sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
208ffc39e5dd52cec67b06b9c5b9a6c7800191ad7a993f0d9381fe917ed9665a | Shell | 870 | 33 | #!/bin/bash
set -e
set -o pipefail
set -o verbose
root=`dirname $(pwd)`
# Get data_folder path
SETTINGS_FILE=$root/settings.ini
if [ ! -f "$SETTINGS_FILE" ]; then
SETTINGS_FILE="$root/settings.ini.default"
fi
DATA_FOLDER=$(grep -E "^data_folder" "$SETTINGS_FILE" | awk -F ' = ' '{print $2}' | sed "s|\[path\]|${roo... |
f6035979feb1158c5a27f12c1df302a84cbb5fe7e37bb58dd1300eef388ebb2e | Shell | 870 | 10 | #!/bin/bash
# calculate the total length of unassigned contigs after correlation-based assignment
awk 'FILENAME==ARGV[1] && $0 !~ "#" {len[$7]=$10} \
FILENAME==ARGV[2] && $1 in len {tlen+=len[$1]} \
END{print tlen}' <(cat /Users/siyuansmac/test/GCA_013340165.1_LBDM_Dsuz_2.1.pri_assembly_report.txt) <(awk '$3 == "ambigu... |
85c5bda0cc098a0212c99c4791af08629a63e62b9992083d900b16018bd7396c | Shell | 872 | 17 |
# (c) Coraline Rinn Iordan 07/2017, 10/2017, 10/2019
# Align prototype after skull stripping
# $1 : PARAMS.TEMPLATEDIR
# $2 : PARAMS.LOCALIZERANAT
# $3 : PARAMS.CURRENTANAT
# $4 : PARAMS.LOCALIZERTEMPLATE
# $5 : PARAMS.NIFTIDIR
# $6 : PARAMS.PROTOTYPE.FINALFILE
3dSkullstrip -input "$1"/"$3"+orig -prefix "$1"/"$3"_st... |
600657a4bd568d13ac036daf735cf219e0a6588377d030e83dec4f5cce366d2b | Shell | 873 | 18 | #!/bin/bash
autopep8 scenario_runner.py --in-place --max-line-length=120
autopep8 srunner/scenariomanager/*.py --in-place --max-line-length=120
autopep8 srunner/scenariomanager/actorcontrols/*.py --in-place --max-line-length=120
autopep8 srunner/scenariomanager/scenarioatomics/*.py --in-place --max-line-length=120
aut... |
75966878fbcc88924b08d719520d9a2140430c3ea33e52803bba0732948681f1 | Shell | 873 | 10 | smr_Linux --eqtl-summary EAS.eQTL --qtltools-nominal-format --make-besd --out EAS
#snp.frq is a text file contains the frequency information which generated from plink
cat EAS.esi | awk 'NR==FNR{a[$2]=0;b[substr($2,length($2))]=0}NR>FNR&&($2 in a){if($3 in b){split($2,c,"_");print $1"\t"$2"\t"0"\t"c[2]"\t"c[4]"\t"c[3]... |
839a9137ce2186cd62c19e2b249df9c062b80ea94a81ba186e66a20dff1bc057 | Shell | 873 | 39 | #MOLGENIS walltime=02:00:00 mem=2gb ppn=1
#string pythonVersion
#string beadArrayVersion
#string gapVersion
#string bpmFile
#string projectRawTmpDataDir
#string intermediateDir
#string tmpTmpdir
#string tmpDir
#string workDir
#string tmpName
#string Project
#string logsDir
#string arrayFinalReport
#string samplesheet
... |
013d2676ac9db472d0d2d1875ec7bdec4379a75fd5175807b73f4c3db1f89418 | Shell | 877 | 20 | #!/bin/bash
if [ $# -ne 1 ]
then
echo "Please, give input fq.gz file"
fi
file=$1
email=a.alemany@hubrecht.eu
path2star=/hpc/hub_oudenaarden/avo/nascent/STAR-2.5.3a/bin/Linux_x86_64
starMouseRef=/hpc/hub_oudenaarden/group_references/ensembl/93/mus_musculus/star_index_75
intron=/hpc/hub_oudenaarden/group_reference... |
a2f1a659abfaadb2d23746064a98117120eebb5cc215a819e6e2404f6f1873ac | Shell | 878 | 24 | #!/bin/bash
# Copyright 2026 The Google Research Authors.
#
# 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/licenses/LICENSE-2.0
#
# Unless required by applicable ... |
e69af8f4b6c9437168b6a3355df6cdc8e77ce067bba5eee6a4ddc4978dd62c2e | Shell | 878 | 39 | #!/bin/bash
# Run feature selection experiments across a few genes, with selected cancer
# types held out (either partially or completely)
RESULTS_DIR=./08_cell_line_prediction/results/tcga_ccle_nn
ERRORS_DIR=./tcga_ccle_nn_errors
mkdir -p $ERRORS_DIR
# number of features to "preselect" to by mean absolute deviation... |
59380752d3545d959a0ebace9b04479d53c24b0ddc0b25486903d8aa781de8ff | Shell | 880 | 26 | #!/bin/bash
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable ... |
a50e2f554d4a0fb32d55e4c15a187e8b3f759d0c792e77c47b046669a16c5563 | Shell | 881 | 28 | load_app() {
if lsmod | grep -q "dma_proxy"; then
sudo rmmod dma_proxy
fi
if [ "$BIOEMUM_TARGET" = "vpk120" ]; then
sudo fpgautil -R -n full
sudo fpgautil -b "/lib/firmware/xilinx/$BIOEMUM_TARGET-bioemum/$BIOEMUM_TARGET-bioemum.pdi" -o "/lib/firmware/xilinx/$BIOEMUM_TARGET-bioemum/$B... |
7c75c12cf93948e9f02a3914208df4c7da42e267868f01c5e2ccc2c62396c46c | Shell | 882 | 29 | #!/bin/bash
# Copyright 2026 The Google Research Authors.
#
# 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/licenses/LICENSE-2.0
#
# Unless required by applicable ... |
9a29f39b516130ea2379987587884f35d10ff92f499a0b017670ad10ca8331da | Shell | 885 | 57 | #!/bin/bash
scriptpath="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
nocolor=false
brief=false
while [[ $# > 0 ]]
do
key="$1"
case $key in
-nocolor)
nocolor=true
;;
-brief)
brief=true
;;
*)
break
;;
esac
shift
done
if [ "$#" -eq 0 ]; then
DIR="$(dirname "$scriptpath... |
19d77ab4b2955004a0b89a00ced9fc21f7db3a68c08c7642f842b5ad66aebee5 | Shell | 887 | 26 | #!/bin/bash
set -e
set -o pipefail
set -o verbose
#General description:
# https://wiki.dnanexus.com/scientific-notes/human-genome
#Description of decoy sequences:
# ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/README_human_reference_20110707
src=`pwd`/../src/
if [... |
34b8e722b544d151fc02c8bd4d792b36048b6aeed4814b3f3311f8f6df2f2d77 | Shell | 888 | 27 |
source scripts/samples.sh
for i in ${SAMPLES[@]};
do
mkdir results/star_pass2/${i};
STAR --runThreadN 16 \
--outSAMtype BAM Unsorted \
--sjdbOverhang 124 \
--outFilterType BySJout \
--outFilterMismatchNoverLmax 0.04 \
--alignEndsType EndToEnd \
--alignSJDBoverhangMin 4 \
--alignIntronMax 1000000 \
-... |
3f9a9022a4c29e69d5fd3aeb48b31442a5949105584c62b3e2f88a14f39e1be7 | Shell | 896 | 25 | #!/bin/sh
current_dir=`pwd`
code_dir="./../../../Core_code/"
ncores=82
output_folder="/home/asantoro/COST/Project2_Higher_Order_Brain/Brain_HORS/Figure2/Results/HO_indicators/"
#file_input="/home/asantoro/HCP/100307/rfMRI_REST1_LR/Schaefer100/TS_Schaefer100S_gsr_bp_z.mat"
cd ${code_dir}
taskname="EMOTION"
for sub... |
02e538aa1831d4c0ac75262590bc5782300a66b2a0c3cc7737af5457c9f00dae | Shell | 897 | 24 | #!/bin/bash
set -ex
## Create a file for the environmental variables
if [ -f soft/bashrc_pyseg_sys ]
then
rm soft/bashrc_pyseg_sys
fi
printf -v date '%(%d.%m.%Y)T\n' -1
printf "\n## PySeg system "$date" \n" >> soft/bashrc_pyseg_sys
printf "\n## DisPerSe \n" >> soft/bashrc_pyseg_sys
printf "export PATH="$PWD"/sof... |
aea882f867943dcfcf255f00ef4fbf341ca2004c4fcab98b803931f1b6292479 | Shell | 898 | 37 | #!/bin/bash
# Copyright 2026 The Google Research Authors.
#
# 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/licenses/LICENSE-2.0
#
# Unless required by applicable ... |
eabf7a48ea07371ea405cb5baeb656544267f27fb43aa72def4bd0f9dc76eada | Shell | 898 | 27 | #!/bin/bash
# Copyright 2026 The Google Research Authors.
#
# 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/licenses/LICENSE-2.0
#
# Unless required by applicable ... |
e4c2a462d60dfca221b2a710b81fb2d1fa5156140a7bbb4caaac2bd1b00a0a41 | Shell | 899 | 30 | #!/bin/bash
# Copyright 2026 The Google Research Authors.
#
# 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/licenses/LICENSE-2.0
#
# Unless required by applicable ... |
95c3d1be0d92e2624ebb77206f4700377e6e230dff5b526dda3b7db3c71796b7 | Shell | 901 | 18 | #!/bin/bash
# Copyright 2026 The Google Research Authors.
#
# 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/licenses/LICENSE-2.0
#
# Unless required by applicable ... |
6a40d0947c5dbcf4ef1a022058024c31b8b57a86a713ad654b072dc9d1a5bff4 | Shell | 902 | 37 | #!/bin/bash
# Copyright 2026 The Google Research Authors.
#
# 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/licenses/LICENSE-2.0
#
# Unless required by applicable ... |
19b826da0571bd50d5f6dea9e315ef488b6d842bf3f4409ebcd78b628eb51e5c | Shell | 903 | 27 | #!/bin/bash
# Set your paths here
HOME=/fslgroup/fslg_spec_networks/compute
code_DIR=${HOME}/code/NSD_analysis/CBIG2016_preproc
data_DIR=/fslgroup/fslg_fun_conn/compute/NSD_analysis/NSD_BIDS
# Create that special CBIG subjids text file for each subject (data must be in BIDS format)
# CBIG example format: 001 /fslhome... |
9ab1e2bbfd8cf5143e84192b8faa39809947dd422b00bbce48a5eaafc6586e34 | Shell | 907 | 30 | #!/bin/bash
# Copyright 2026 The Google Research Authors.
#
# 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/licenses/LICENSE-2.0
#
# Unless required by applicable ... |
91e61cc02b6fc68e84842e89baa53140c7ea8ef0c91d7f65666369dfdb12b493 | Shell | 908 | 41 | #!/bin/bash
trap 'kill 0' INT TERM
if [ -n "$1" ]; then
TOP_LOG_DIR="$1"
else
TOP_LOG_DIR=.
fi
echo "[TOP_LOG_DIR]=${TOP_LOG_DIR}"
echo
FUNC=save3DImage_uint16
SIZE_Z=250
for n in 500 1000 1500 2000 2500 3000; do
echo "===== ${FUNC}(): n = $n"
TOP_LOG=${TOP_LOG_DIR}/top-${FUNC}-xy-${n}-z-${SIZE_Z}.lo... |
52d95e883d2a6575909d245b68bba8878c923af35e5a06123e588710c15ebc58 | Shell | 910 | 44 | #!/bin/bash
if [ -z ${AWS_SSH_PRIVATE_KEY_FILE} ]
then
echo "ERROR: You must set AWS_SSH_PRIVATE_KEY_FILE in the environment."
exit 1
fi
i=0
maxRetries=12
retries=0
for publicDnsName in $(cat nodes-public)
do
if [ ${retries} -ge ${maxRetries} ]
then
echo "ERROR: Too many ssh retries."
... |
3b1d93c8a918a93df1061a653cc9e517c36ea5442707c64659fb1e27ca51fbce | Shell | 912 | 30 | #!/bin/bash
#SBATCH --job-name=Shallow_Grid_1_N_Link_Simulation_Stage
#SBATCH --partition=general1
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=10
#SBATCH --cpus-per-task=4
#SBATCH --mem-per-cpu=4400
#SBATCH --extra-node-info=2:20:1
#SBATCH --time=32:00:00
#SBATCH --mail-type=FAIL
#SBATCH --array=0-9
#SBATCH --output=... |
bf0a30be14a1d6d63fb263a19a3759479c8e22cce6aa438e30262c587ce8bd01 | Shell | 912 | 30 | #!/bin/bash
#SBATCH --job-name=Shallow_Grid_1_Rule_Kern_Inference_Stage
#SBATCH --partition=general1
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=2
#SBATCH --cpus-per-task=20
#SBATCH --mem-per-cpu=4400
#SBATCH --extra-node-info=2:20:1
#SBATCH --time=24:00:00
#SBATCH --mail-type=FAIL
#SBATCH --array=0
#SBATCH --output=... |
807504f40bf6a8bf7edc50a5f04019a789a5ad968904de12078a7b3d4e54c73a | Shell | 913 | 23 | #!/bin/bash
# Copyright 2026 The Google Research Authors.
#
# 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/licenses/LICENSE-2.0
#
# Unless required by applicable ... |
ef1f67a147caf3a2c1267c2bad400fab3d1f8b50eecf88147dfd3904b750d6b6 | Shell | 915 | 30 | #!/bin/bash
#SBATCH --job-name=Shallow_Grid_1_Rule_Kern_Simulation_Stage
#SBATCH --partition=general1
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=10
#SBATCH --cpus-per-task=4
#SBATCH --mem-per-cpu=4400
#SBATCH --extra-node-info=2:20:1
#SBATCH --time=32:00:00
#SBATCH --mail-type=FAIL
#SBATCH --array=0-9
#SBATCH --outp... |
23f5e77cd60f877ee8addbb7721de35c39b510aa55d6eb3893f7be33a8ba5b53 | Shell | 916 | 26 | #!/bin/bash
declare -a
sims=("BlobStimReliability_O1v5-SONATA_RecipRemoval_StructDim56"
"BlobStimReliability_O1v5-SONATA_RecipRemoval_StructDim56_456"
"BlobStimReliability_O1v5-SONATA_RecipRemoval_StructDim456"
"BlobStimReliability_O1v5-SONATA_RecipRemoval_Unstruct-0"
"BlobStimReliability_O1v5-SONATA_RecipRemoval_Uns... |
dc41b484bdb4d3089e7c749976a225077f29e61a66d400f2405dd6ab6c99e738 | Shell | 919 | 12 | #!/bin/bash
echo -e "Running: ./seqc -if=5edw.fasta -select::sequence::long_at_least=10 -select::sequence::nucleic -out::fasta"
./seqc -if=test_inputs/5edw.fasta -select::sequence::long_at_least=10 -select::sequence::nucleic -out::fasta
echo -e "Running: ./seqc -if=5edw.fasta -select::sequence::long_at_least=100 -sele... |
3f809bb0654747d6f5d3591124dc43898fad26b72fac95b36bf84abd9eb7a663 | Shell | 920 | 42 | #!/bin/bash
trap 'kill 0' INT TERM
if [ -n "$1" ]; then
TOP_LOG_DIR="$1"
else
TOP_LOG_DIR=.
fi
echo "[TOP_LOG_DIR]=${TOP_LOG_DIR}"
echo
# 1e9 causes out-of-memory
for n in 1e7 0.2e8 0.4e8 0.6e8 0.8e8 1e8; do
echo "===== quantilenorm(): n = $n"
TOP_LOG=${TOP_LOG_DIR}/top-quantilenorm-nrows-${n}.log
... |
93d4de2e4aa47beab816dd5c9ecfeb36fbcea546c8f85aff46a3ae44294afe86 | Shell | 921 | 24 | #!/bin/bash
# Copyright 2026 The Google Research Authors.
#
# 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/licenses/LICENSE-2.0
#
# Unless required by applicable ... |
1a91003b19dd8b25ddd4ab51112d9b58e2f1dc857a9d5d9ff7a817ec7531e04a | Shell | 924 | 24 | #!/bin/bash
./ffmpeg2gif.sh APTStart.mp4 APTStart.gif "setpts=0.5*PTS,fps=10,scale=1920:-1"
./ffmpeg2gif.sh newproj.mp4 newproj.gif "setpts=0.5*PTS,fps=10,scale=1920:-1"
./ffmpeg2gif.sh LabelSequential.mp4 LabelSequential.gif "fps=20,scale=1920:-1"
./ffmpeg2gif.sh LabelMore.mp4 LabelMore.gif "setpts=2*PTS,fps=15,sc... |
1ee3157698df9f6ea7b89dca24c44d00d3e7b13022f6b46b1586df0a337379d4 | Shell | 928 | 18 | #!/bin/bash
### 1. configure the conda enviroment ###
source /home/siyuan/biosoft/miniconda3/bin/activate wgs_suzukii
### 2. set parameters ###
rscript=/home/siyuan/jobs/suzukii_WGS/genetic_diff/ML_tree/plot/mincount_10_no_se_auto_X_over10/plot_ML_tree.R
wd=/home/siyuan/jobs/suzukii_WGS/genetic_diff/ML_tree/plot/minc... |
9636ffa5af5890859a87ea714034a10a5308d4d3c4c7a2f2c2125b17ff48be74 | Shell | 928 | 28 | #!/bin/bash
# examine the number of transcripts that were assembled that appear to be full-length or nearly full-length.
# Store the diamond output file name
diamond_output_file=$1
# Initialize variables
total_hits=$(wc -l < "$diamond_output_file")
cumulative_count=0
# Print table header
echo -e "perc_cov_bin\tcount... |
64823548bb49296f8856dd6634352f57fecf9dc7ff68cd69e7c95324fdcdade5 | Shell | 930 | 19 | #!/bin/bash
### 1. configure the conda enviroment ###
source /opt/miniconda3/bin/activate WGS_analysis
### 2. set parameters ###
rscript=/home/siyuan/jobs/suzukii_WGS/genetic_diff/PCA/plot/plot_PCA.R
wd=/home/siyuan/jobs/suzukii_WGS/genetic_diff/PCA/plot
dd=/home/siyuan/jobs/suzukii_WGS/genetic_diff/PCA/results
### ... |
cc5484311d80fbc02a755c540527e1e44033043b9b2a4c970ce3079d18ceb937 | Shell | 930 | 41 | #!/bin/bash
trap 'kill 0' INT TERM
if [ -n "$1" ]; then
TOP_LOG_DIR="$1"
else
TOP_LOG_DIR=.
fi
echo "[TOP_LOG_DIR]=${TOP_LOG_DIR}"
echo
FUNC=phaseOnlyCorrelation
SIZE_Z=250
for n in 500 1000 1500 2000 2500 3000; do
echo "===== ${FUNC}(): n = $n"
TOP_LOG=${TOP_LOG_DIR}/top-${FUNC}-xy-${n}-z-${SIZE_Z}.... |
1f90032e4b9c7dd74757a56cbecda956b3a67366bcf53ba53d82b33015dfaa65 | Shell | 931 | 18 | #!/bin/bash
# Copyright 2026 The Google Research Authors.
#
# 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/licenses/LICENSE-2.0
#
# Unless required by applicable ... |
04412f96b669ed26fc3a97419d324746aa5dd8b2ecbe4140be4331e44bd1d27b | Shell | 935 | 29 | #! /bin/bash
set -ex
cat << EOF | debconf-set-selections
slapd slapd/internal/generated_adminpw password admin
slapd slapd/internal/adminpw password admin
slapd slapd/password2 password admin
slapd slapd/password1 password admin
slapd slapd/dump_database_destdir string /var/backups/slapd-VERSION
slapd slapd/domain st... |
a625fa43952b6973ba783f2952a6368ec7206e8bcfb57003423926785406cadd | Shell | 938 | 32 | #!/bin/bash
# Copyright 2026 The Google Research Authors.
#
# 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/licenses/LICENSE-2.0
#
# Unless required by applicable ... |
4fdfe023f10a6a2899d3ae5f6c53a23bd0314f601db528c7290b441f44a72303 | Shell | 939 | 27 | #!/bin/bash
# Copyright 2026 The Google Research Authors.
#
# 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/licenses/LICENSE-2.0
#
# Unless required by applicable ... |
c59be1ad24df86d0c69e5edc7950fb9f32cd43bdb05f36a538b600b5bbc5538e | Shell | 939 | 29 | #!/usr/bin/env bash
# Configure below, then run: ./scripts/run_compute_seg_metrics.sh (paths are relative to your cwd)
GT_DIR="path/to/ground_truth"
SEG_DIR="path/to/segresnet_preds"
OUTPUT_CSV="./seg_metrics.csv"
PATTERN="*.nii.gz"
NAMING_SCHEME="identical" # identical or braintracking
CONNECTIV... |
5f1f56a528694c49fde9cc46bf5a77efcaebf13645477c3d110e30edef43d932 | Shell | 947 | 29 | #!/bin/bash
path2star=/hpc/hub_oudenaarden/avo/nascent/STAR-2.5.3a/bin/Linux_x86_64
if [ $# -ne 2 ]
then
echo "Please, give:"
echo "1) fastq file to map"
echo "2) root for output file (no .sam or .bam extension)"
echo "3) reference genome"
fi
file2map=$1
outfq=$2
ref=$3
if [ $ref == 'mouse' ]
then
... |
738d9a8c3491f9a0bd4017504f4845025423070442e346507154c35dbe56bc47 | Shell | 948 | 20 | #######################
### Pseudobulk data ###
#######################
Rscript ML_scripts/Pseudobulk.R --inputPath SLE/data/SLE_Science/ --sampleColumn ind_cov
Rscript ML_scripts/Pseudobulk.R --inputPath SLE/data/SLE_pediatrics/ --sampleColumn ind_cov
###################
### Run models ###
###################
algo... |
631bbfe012b4c768b085a7021f50b50778ba4ac8a4c96b302be3b2f0b9ea4e9f | Shell | 949 | 22 | #!/bin/bash
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable ... |
4c97ff0947d4c7f7cd7f903087cd38fe54b6b07a69feb64ec9e84bc06fe97057 | Shell | 950 | 41 | #!/bin/bash
PYTHONPATH=".:$PYTHONPATH"
trap 'kill -INT -$pid && exit 1' INT
working=()
failing=()
examples=$(find examples -name '*.py' -not -name '__init__.py')
echo 'Running all the examples...'
for f in $examples; do
timeout 15s python2 $f > /dev/null 2>&1 & pid=$!
wait $pid
status=$?
if [ $statu... |
fe226c2a7d9a168f3882f86fd789f7f31875b8377b4da9fa159fd7089937594a | Shell | 950 | 25 | #!/bin/bash
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable ... |
7d6cd99851b8767f01fcf329fcea159268bbfae53dd85e78fa4809dfed331915 | Shell | 953 | 40 | #!/bin/bash
set -ex
#no final slash !!
targetFold=$PWD/../../../soft/disperse/latest
if [ -d "$targetFold" ]; then
echo "removing $targetFold before installing !!"
rm -r $targetFold/*
fi
mkdir -p $targetFold
buildFold=$targetFold/build
infrFold=${targetFold}/infrstr
mkdir $infrFold
mkdir $buildFold
# Setting up ... |
104edde820d4017a7a874929faf73587d1742885bcc80ff4b71ca5fe4c98dba2 | Shell | 959 | 38 | #!/bin/bash
#=====================================
# prep for PC-AiR on related data set
#=====================================
prefix=adc
prefix_out="$prefix"_np
# keep only european subjects
plink \
--bfile tmp/"$prefix"_qc1.tmp \
--keep data/"$prefix"/ids_qced.txt \
--make-bed \
--out tmp/"$prefix"_qc3.tmp
... |
4b5359a2f9158c662600573a6a67beb37dfb10b2eee797bbb5f1f6ddd147f7c3 | Shell | 961 | 24 | #!/bin/bash
HOME=/fslgroup/fslg_spec_networks/compute
code_DIR=${HOME}/code/HCP_analysis/CBIG2016_preproc
output_DIR=/fslgroup/grp_spec/compute/HCP_analysis/CBIG2016_preproc_FS6
output_DIR2=/fslgroup/fslg_HBN_preproc/compute/HCP_analysis/CBIG2016_preproc_FS6
output_DIR3=/fslgroup/fslg_autism_networks/compute/HCP_analy... |
7949de7e226ceb5b98995b4d7e2c6c1089adbbf2c6aa7da8b2be5672877aa155 | Shell | 961 | 41 | #!/bin/bash
trap 'kill 0' INT TERM
if [ -n "$1" ]; then
TOP_LOG_DIR="$1"
else
TOP_LOG_DIR=.
fi
echo "[TOP_LOG_DIR]=${TOP_LOG_DIR}"
echo
FUNC=load3DImage_uint16
SIZE_Z=250
for n in 500 1000 1500 2000 2500 3000; do
echo "===== ${FUNC}(): n = $n"
TOP_LOG=${TOP_LOG_DIR}/top-${FUNC}-xy-${n}-z-${SIZE_Z}.lo... |
c50874e67a52f96c30992dd0e1539ce864a8e359fb08d3a40c49f5bd88a0ad6a | Shell | 961 | 46 | # fba; directional
fba map \
-1 $READ1 \
-2 $READ2 \
-w $CELL_BARCODE \
-f $FEATURE_REF \
-o matrix_featurecount.csv.gz \
-r1_coords 0,16 \
-cb_m 1 \
-al bwa \
--mapq 10 \
-us 16 \
-ul 12 \
-um 1 \
-ud directional \
--output_directory barcode_mapping
# fba; perc... |
eeb290fca9deddcfda28dee303cb4745a7f514184c919e0428e262031272588d | Shell | 961 | 30 | #!/bin/bash
#SBATCH --time=1:00:00 # walltime
#SBATCH --ntasks=1 # number of processor cores (i.e. tasks)
#SBATCH --nodes=1 # number of nodes
#SBATCH --mem-per-cpu=405000M # memory per CPU core
#SBATCH -J "ind_AI" # job name
# Set the max number of threads to use for programs using OpenMP. Should be <= ppn... |
1f2413a1a61ce1b8f9c823dff6d256f29fc0347a8734ab9ec5c7ef93923d5a09 | Shell | 965 | 27 | #!/bin/bash
# Copyright 2026 The Google Research Authors.
#
# 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/licenses/LICENSE-2.0
#
# Unless required by applicable ... |
a4a57cb01ec64af27d4b653f1561d98dfa5f77dc1f56c6e6d540052a6d08eb3c | Shell | 965 | 28 | #!/bin/bash
ftrait=$1
fannot=$2
foutput=$3
fbaseline=$4
trait=$(basename "$ftrait")
annot=$(basename "$fannot")
echo "*** Beginning LDSC partitioned heritability..."
echo "Trait: $trait"
echo "Annot: $annot"
echo "Output: $foutput"
echo "Baseline: $fbaseline"
module load python/2.7.15
python /home/gokala/programs/... |
d5af271a7a76a681575bd59fa5301de36b86e47d737488f6cee41504e3b78b0f | Shell | 969 | 16 | #! user/bin/bash
day=$1
path=/m/cs/archive/networks-pm/cognitive;
mv_path=/m/cs/project/networks-pm/cognitive;
cp ${path}/sub-01_day-${day}_task-_1back_rawdata.txt ${mv_path}/sub-01_day-${day}_task-nback_run-1_pres.txt
cp ${path}/sub-01_day-${day}_task-_1back_summary.txt ${mv_path}/sub-01_day-${day}_task-nback_run-1_... |
46b15efa976525e6c63cd75f785a28cf8552a9dc2fe37e8b5b3359143e6db885 | Shell | 970 | 34 | #!/bin/bash
function run_paratest(){
mincov=$1
min_count=$2
wd=/home/siyuan/jobs/suzukii_WGS/genetic_diff/PCA/results/mincov_$mincov\_mincount_$min_count
dir_snp=/home/siyuan/jobs/suzukii_WGS/call_snp/amb/updated_poolsnp/paratest/test_maxcov/call_snp_maxcov_99/mincov_$mincov\_mincount_$min_count
dir_mpileup=/home/siyu... |
3272d74b46cdb3f83e2c02a7f4cbb3adc5c323ccfdb1ca674585eec5521f3d32 | Shell | 971 | 29 | #!/bin/bash
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable ... |
73fde76414361b4ca468a2b130095b2c96c27a19b05308b25bd5256daa535198 | Shell | 974 | 31 | #!/bin/bash
# Set your paths here
HOME=/fslgroup/fslg_spec_networks/compute
code_DIR=${HOME}/code/NSD_analysis/CBIG2016_preproc
data_DIR=/fslgroup/fslg_fun_conn/compute/NSD_analysis/NSD_BIDS
# Create that special CBIG subjids text file for each subject (data must be in BIDS format)
# CBIG example format: 001 /fslhome... |
23efbf4d9f0e9b53593252a8a0f07a49e619b1bf62169b444492a955fd9cb7f9 | Shell | 975 | 25 | #!/bin/bash
# Copyright 2026 The Google Research Authors.
#
# 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/licenses/LICENSE-2.0
#
# Unless required by applicable ... |
697fbde8c53c1653f5175be8f8a609f5bbfca82f539943c749b60f6e57af5a83 | Shell | 978 | 17 | #!/bin/bash
cd /m/cs/scratch/networks-pm/effects_externalfactors_on_functionalconnectivity/data/mri/glm
Text2Vest contrast.txt contrast.con
Text2Vest nback_awake_time_design.txt nback_awake-time_design.mat
Text2Vest nback_inactive_time_design.txt nback_inactive-time_design.mat
Text2Vest nback_restless_sleep_design.tx... |
fb5a0d6e0f5629f125fa58b56a19a8d4cdf60b6e58a4473fcbe7572fca6ddba4 | Shell | 979 | 26 | #!/bin/bash
# Copyright 2026 The Google Research Authors.
#
# 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/licenses/LICENSE-2.0
#
# Unless required by applicable ... |
0aebcdb0f4940ff4bc88d182085f2c5414094952b62a38ee3fbbf6d4d0016308 | Shell | 982 | 24 | #!/bin/bash
#
# Gokberk Alagoz - 02.03.2023
#
# This script will extract partherit results from all LDSC partitioned
# heritability analysis .results file and annotate each result's
# annotations and trait.
#
########################
# PATHS
inDir="/data/clusterfs/lag/users/gokala/beat-dyslexiaevol/results/partherit/"
... |
7019cf9def213ad8cc583395cd5df4433d8e67eb64618db59754ec268ab0af83 | Shell | 983 | 25 | #!/bin/bash
# Copyright 2026 The Google Research Authors.
#
# 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/licenses/LICENSE-2.0
#
# Unless required by applicable ... |
f2082cb6eb71fd234dda70b5ccbdb18d856ebeed763311ccb3b9d3490dcbcec2 | Shell | 986 | 51 | #!/bin/bash
# Run feature selection experiments across a few genes, with selected cancer
# types held out (either partially or completely)
RESULTS_DIR=./08_cell_line_prediction/results/tcga_ccle_nn_hsize_range
ERRORS_DIR=./tcga_ccle_nn_errors
mkdir -p $ERRORS_DIR
# number of features to "preselect" to by mean absolu... |
a81d8d8c909fd77d033d3732feef3293d845cdc6d1364ec9b66b6b1a4e2b478f | Shell | 988 | 17 | #!/usr/bin/env bash
# LiquidAion Neural Observatory: download-and-run launcher for Linux.
# First run: installs uv (pinned) and Python 3.12 into .tools/, then PyTorch and dependencies into
# .liquidaion-env/ (CUDA build if an NVIDIA GPU is visible, else CPU). Options: see scripts/bootstrap.py.
set -euo pipefail
root="$... |
fe305f3028811397dffa48927dfefcfc309bb5cd31abaec4e11303538dd9e9e3 | Shell | 989 | 29 | #--------------------------
#---- Clumping w/PLINK ----
#--------------------------
# clump sumstats before plotting phastCons
# vs. GWAS_pvalues.
#-----Variables-----
sumstats="/data/clusterfs/lag/users/gokala/beat-dyslexiaevol/results/gSEM/GenomicSEM_multivarGWAS_CPM_dys_rhyimp_GCcorr_withN.tab"
outDir="/data/clust... |
fe1b8f23dfb6fdac88b94af1872d4d7be07e6e1cc14765fbd16becbf707393e5 | Shell | 991 | 43 | #!/bin/bash
trap 'kill 0' INT TERM
if [ -n "$1" ]; then
TOP_LOG_DIR="$1"
else
TOP_LOG_DIR=.
fi
echo "[TOP_LOG_DIR]=${TOP_LOG_DIR}"
echo
NCOLS=640
# 1e6 causes out-of-memory
for n in 1e4 0.2e5 0.4e5 0.6e5 0.8e5 1e5; do
echo "===== pdist2(): n = $n"
TOP_LOG=${TOP_LOG_DIR}/top-pdist2-nrows-${n}.log
... |
002ff780c315044e47e35d21b832845c2cb566bc7c65372cf13ac27072cb618b | Shell | 992 | 11 | #!/bin/bash
# make a dataset_Dscription.json
echo '{"Name":"Expert persuasion on sugar", "BIDSVersion":"1.0.2", "Authors":["Ioannis Ntoumanis", "Julia Sheronova", "Alina Davidova"], "Funding":["list here"]}' > ../data_bids/dataset_description.json
echo '{"TaskName": "Narrative"}' > ../data_bids/task-narrative_bold.js... |
5728ba4590c1164d99d422feb685c010d6a8fce04afd81755398273db6f6ca89 | Shell | 993 | 31 | #!/bin/bash
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable ... |
d918912f31daac964817314234e77513a98cec0fa0f1096f99903f6ceacda0f5 | Shell | 993 | 23 | #! /bin/bash
################################################################################
# bash script for ASL registration. Written for Unix, FSL v6.0 #
# Author: Sofie Tapper, IMT, Link\"oping University, sofie.tapper@liu.se #
# February 2022 ... |
7aaa656cee930d2eac27401dc30216cddeff6381f084429dcd8dbc21e08ba452 | Shell | 994 | 36 | #!/bin/bash
# read the list of cancer genes from tsv file
filename="data/vogelstein_cancergenes.tsv"
read_genes_from_file() {
# create global gene array
declare -a -g genes
# read tab-separated file, genes should be the first column
while IFS=$'\t' read -r gene class; do
genes+=("$gene")
... |
80e592e9e26159cd299c8f35fd23084ac6caa696d15a00b78565dc381b263172 | Shell | 997 | 18 | #!/bin/bash
mkdir -p TargetCall
#Download refs and fast5 files
wget https://zenodo.org/record/7334592/files/simulated-virus.tar.gz; tar -xzf simulated-virus.tar.gz; rm simulated-virus.tar.gz
wget https://zenodo.org/record/7335539/files/real-virus.tar.gz; tar -xzf real-virus.tar.gz; rm real-virus.tar.gz
wget https://z... |
687e02f89af0b84aad8b14638412c626a7f28df49ead24f194b4b791e7cae669 | Shell | 1,000 | 37 | #!/bin/bash
TAG_COLOR="\e[95m"
END_COLOR="\e[0m"
TAG_NAME="Bioemum"
TAG="[$TAG_COLOR$TAG_NAME$END_COLOR]"
echo -e "$TAG Setup environment variables and scripts permissions"
# Check command-line argument
case $1 in
kr260|kv260|vpk120)
export BIOEMUM_TARGET=$1
;;
*)
echo "Invalid option:... |
d9c7538fb6d7ad3bb7e0d262276e0ae5cadb0f21f238fc0ce914020c5114864c | Shell | 1,006 | 27 | #!/bin/bash
# Copyright 2026 The Google Research Authors.
#
# 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/licenses/LICENSE-2.0
#
# Unless required by applicable ... |
39de4dd73322d724c40ecc895eec82093568d8ac30c07d5ac659e60544a2c336 | Shell | 1,008 | 43 | #!/bin/bash
trap 'kill 0' INT TERM
if [ -n "$1" ]; then
TOP_LOG_DIR="$1"
else
TOP_LOG_DIR=.
fi
echo "[TOP_LOG_DIR]=${TOP_LOG_DIR}"
echo
FUNC=watershed
SIZE_Z=250
NUM_PT=10000
for n in 500 1000 1500 2000 2500 3000; do
echo "===== ${FUNC}(): n = $n"
TOP_LOG=${TOP_LOG_DIR}/top-${FUNC}-xy-${n}-z-${SIZE_Z... |
e7b945c90cd35fc3dc99b30cd5304cb14183282811b2dc594fd98e40e5f9ee2d | Shell | 1,008 | 24 | #!/bin/bash
# Copyright 2026 The Google Research Authors.
#
# 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/licenses/LICENSE-2.0
#
# Unless required by applicable ... |
a3204d38095f2653ddf707fb77a513d802d9d55ecd9be915ac0f83a453457153 | Shell | 1,011 | 27 | #!/bin/bash
current_dir=`pwd`
code_dir="./../../../Core_code/"
ncores=82
output_folder="/home/asantoro/COST/Project2_Higher_Order_Brain/Brain_HORS/Figure2/Results/HO_indicators/"
tasklist=( "GAMBLING" "LANGUAGE" "MOTOR" "RELATIONAL" "SOCIAL" "WM" )
#file_input="/home/asantoro/HCP/100307/rfMRI_REST1_LR/Schaefer100/TS... |
b4ddbeadf3f1598df5b1bf0cf5c2f2a50e21f61f8e4e6302f2a21f7b167c350d | Shell | 1,012 | 30 | #!/bin/bash
# Activate environment
source activate sampl6_pKa
# Update requirements
conda list --export > requirements.txt
# Run first step of analysis and create collection file
python typeI_analysis.py
# Compile LaTeX statistic table for Closest matching approach twice for better rendering
pdflatex ./analysis_out... |
3a51c43beb5d6e5e8859d8c3957c62a04da2c32ee303046798e1dd78e5aedf1a | Shell | 1,013 | 44 | #!/bin/bash
trap 'kill 0' INT TERM
if [ -n "$1" ]; then
TOP_LOG_DIR="$1"
else
TOP_LOG_DIR=.
fi
echo "[TOP_LOG_DIR]=${TOP_LOG_DIR}"
echo
FUNC=imresize3
SIZE_Z=250
for n in 1000 2000 3000 4000 5000; do
echo "===== ${FUNC}(): n = $n"
TOP_LOG=${TOP_LOG_DIR}/top-${FUNC}-0.5-xy-${n}-z-${SIZE_Z}.log
if ... |
929e4873e0ab3aabd0e55adbe0b804a07ed00b7dbb93847ce800be650d81bd7b | Shell | 1,014 | 31 | #!/bin/bash
# Copyright 2026 The Google Research Authors.
#
# 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/licenses/LICENSE-2.0
#
# Unless required by applicable ... |
89e3f163e18bc9a518f3641a36251fd14a89574410e7e875ec7a2a0a8d8a0af9 | Shell | 1,016 | 30 | #!/bin/bash
# Activate environment
source activate sampl6_pKa
# Update requirements
conda list --export > requirements.txt
# Run first step of analysis and create collection file
python typeIII_analysis.py
# Compile LaTeX statistic table for Closest matching approach twice for better rendering
pdflatex ./analysis_o... |
62a238d72f5abcbb660f5401125e9eab70b1589546ec40536e3d3955a8f75259 | Shell | 1,017 | 26 | #!/bin/sh
current_dir=`pwd`
code_dir="./../../../Core_code/"
ncores=90
output_folder="/home/asantoro/COST/Project2_Higher_Order_Brain/Brain_HORS/Figure3/Results/"
#file_input_format="TS_Schaefer100S_gsr_bp_z_rest300_tasks_EMO_GAM_LAN_MOT_REL_SOC_WM"
cd ${code_dir}
for subjID in `ls -d /home/asantoro/HCP/* | cut -f... |
a90d52cda0cead0175be00cda35c266714396d3ed77c321d8d234dea9977f38b | Shell | 1,018 | 45 | #!/bin/bash
trap 'kill 0' INT TERM
if [ -n "$1" ]; then
TOP_LOG_DIR="$1"
else
TOP_LOG_DIR=.
fi
echo "[TOP_LOG_DIR]=${TOP_LOG_DIR}"
echo
FUNC=imtranslate
SIZE_Z=250
for n in 1000 2000 3000 4000 5000; do
echo "===== ${FUNC}(): n = $n"
TOP_LOG=${TOP_LOG_DIR}/top-${FUNC}-xy-${n}-z-${SIZE_Z}.log
if [ ... |
e6fdbaf3ee4fd365d1f4f6b40529ea4e95824f17ebcb9262cba916742c23940d | Shell | 1,018 | 26 | #!/bin/bash
current_dir=`pwd`
code_dir="./../../../Core_code/"
ncores=94
output_folder="/home/asantoro/COST/Project2_Higher_Order_Brain/Brain_HORS/Figure2/Results/HO_indicators/"
file_input_format="TS_Schaefer100S_gsr_bp_z_rest300_tasks_EMO_GAM_LAN_MOT_REL_SOC_WM"
tasklist=( "GAMBLING" "LANGUAGE" "MOTOR" "RELATIONAL" ... |
fabd6b38a8879302c903c094676c21b15aba4bc1f951f0a3a1732b3b4e0f4a1e | Shell | 1,019 | 43 | # cat output/gwas/mega/polmm/atheroscler_polmm_results.txt | \
# ~/software/locuszoom/bin/locuszoom \
# --metal - \
# --markercol SNPID \
# --pvalcol pval.spa \
# --chr 13 \
# --refsnp rs2000660 \
# --flank 500000 \
# --source 1000G_March2002 \
# --build hg19 \
# --pop EUR \
# ... |
2d06127c9a3ba9d4de27d89f5394d2820a1f7129ad723b201bdc0c55ae0872ac | Shell | 1,020 | 24 | #! /bin/sh
# Last successfully run on May 2nd 2017
# DO NOT CHANGE: This clears old freesurfer variables if they previously exists
if [ -n "$FREESURFER_HOME" ]; then
$FREESURFER_HOME/bin/clear_fs_env.csh
fi
# PLEASE CHANGE: Please specify location of CBIG repository
export CBIG_CODE_DIR=/data/users/xzhang/storage/C... |
7d1daa9c251e9a5f03ea13ad118e164b5870bcbc6ff17747803336d4989ecdf4 | Shell | 1,020 | 34 | #!/bin/bash
# Copyright 2026 The Google Research Authors.
#
# 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/licenses/LICENSE-2.0
#
# Unless required by applicable ... |
2ae8520ff784595db5a6a0e67fe91bdd3e9d3f84850dc4555da1a123a23a7103 | Shell | 1,024 | 36 | #!/bin/bash
#SBATCH --time=2-23:00:00
#SBATCH --mail-type=ALL
#SBATCH --cpus-per-task=1
#SBATCH --partition=ga100
#SBATCH --mem=200G
#SBATCH --gres=gpu:1
#SBATCH --output=slurm-nucleus2-%j.out
# replace <labname> and <username>
# submit as sbatch run_nucleus.sh
ml foss
ml Anaconda3
pip install uv
uv venv /nemo/lab... |
d692ed61972743e3c9cd52e5962a02c9aa23bf8ad60b97662b841fe4e7e60185 | Shell | 1,024 | 30 | #!/bin/bash
# Activate environment
source activate sampl6_pKa
# Update requirements
conda list --export > requirements.txt
# Run first step of analysis and create collection file
python typeI_analysis.py
# Compile LaTeX statistic table for Closest matching approach twice for better rendering
#pdflatex ./analysis_ou... |
90543e6e0cf8d2c3d8da1a1ef04912ca8481f626ab57c195dd65f684e0220c90 | Shell | 1,025 | 43 | #!/bin/bash
# Copyright 2026 The Google Research Authors.
#
# 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/licenses/LICENSE-2.0
#
# Unless required by applicable ... |
1f1cab66fc266f86103b1b935a901399261bce67a74d2e7f8112d3ff67442770 | Shell | 1,026 | 27 | #!/bin/bash
#Purpose: Create SNR maps using fslmaths.
#Input: CBIG2016 preproc output.
#Output: SNR maps.
#Written by M. Peterson, Nielsen Brain and Behavior Lab under MIT License 2023
#PATHS:
CODE_DIR=/fslgroup/fslg_spec_networks/compute/code/HCP_analysis/tSNR/ALL
PREPROC_DIR=/fslgroup/fslg_autism_networks/compute/... |
c7f3cc04bac928cd488a436de3dbc5d5a70723ae98ea986b230070fabae96178 | Shell | 1,026 | 42 | #!/bin/bash
# Copyright 2026 The Google Research Authors.
#
# 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/licenses/LICENSE-2.0
#
# Unless required by applicable ... |
a36f5ed7227c65aadd04c45a44268bf30a1bf9b67ad56b05f538ef29c03444c6 | Shell | 1,028 | 50 | #!/bin/bash
# Run feature selection experiments across a few genes, with selected cancer
# types held out (either partially or completely)
RESULTS_DIR=./08_cell_line_prediction/results/tcga_ccle_nn_lr_range
ERRORS_DIR=./tcga_ccle_nn_errors
mkdir -p $ERRORS_DIR
# number of features to "preselect" to by mean absolute ... |
72ffe12f804e403a28e5e0abf1fe9812a58176fab7b6a6fe127a59cd6c14bdf1 | Shell | 1,030 | 42 | #!/bin/bash
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable ... |
079543d066494c74b64183b3969df14b4312f5f3e09bc2706ce3c3db710ba3c6 | Shell | 1,032 | 29 | #!/bin/bash
PYTHONPATH="${PYTHONPATH}:$PWD/.."
echo $PYTHONPATH
cp ../../data/tutorials/exp_ssmb/tracing/mb_single/pick/cyto/fil_mb_sources_to_cyto_targets_net_parts.star ../../data/tutorials/exp_ssmb/tracing/mb_single/pick/cyto/0_fil_mb_sources_to_cyto_targets_net_parts.star
cp ../../data/tutorials/exp_ssmb/tracing... |
e7ebfe0ed2782762ec612c1d89dbac7589128032290fa2a6c30218b0aafbfeef | Shell | 1,032 | 43 | #!/bin/bash
# This script is designed as a wrapper for
# 03_cross_cancer_classification/run_cross_cancer_classification.py,
# to run cross-cancer prediction experiments for TP53 across commonly
# mutated cancer types.
RESULTS_DIR=./03_cross_cancer_classification/results/p53_stability_pilot
ERRORS_DIR=./p53_stability_... |
09e122b7f199b930ed5a76eebe2ff49c177d84780f8d7cab8d11633b863e4883 | Shell | 1,037 | 38 | #--------------------------
#---- Clumping w/PLINK ----
#--------------------------
# Gokberk Alagoz, 2021 - last updated April 2022
# Clump sumstats before the overlap analysis.
#-----Variables-----
# ssh to gridmaster, run this script as: bash clump.sh
sumstatsList="/data/clusterfs/lag/users/gokala/beat-dyslexiae... |
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