#### AF ... |
d46d5cd5475fd1a58c9e9d9d885b6fc57d7990001f0a8db21f55d0331cafd964 | Shell | 15,490 | 531 | #! /bin/bash
# AnaCOM2 - Serge Kinkingnéhun & Emmanuelle Volle & Michel Thiebaut de Schotten
# & Chris Foulon
[ $# -lt 9 ] && { echo 'Usage $0 :
$1: csvFile
$2: LesionFolder
$3: ResultFolder
$4: threshold
$5: controlScores
$6: test (Kruskal-Wallis, Mann-Whitney, t-test, Kolmogorov-Sm... |
4a02fcb343d1f965482faf67b614aa4314250c19cbd8ceb507f019f888ca7c12 | Shell | 16,539 | 394 | workspace='./MCA_BatchRemove_dge/rmbatch_dge/'
TAG='Bladder'
f1=$workspace$TAG\_rm.batch_dge.txt
python 1combine.py $workspace$TAG\_com.txt $f1
python 2getAnno.py $workspace$TAG\_com.txt
python 3compress.py $workspace$TAG\_com.txt.anno.txt ./OUT/$TAG\_ref_mouse.txt
python mouse2human.py ./OUT/$TAG\_ref_mouse.txt ./OUT... |
8648dd5bc4f0c6642a6a71818e29b7483a36df536286fcd25da63c08e550cfb8 | Shell | 16,665 | 570 | #! /bin/bash
#AnaCOM2 - Leonardo Cerliani & Michel Thiebaut de Schotten & Chris Foulon
[ $# -lt 5 ] && { echo "Usage : $0 T1Folder RSFolder resultsFolder \
sliceCorrection saveTmp [LesionsFolder]"; exit 1; }
#Those lines are the handling of the script's trace and errors
#Traces and errors will be stored in $3/logAna... |
7344a51cb003b4d865b24bfdaefced8ca5bc8abd34c2d6138e67f3a8651babb5 | Shell | 18,516 | 641 | #!/bin/bash
######################################
#### SumstatsQC Dev version 2 ########
#### visualization step ######
#### required parameters : #
#### sumstats #
#### pop #
#### prefix #
#### AF ... |
4dda672ce13db277a0a06bf2584a95ae40c7369e177b68753a16d2036ad38104 | Shell | 21,018 | 805 | #!/usr/bin/env bash
# Copyright 2009 The Go Authors. All rights reserved.
# Use of this source code is governed by a BSD-style
# license that can be found in the LICENSE file.
# Generate Go code listing errors and other #defined constant
# values (ENAMETOOLONG etc.), by asking the preprocessor
# about the definitions.... |
2bc7226cb7995f7bb250aab3e038cdee578edead2cd1dd68bd555533e9b8f8f1 | Shell | 23,204 | 731 | #!/bin/bash
set -x
# @ Ahmed Radwan -> ahmed.radwan@kuleuven.be, radwanphd@gmail.com
# @ Stefan Sunaert -> stefan.sunaert@kuleuven.be
# KUL_synth_cohort_gen.sh
# v=0.25 - 11092021
cwd="$(pwd)"
# function Usage
function Usage {
cat <<USAGE
`basename $0` Runs whole brain TCK segmentation using an input config ... |
cba2b5afe92c974f9043339b9ed74c000ed2516aa6f79506354b4a216e57df2d | Shell | 25,161 | 446 | #!/bin/bash
function print_usage {
echo -e "USAGE: aws-igenomes.sh\n" \
"\t\t[-g <genome name>]\n" \
"\t\t[-s <source name>]\n" \
"\t\t[-b <build name>]\n" \
"\t\t[-t <reference type>]\n" \
"\t\t[-o <output directory>]\n" \
"\t\t[-d (dry run, no downloads)]\n" \
... |
ce32cf0132184101930fb1c587e1a01cd7813ecd90e3e871e58e0c9beb7dceed | Shell | 26,438 | 258 | sumstats=$1
Reference_Allele=$2
output=$3
### SumstatsQC utility
printf "\n#############################################\n#### SumstatsQC Utility for Generating Batch File \n#############################################\n\n" 2>&1 | tee $output.batch.log
printf "\nAnalysis Initials = $(id -u -n)\n" 2>&1 |... |
be1c1d914e83ea0f6a8334273d4b8782e8cce2ecc6bcabfcba2ee65915c05035 | Shell | 28,606 | 655 | #!/usr/bin/env bash
# =============================================================================
# run_disco.sh — Disconnectome Maps Runner for BCBToolKit
# =============================================================================
#
# SYNOPSIS
# Folder mode : run_disco.sh -l DIR -o OUTDIR [-r FROM:TO] [optio... |
8671a7a9fca0719f06150b3a0cf602165afabd407bfe8394a7921c98be696b22 | Shell | 29,975 | 508 | ################################################
#### HESS wrapper
# The following scripts would carry out HESS local genetic correlations according to
# instructions found in https://huwenboshi.github.io/hess/
function helpscript {
echo "The following wrapper script will carry out steps that h... |
306b26564e63acd92a3c7131506aee6b02047ad213eb62b3030f757675fc3d6c | Shell | 35,282 | 568 | #!/bin/bash
######################################
#### SumstatsQC Dev version 2 ########
#### Post processing step ######
#### required parameters : #
#### sumstats #
#### pop #
#### prefix #
#### AF ... |
a25e1a5f5e0d854872b15621bea4ce7f36f2783bbdb253d433ada8b36690bdd7 | Shell | 43,921 | 1,010 | #!/usr/bin/env bash
# End-to-end tests for an installed Kraken 2.
#
# Usage: tests/e2e.sh INSTALL_DIR [WORK_DIR]
#
# INSTALL_DIR is a directory produced by install_kraken2.sh. WORK_DIR holds
# every database, output file and log the run produces; it defaults to a new
# temporary directory and is kept afterwards so CI ... |
062b7e586624f37801d30cf624e665db5538a9cff67a37459b67971e930c512c | Shell | 49,975 | 1,546 | #!/bin/bash
# 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 (the
# "License"); ... |
8a20d0101f35ad7373a869ee90a0d4eb62b7d42c94b5517c773cffcf4838fd28 | Shell | 59,733 | 1,112 | #!/bin/bash
###############################################################
#### SumstatsQC Dev version 2 #################################
###############################################################
################################################################
##### Define help script ####################... |
a6eebb0ba26dca6ebeab4d93243b3713959c9fc0f7bf156811b4f9503f98c668 | Shell | 107,101 | 3,342 | #!/bin/bash
# set -x
# Ahmed Radwan ahmed.radwan@kuleuven.be
# Stefan Sunaert stefan.sunaert@kuleuven.be
# this script is in dev for S61759
#####################################
v="0.61_23112021_beta"
# This script is meant to allow a decent recon-all/antsMALF output in the presence of a large brain lesion
# T... |
30704c399d9a78f18f33733f8f41329d69b6ba46f748d283ba3cea97fd7c0134 | Shell | 200,000 | 828 | #!/bin/bash
CURL_VERSION=$(curl --version | grep -oie "curl [0-9][0-9.]*" | head -n 1 | awk '{print $2}')
if [ -z "$CURL_VERSION" ]
then
CURL_VERSION=PARSE_ERROR
fi
CURL_USER_AGENT="curl/$CURL_VERSION/esg/3.0.50-20220222-202404/created/2022-02-28T07:28:01-07:00"
####################################################... |
bdcd4b283fa12d0116fb2eb1e81b98da4e693299f954197b695f028afc09a7d3 | Text | 9 | 1 | # public
|
87d50e626b51570cbc3d68f51c36d09f41a5d77a5c0789c74905aaad695e68ea | Text | 11 | 1 | # SCFA_wmgx |
7638086acc27304f8ccda67152ec3abbbb14256e6ccfd106d40568c26335ee55 | Text | 12 | 2 | # Raw-data
|
c2de5161a9232df54ae71501f25747871e4e4c2a8ed90deb7dc2692da036e674 | Text | 15 | 1 | # Chunyan-Shuai |
56c88bfc8d69657b7519c57e92e9ed06246ed1ea1b115ccf8530aabfd47b76ce | Text | 18 | 2 | # Psycho-PPI
none
|
cfdcd9afc1c7affc4f730084032e5ab30ddafec53baee10a9e655a11294db97a | Text | 19 | 1 | # Fisher_info_codes |
471aacf04de1cf843c4ebaa40f475c4e3e45444ab1b9bb2be3e75fa52fbd162e | Text | 21 | 1 | # MIBI_Brain_Analysis |
04879310e479c720d111d68ec5be12f0515605f52fc494d2a3a185ff106a5797 | Text | 33 | 1 | # Lowet-Nature-Communication-2022 |
46440bac20981bbc155faf509d65580ed1620a18c9efd4d9021fa5503b226608 | Text | 36 | 2 | # widefield
widefield_data_analysis
|
a8673a775fb3cb51e2322ff8e45f3b124c5f85feb5eab88528dda06ce37f7565 | Text | 47 | 2 | # NES
Glioblastoma Natural Evolution Signature
|
8d4a7bc6f2852b757a8cff83ad2d9db51eb76166d018d9ba3dea44af64c87104 | Text | 48 | 3 | ===============
neurogenesis-dl
===============
|
a90beacf958deb18f86583d7727a5bf0a50d0eefae01e80d59face8b2eab5f53 | Text | 54 | 2 | # Stroke_cancer_immune
brain and skull injury-ran-seq
|
91b20aef2e1f317aae0a256793fd89a07fe219c876302d2396b558307fb0a36f | Text | 56 | 2 | # SNN-Kalman-Filtering
Code of snn-based Kalman filter.
|
640e49599a08507fcf9dca8b4db4e2e1b37f22c94ae41e2c47b7ce89849970c1 | Text | 58 | 2 | # rcaExtra
RC Analysis add-ons (plotting, averaging, etc)
|
29bd2a724cc09b87a9a4d1cb624a9722fd7e43742d354749a62d0cb226fa1c30 | Text | 65 | 1 | # https-github.com-IdlingBrainUT-Nomoto2022_NatureCommunications
|
da7c6a489a30e9acffc4105b7ee4a1a0eb94fc10dcba38a0e94070c3e62b6a3a | Text | 70 | 3 | # Math23k
The original partition of Math23k dataset for downloading.
|
161c968e6c07b8350f7e536000369aad69ee1cec91de765eba59f2d69fef5cbf | Text | 80 | 1 | # A machine learning based approach towards high-dimensional mediation analysis
|
5bae40893d41d65cb83b72627b3b40f811b198f0b512658a16ef517013e5c53d | Text | 82 | 2 | # verbal.irony.behavioral
Creation of verbal irony stimuli for Mexican popularion
|
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