sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
16b87f2f2e7390a52784bd66307dbc7963bda775ef00f86a9e9172297def4820 | Shell | 2,701 | 77 | #!/usr/bin/env bash
##################################################################################
#
# MIT License
#
# Copyright (c) 2025 Kevin Rockenbach, Agnieszka Golicz
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "S... |
258b2892b0c0626be66612e597ebb9b4ca7cf29fbdb68c8c1025468755648047 | Shell | 2,840 | 80 | #!/usr/bin/env bash
##################################################################################
#
# MIT License
#
# Copyright (c) 2025 Kevin Rockenbach, Agnieszka Golicz
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "S... |
fedda642c367c3b414bb321293c0558b9cdfa39b5ab71a8b0789895422d9b381 | Shell | 2,840 | 57 | #git checkout 1b88b4332b7afe044820ee5eff575b13006fa04c mqparTTPdda.xml mqparTTPdia.xml scratch.slurm slurmMQrunTTP.sh
#dos2unix mqparTTPdda.xml scratch.slurm slurmMQrunTTP.sh
#cp $HOME/PD/TIMSTOF/LARS/2025/25*Mit*/*opy*xml .
#mv *Copy*xml mqpar.mitra.xml
#cp $HOME/PD/TIMSTOF/LARS/2024/240819_Mitra/*.fas* $HOME/cluste... |
fbfa5468096dcd6423a4eda4bacb381b1698726b577c1257164eba01f8caed70 | Shell | 2,845 | 50 | # split voxel indices into equally spaced $parts. Each part will be computed in a separate MATLAB instance. If a part file already exists, the analysis will not be run except reRun is set to 1 in the config file. The same is true if the combined results file already exists. If a part is computed, an indicator of which ... |
0da78c5a13183e3fab52f2c02b04cf12a3ba97253999617160ae407f3e48e14b | Shell | 2,882 | 77 | #!/usr/bin/env bash
##################################################################################
#
# MIT License
#
# Copyright (c) 2025 Kevin Rockenbach, Agnieszka Golicz
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "S... |
3c47b23fe4723c4e55d98ec34b98960cd8c2b467ec4d76bae30939e1db94fd56 | Shell | 3,075 | 40 | cp -a $teamplateFolder/. $presentationFolder/
# sequence in steps of $scnSteps, indicating the start of a trial, before scanning $scnSteps volumes
scanOrderBlock=($(seq $scnSteps $scnSteps $trialsPerBlock))
scanOrderPractice=($(seq $scnSteps $scnSteps $trialsPractice))
# create sequence of odd ball stimuli for all ex... |
864080996108b47ae581cf07a6599236ffa98f98435928589e8af4fca79ae366 | Shell | 3,114 | 102 | #!/bin/bash
# brain mask and mid block realignment using mcflirt
ret_counter=0
task_counter=0
inv_counter=0
transmatNames=()
rawFileNames=()
mkdir $workingDir/stage1
for f in $functionalsDir/*.nii* $invertedDir/*.nii*; do
case "$f" in
*RetinotopyR2x2s1s*)
filename=ret
counter=$ret_counter
r... |
6ccc1ff2bc616bd7b880a5240cbd937352947de2e1578b255a8313b377b746fe | Shell | 3,140 | 103 | #!/bin/sh
repo_dir="${1:-.}"
output_file="${2:-AIDAmri_git_information.txt}"
unknown="unknown"
sanitize() {
value="$1"
value=$(printf "%s" "$value" | tr "\r\n" " ")
if [ -n "$value" ]; then
printf "%s" "$value"
else
printf "%s" "$unknown"
fi
}
git_output() {
git -C "$repo_dir... |
a2bc4459b74b1661fe2c2a2336cb4ac2364b391fc2c0e0943007b7dac6424dc9 | Shell | 3,204 | 130 | #!/usr/bin/env bash
SCRIPT=run_network_simulations.py
cpus1="41-48"
counter=1
while [ $counter -le 10 ]
do
numactl --physcpubind=$cpus1 \
--localalloc \
python $SCRIPT \
-t "deg_vs_del" \
-m "minimal_SLSTDP_synapse" \
-s $counter \
... |
ccdecb8efc1b194ddecae337e4a3a99406592756425b31350f9abc0cd29064dc | Shell | 3,241 | 81 | #!/usr/bin/env bash
set -euo pipefail
PROJECT_ROOT="$(cd "$(dirname "${BASH_SOURCE[0]}")/../.." && pwd)"
BUILD_ROOT="${XDG_CACHE_HOME:-$HOME/.cache}/SMILES2DockingBuild"
DIST_ROOT="$BUILD_ROOT/dist"
WORK_ROOT="$BUILD_ROOT/build"
RELEASE_ROOT="$PROJECT_ROOT/release/linux"
APPDIR_ROOT="$RELEASE_ROOT/SMILES2DockingDeskto... |
fc79500fa6f61fb6aa75bfdd1cbe3ba945ea40a8c5d4e5bc6a2c06ec6eabc82d | Shell | 3,353 | 103 | #!/bin/bash
mkdir genome_files
cd genome_files
##get the fasta file
wget https://ftp.ensembl.org/pub/grch37/release-87/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.dna.primary_assembly.fa.gz
##unzip fasta file
gzip -dk Homo_sapiens.GRCh37.dna.primary_assembly.fa.gz
#filter fasta file for chromosomes in vcf
samtools... |
f719518fd5d885ded1ff410a8151cba8d85160f187fece165c93329d48799066 | Shell | 3,402 | 32 | #cd /mnt/promec-ns9036k/raw
#bash $HOME/scripts/fprunTTP.sh /mnt/promec-ns9036k/NORSTORE_OSL_DISK/NS9036K/promec/promec/TIMSTOF/LARS/2025/250214_HISTONE $HOME/scripts
#grep "Histone H" 250213_H1_DDA_Slot1-19_1_9546.d.FPv22macetprop/250213_H1_DDA_Slot1_19_1_9546/protein.tsv | wc
# 18 505 8754
#wc 250213_H1... |
e2a19f397440953f79cda35dd362e91a917adde4fa595d376d17a912181e6ba7 | Shell | 3,439 | 45 |
OUTPUT_DIR=/flywheel/v0/output/
WORK_DIR=/flywheel/v0/work/
age=30
# Extract volumes of segmentations
output_csv=${WORK_DIR}/All_volumes.csv
# Initialize the master CSV file with headers
echo "template_age, supratentorial_tissue, supratentorial_csf, ventricles, cerebellum, cerebellum_csf, brainstem, brainstem_csf, l... |
4f298ac226befc955351392db77b8e2bfd3dde4a49f9e7d3c810e32e21461c90 | Shell | 3,465 | 104 | #!/bin/bash
module load ANTs
DIR=/project/3018037.01/Experiment3.2_ERC/AnalysisFolder/scripts
cd $DIR
workingDir=/project/3018037.01/Experiment3.2_ERC/AnalysisFolder/scripts/../subjectData/S49/1_realignment
functionalsDir=/project/3018037.01/Experiment3.2_ERC/AnalysisFolder/scripts/../rawData/S49/niftis/functionals
r... |
2392944320830cf41ab64a40fab2da464e04e361ea69513e8b12adf517f542d9 | Shell | 3,466 | 8 |
python3 $1/isoquant_tests/github/run_until.py "python3 "$1"/splisoquant.py -o /abga/work/andreyp/ci_isoquant/data/resume/SRIV.Set4.ONT_R10.resume1/ -r /abga/work/andreyp/ci_isoquant/data/ref/SIRV4/SIRV_isoforms_multi-fasta_200709a.fasta -d ont -p SRIV.Set4.ONT_R10 --genedb /abga/work/andreyp/ci_isoquant/data/ref/SIRV... |
e6318f19d689691c58d8b56944a893a1f4234eea842a1b2b49e599cd8a8ee33c | Shell | 3,543 | 103 | smoothing=30 # in mm
workingDir=.
raw_ret=$workingDir/ret-test.nii.gz
raw_tas=$workingDir/task-test.nii.gz
rm -R -v !(*test.nii.gz)
# pre alignment
raws=("$raw_ret" "$raw_tas")
withins=()
for raw in ${raws[@]};do # within block realignment
filename=$(basename $raw)
filename=${filename%%.*}
filename=$workingDir/... |
667622e600c1bc76a33f8e6fa2e0103c0c6991e4269564da0342fe6e67556d3e | Shell | 3,682 | 148 | #bash compareFastq.sh "/cluster/projects/nn9036k/TK/TK10*.fq.gz" "/cluster/projects/nn9036k/TK/sra/fastq/SRR31089075*" --dry-run
# Always use cluster scratch, never /tmp
TMPDIR="/cluster/work/users/$USER/tmp"
mkdir -p "$TMPDIR"
set -euo pipefail
usage() {
echo "Usage: $0 <reads_pattern> <sra_pattern> [--dry-run]"
... |
a18986aa40a82fdb9018aec5841ef9f3c5c02c341c7fb26ebae996a9e3855cd0 | Shell | 3,704 | 119 | #!/bin/bash
# current working directory of this script
DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
# locate raw and processed data directories
while IFS='' read -r line || [[ -n "$line" ]]; do # loop over lines
for i in $(echo $line | sed "s/,/ /g"); do # loop over comma separation
eval $i
do... |
c8ab43614e647ab973b2bf1db1855dacbfec9695de1ce2f1f928b4f0ff4636ca | Shell | 3,754 | 101 | #!/usr/bin/env bash
##################################################################################
#
# MIT License
#
# Copyright (c) 2025 Kevin Rockenbach, Agnieszka Golicz
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "S... |
51dba9f98462023580704ced5d18d815a4f29c74b35a6338be32e9c4d490e419 | Shell | 3,773 | 49 | #git checkout 8c9b98c1ef58fa67355743da3bf78516467fd85f scratch.slurm slurmSR.sh
#dos2unix scratch.slurm slurmSR.sh
#cat slurmSR.sh
#ls -ltrh /cluster/projects/nn9036k/scripts/TK/mergeHISAT/ >> slurmSR.sh
#bash slurmSR.sh hg38v110/Homo_sapiens.GRCh38.110.gtf /cluster/projects/nn9036k/scripts/TK/mergeHISAT
# 1005 2023-... |
07d62152cd7e73503df893b445759352f6240a15ab269718e31f4bdb1ab83fab | Shell | 3,923 | 121 | alias lh='ls -Ap | grep -v / | egrep "^\."'
export GOROOT=$HOME/go
export GOPATH=$HOME/gopath
export PATH=$GOPATH:$GOPATH/bin:$GOROOT:$GOROOT/bin:$PATH
# ~/.bashrc: executed by bash(1) for non-login shells.
# see /usr/share/doc/bash/examples/startup-files (in the package bash-doc)
# for examples
# If not running inter... |
805348a63ff3bbacdc12ee016c6c74b8945243d0505af6f559c8e23fc1fe6a6c | Shell | 3,951 | 115 | #!/bin/bash
# by Anoushka Joglekar. Edited March 2020, July 2020
# Required input args:
function checkForFile {
file=$1;
if [ ! -f $file ]
then
echo "ERROR:"$file" is not a regular file ... exiting "
exit;
fi
}
function checkForDirectory {
dir=$1... |
98173bee60b4e18729af9282ed7f82faa40e07878471294bc54554819bc4a071 | Shell | 4,032 | 96 | #!/usr/bin/env bash
##################################################################################
#
# MIT License
#
# Copyright (c) 2025 Kevin Rockenbach, Agnieszka Golicz
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "S... |
46a5b9d93b5ef9f9b1c34a872d129d50197f588e15bb2ddf816326bd5903eeef | Shell | 4,174 | 165 |
module load ANTs
module load c3d
module load itk
realign=$DIR/tmp-$RANDOM-antsRegistrationSyN.sh
cp $DIR/toolboxes/misc/antsRegistrationSyN.sh $realign
nvols=$(( $(fslnvols ${invol}) - 1 ))
if [[ $single_ref == 0 ]];then
initrefvol=${outvol}-within-first.mat/vol0002.nii.gz
applyinitmask=0
else
initrefvol=$single_re... |
a76a44b8f85560dd0efd55981821d0662489bf678a7929a5c5fba3caba1b86ca | Shell | 4,209 | 40 | cd /cluster/home/ash022/scripts/TKSB
module load SAMtools/1.17-GCC-12.2.0
samtools mpileup -f ../hg38v110/genome.fa TK16_R1_.sort.bam > TK16_R1_.sort.bamoutput.pileup 2>t #https://decodingbiology.substack.com/p/a-diy-guide-genomic-variant-analysis?utm_source=substack&utm_medium=email except for -u
module load BCFtools/... |
619bf29cb998ad7804bd2a963dee1dec5062ceb3a7a39de5028ebb676a10d279 | Shell | 4,260 | 110 |
module load ants
rm -r $workingDir/*
realign=$DIR/tmp-$RANDOM-antsRegistrationSyN.sh
cp $DIR/toolboxes/misc/antsRegistrationSyN.sh $realign
T1=$freesurferDir/mri/brain.mgz
T1ref=$workingDir/T1.nii.gz
taskVol=$workingDir/../1_realignment/task0-mcf-between.nii.gz
# convert reference brain to LSP space (ANTs) and to... |
e650c3065cfb9a11f308460607399be70af010ccf0f3661e0b41c6d29eaca91d | Shell | 4,610 | 178 | #!/bin/bash
# current working directory of this script
DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
DIR=$DIR/..
# locate raw and processed data directories
while IFS='' read -r line || [[ -n "$line" ]]; do # loop over lines
for i in $(echo $line | sed "s/,/ /g"); do # loop over comma separation
... |
6ca33da0c1076020a0a8fd512277e0ef23cd7ec271c5fbab4fccbb757bef8f02 | Shell | 4,903 | 163 | #!/bin/sh
# Generate mova.md, a file containing patterns that can be implemented
# using the h8sx mova instruction.
echo ";; -*- buffer-read-only: t -*-"
echo ";; Generated automatically from genmova.sh"
# Loop over modes for the source operand (the index). Only 8-bit and
# 16-bit indices are allowed.
for s... |
2b74916319b804ede4cbae302102c4d29a3ce73808413339cef1279991699074 | Shell | 5,191 | 220 | #!/usr/bin/env bash
set -euo pipefail
# ==============================
# SETTINGS
# ==============================
AREAS=("AF" "IFO")
DIFF_RAW="PATH_TO_DIFFUSION_DATA_SOURCE_DIRECTORY"
STRUCT_RAW="PATH_TO_STRUCTURAL_DATA_SOURCE_DIRECTORY"
WORK="PATH_TO_WORKING_DIRECTORY"
DERIV="PATH_TO_DERIVATIVES_DIRECTORY"
ATLAS="... |
f7e0e6dec346fa00634647e388e19154a33d0c17e34f786cd3403c0042e36061 | Shell | 5,226 | 128 |
module load ANTs
module load c3d
module load itk
# within block realignment
echo $(date +"%D %T") "preparing within block correction for $invol" >> $workingDir/log.txt
fslmaths ${invol} -inm 1000 ${outvol}-pre
echo $(date +"%D %T") "starting within block correction for $invol" >> $workingDir/log.txt
mcflirt -in ${ou... |
07e3725f2a26acb21e555a6debd535b3125ee2a150e7952645b5ebb23caf78a6 | Shell | 5,450 | 81 | #https://nf-co.re/rnaseq/3.14.0/docs/usage#reference-genome-options
#latest_release=$(curl -s 'http://rest.ensembl.org/info/software?content-type=application/json' | grep -o '"release":[0-9]*' | cut -d: -f2)
#wget -L ftp://ftp.ensembl.org/pub/release-${latest_release}/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna_sm.p... |
d769ec4db0d517ae8603d6083d9e90cb4359e9457ad1659bf90e0190dd2925b2 | Shell | 5,495 | 80 | #perl -pi -e's/\015\012/\012/g' slurmMQrun.sh
#perl -pi -e's/\015\012/\012/g' scratch.slurm
#perl -pi -e's/\015\012/\012/g' mqpar.xml
#bash slurmMQrun.sh /cluster/projects/nn9036k/MaxQuant_v2.1.4.0/bin/MaxQuantCmd.exe $PWD/MM /cluster/projects/nn9036k/FastaDB/sORFidAAleeGaoComb.unstar.fasta mqpar.K8R10.xml scratch.slur... |
6390390ac52f97aab03b10fbc540a2abf9a1560fb6112bc5e4f4618b3172aafd | Shell | 5,537 | 185 | rm -r $workingDir/*
ls $functionalsDir/*.nii* > $workingDir/volumes.txt
# merge volumes to single file and realign
mkdir $workingDir/stage1
first_step=$workingDir/stage1/all-pre.nii.gz
fslmerge -t $first_step $(ls $functionalsDir/*.nii*)
fslmaths $first_step -s 2.12314225053 $first_step
mcflirt -in $first_step -stage... |
55cda9ccaebbd943f915c979bf9ab2f106de044c207d6995b57ddd92f251e926 | Shell | 5,642 | 160 |
#!/bin/bash
# ==============================================================================
# DICOM → NIfTI conversion + BIDS organization for Caroline_Full_Dataset
# ==============================================================================
# Input : sourcedata/sub-*/ses-1/<series>/
# Output : rawdata/sub-*/se... |
6c449976ff822abd459f555435079bb34215fee0e40b5eb36f513dde3ac6edad | Shell | 5,812 | 135 | #!/usr/bin/env bash
##################################################################################
#
# MIT License
#
# Copyright (c) 2025 Kevin Rockenbach, Agnieszka Golicz
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "S... |
ecc74d5e12fc3231aeff8ba5d3d6a87cade485364cdccae4a1a3c27c1ebaa937 | Shell | 5,831 | 76 | #!/bin/bash -l
CHEMPROP_ENV=$1
CHEMPROP_PATH=$2
if [ -z "${CHEMPROP_ENV}" ] || [ -z "${CHEMPROP_PATH}" ]; then
echo "Usage: regenerate_models.sh <CHEMPROP_ENV> <CHEMPROP_PATH>"
exit 1
fi
conda activate $CHEMPROP_ENV
data_dir="$CHEMPROP_PATH/tests/data/mol_atom_bond"
save_dir="save_dir"
rm -rf $save_dir
che... |
d567ad54214913b2e53f3a66f86bf18dab4302b081768ef89bc1b387d50e572a | Shell | 5,940 | 106 |
############################################################################
# Copyright (c) 2022-2024 University of Helsinki
# All Rights Reserved
# See file LICENSE for details.
############################################################################
#!/usr/bin/env bash
# dataset settings
DATASET_NAME="ONT_R10"... |
eae2fc9f08c72ce3b1c2d022b2c559b154744460a2e6510b4d8a212567b75c38 | Shell | 5,994 | 130 | #!/bin/bash
# by Hagen Tilgner 5/2014
# Edited 07/2020 AJ
function checkForFile {
file=$1;
if [ ! -f $file ]
then
echo "ERROR:"$file" is not a regular file ... exiting "
exit;
fi
}
function checkForDirectory {
dir=$1;
if [ ! -d $dir ]
then
echo "ERROR:"$dir" is not a r... |
05157f67d90d55e7083c5264c4712683cec118e1e72e2e4613630c14e5e487d9 | Shell | 6,200 | 179 |
#cd /project/3018037.01/Experiment3.2_ERC/AnalysisFolder/scripts
#workingDir=/project/3018037.01/Experiment3.2_ERC/AnalysisFolder/scripts/../subjectData/S3/1_realignment
#functionalsDir=/project/3018037.01/Experiment3.2_ERC/AnalysisFolder/scripts/../rawData/S3/niftis/functionals
rm -r $workingDir/*
ls $functionalsDir... |
2eab5a8cf73cb5b5ab25f93c6cefec1e47484bd7065e82afa3b45f074dd27d7c | Shell | 6,880 | 123 | #!/bin/bash -l
CHEMPROP_ENV=$1
CHEMPROP_PATH=$2
if [ -z "${CHEMPROP_ENV}" ] || [ -z "${CHEMPROP_PATH}" ]; then
echo "Usage: regenerate_models.sh <CHEMPROP_ENV> <CHEMPROP_PATH>"
exit 1
fi
conda activate $CHEMPROP_ENV
# test_cli_classification_mol
rm -rf test_cli_classification_mol
chemprop train -i $CHEMPR... |
3d0bbf5bfe334b303a37c47a11bbb299cd10d04452ecabd6288268bc2dcc32a2 | Shell | 7,112 | 117 | #!/usr/bin/env bash
##################################################################################
#
# MIT License
#
# Copyright (c) 2025 Kevin Rockenbach, Agnieszka Golicz
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "S... |
be867226f8840d46e9ce40011ef3441ae86ae06972e55a4de96adb6400a3d327 | Shell | 7,148 | 163 | #!/usr/bin/env bash
##################################################################################
#
# MIT License
#
# Copyright (c) 2025 Kevin Rockenbach, Agnieszka Golicz
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "S... |
f20c0d1ba3328eff726aa7f5c0e757cbec1a9b2ba8d2d6dcb0871ce3f92ebf31 | Shell | 7,563 | 262 | #!/usr/bin/env bash
# Build script for OpenCV.
#
# Run as
# build_opencv.sh \
# version \
# path/to/cmake \
# path/to/ninja \
# path/to/patchelf \
# path/to/conda/bin/python \
# path/to/opencv/CMakeLists.txt \
# path/to/dest/cv2.so
VERSION="$1"
shift
CMAKE=$(realpath -sL "$1")
shift
NINJA=$... |
eb64bc4fd3f243e0337f706b51e49f9066fb2b153eb3ee2383d140c0f378094e | Shell | 7,622 | 174 | #!/usr/bin/env bash
##################################################################################
#
# MIT License
#
# Copyright (c) 2025 Kevin Rockenbach, Agnieszka Golicz
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "S... |
b305a09b3d486e3489e2b9f88a880dd406ac6242efd90302788d0f5d28668449 | Shell | 7,979 | 52 | # lsf22-gpu01
screen -dm bash -c ". ~/load_env_torch224.sh && CUDA_VISIBLE_DEVICES=3 nnUNetv2_train 3 3d_fullres 0 -tr nnUNetTrainer_noDummy2DDA -p nnUNetResEncUNetMPlans --disable_checkpointing"
screen -dm bash -c ". ~/load_env_torch224.sh && CUDA_VISIBLE_DEVICES=4 nnUNetv2_train 4 3d_fullres 0 -tr nnUNetTrainer_noDum... |
5c5eab2eaf98b1e75964def20c75dffcdfb003b158d158d1f6625fbc6730bf0e | Shell | 8,007 | 214 | # performs realignment using mcflirt.
ret_counter=0
task_counter=0
inv_counter=0
# block to mid of block alignment
echo "performing intra block alignment..."
mkdir $workingDir/stage1
mkdir $workingDir/raw
for f in $functionalsDir/*.nii* $invertedDir/*.nii*; do
case "$f" in
*RetinotopyR2x2s1s*)
filename=re... |
50ca22e7b9a325d15ea385c9271278199c61c4b8d9e09eb9b959799c2e372bd2 | Shell | 9,131 | 221 | #!/usr/bin/env bash
##################################################################################
#
# MIT License
#
# Copyright (c) 2025 Kevin Rockenbach, Agnieszka Golicz
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "S... |
f97f09bdc70ffaa9ebda600ba93d9bd85d8fde96b36d0ede468c39d948dbdd8c | Shell | 10,124 | 256 | #!/bin/bash
# by Hagen Tilgner for mapping of pacBio reads : December 31st, 2011; updated July 2012
# Edited AJ 04/2020
{ echo "#################################";
echo "# RUNNING [$0]";
echo "# Current date: `date`";
echo "# Current dir: `pwd`"; } 1>&2;
###############
# 0. the arguments
echo "+++++++++++++++... |
5fda397c6819e5d9960a8ed59ce58ed64755477a2824841cfd9c70add383395c | Shell | 10,847 | 278 | #bash $HOME/scripts/runFPTTP.sh /mnt/promec-ns9036k/NORSTORE_OSL_DISK/NS9036K/promec/promec/TIMSTOF/MIRTA/JonCooper ~/scripts 60 '20260513_TO*.d'
# Monitor a folder recursively for new dirs matching a glob pattern and process them
# Conditions: touched within last MAX_AGE_DAYS days AND stable (no content changes) for ... |
4b2be06acb5f551a67bb58496372c619601470a805aaf3f291387e6a1c030e96 | Shell | 12,449 | 32 | # HERVs
# Microglia SN
bedtools window -w 500 -a /Volumes/MyPassport/ASAP/data/ASAP_PMDBS_snRNAseq/results/tables/ciseffect/input/HERVs_cluster_4_DEA_snRNAseq_SN_upreg.bed -b /Volumes/MyPassport/ASAP/data/ASAP_PMDBS_snRNAseq/results/tables/ciseffect/input/gene_cluster_4_DEA_snRNAseq_res_SN.bed > /Volumes/MyPassport/AS... |
17ac75a1a9b10f3226549c4abb62739cad6964c07f0ac3fd60bde368584ad269 | Shell | 13,480 | 99 | #git checkout 8c9b98c1ef58fa67355743da3bf78516467fd85f scratch.slurm slurmSR.sh
#dos2unix scratch.slurm slurmSR.sh
#bash slurmSR.sh $PWD/hg38v110/Homo_sapiens.GRCh38.110.gtf /cluster/projects/nn9036k/scripts/TK/SB
#rename 'sort' 'h8001s8338sort' $PWD/TK9/trimmomatic.1701608001.results/hisat2.1701618338.results/samtool... |
f32d0331cc94272d7a457d32d852597c701b6aed99dab1cc2c864f9afe972c2f | Shell | 15,720 | 85 | ### Overlap upregulated HERVs and L1s with nearby genes
## Purpose:
# This script identifies genes located near upregulated transposable elements (TEs) — specifically HERVs and L1s — in microglia from different brain regions (SN and PUT). It uses bedtools window to find genes within specified distances (windows) of ea... |
908ca624080e8c4a5b0654518fbf873640f2e9a054160e83fdf75fa462cfddf2 | Shell | 15,883 | 335 | #!/bin/sh
set -x
```
# Module: Pipeline for segmenting infant brain images on Flywheel
# Author: Chiara Casella, Niall Bourke
# Overview:
# This script is designed to segment infant brain images on Flywheel. The pipeline consists of the following steps:
# 1. Register the input image to an age-specific template image... |
02f7aa2cab63482ad7ce5746b6efaeab78c5a9ced8cb732384441f52914eaa40 | Shell | 16,114 | 205 | #convert *bam to *[12].fastq for AGS
find . name "*.bam" | parallel "bamToFastq -i {} -fq {}._1.fastq -fq2 {}._2.fastq"
ls -1 22289_GCCAAT_C5E7AANXX_5_20141008B_20141008.bam 22308_ACTGAT_C5E7AANXX_7_20141008B_20141008.bam 22309_ATTCCT_C5E7AANXX_7_20141008B_20141008.bam | parallel "bamToFastq -i {} -fq {}._1.fastq -fq2 ... |
14fa7e391530d484153da0481108e6d890f9971a55884b499826395b29f50edf | Shell | 23,541 | 1,439 | wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/009/914/755/GCF_009914755.1_T2T-CHM13v2.0/GCF_009914755.1_T2T-CHM13v2.0_genomic.gtf.gz
wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/009/914/755/GCF_009914755.1_T2T-CHM13v2.0/GCF_009914755.1_T2T-CHM13v2.0_genomic.fna.gz
gunzip GCF_009914755.1_T2T-CHM13v2.0_genomic.g... |
3f5c5f181a592bad5a67093d3331b0a37a4421f3d2f8f2471894c50142bd1fd6 | Shell | 25,933 | 276 | # this script was provided by Simon Homoelle at the Donders Institute for Brain, Cognition and Behaviour (DCCN), 2018.
# creates all necessary files used to create the EEG source model from the FreeSurfer segmentation
# those results are stored in the FreeSurfer directory of the corresponding subject. This script req... |
05e1e9ea28e8648a293b8ab893ec6c97e2ef65988b573cf7919b5c1d6e24cc35 | Shell | 35,701 | 398 | C:\Users\animeshs\GD\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck
java -jar -Dfile.encoding=UTF-8 -Xmx57G C:\Users\animeshs\GD\fragpipe\tools\MSFragger-3.1\MSFragger-3.1.jar F:\SINTEF\fragger.params F:\SINTEF\200925_SINTEF_sample-T2-M3_positionA8.raw F:\SINTEF\200925_SINTEF_sample-T2-M4_positi... |
67dd66075c89ea59555a8de53bae18f8f2273249e927cf455958fcc4e3826633 | Shell | 57,739 | 757 | #! /bin/bash
#############################################################
# Giuseppe Barisano - barisano@stanford.edu
#############################################################
##### Computing diffusion along perivascular spaces (ALPS) from diffusion-weighted images #####
# REQUIRES: - FSL v. 6.0.3 or newer (htt... |
bcbe00154f28ab2a7c0f543f79a817986c9dbc0a9daadf96ec730d781260ab28 | Stan | 945 | 28 | // http://mc-stan.org/loo/articles/loo2-with-rstan.html
// http://mc-stan.org/users/interfaces/rstan.html
// https://github.com/stan-dev/rstan/wiki/RStan-Getting-Started
// The input data is a vector 'y' of length 'N'.
// The parameters accepted by the model. Our model
// accepts two parameters 'mu' and 'sigma... |
fac84668a5fbc8e79c7918b75085a2971525caad0cf63e4f889ebed368e58e1e | Stan | 1,133 | 47 | // http://www.mrc-bsu.cam.ac.uk/bugs/winbugs/Vol1.pdf
// Page 3: Rats
data {
int<lower=0> N;
int<lower=0> T;
array[T] real x;
array[N, T] real y;
real xbar;
}
parameters {
array[N] real alpha;
array[N] real beta;
real mu_alpha;
real mu_beta; // beta.c in original bugs model
real<lower=0> sigma... |
3f56a5ad359fc94c2e9224cd1f990d651da945e2da06cb1ee6a9391c9a7fdaf7 | Text | 9 | 1 | # jediMEG |
e575bfa6fdc1c1a472b0acd9ecedec17cec8c614e6c9a645399b0ee8e51b6c91 | Text | 44 | 2 | # Image analysis code used for Irala 2024
|
ea46bc01b90e1fe0aa8a7fe877ef925fff5b58b65785d380a0e60e2c02345378 | Text | 45 | 2 | # BrainCovarianceConnectToolkitV2.1
BCCTv2.1
|
f61878063fcc208bb2f38b37519f6bab9b9b605a894b6197c634a9c6a15ce203 | Text | 59 | 2 | # tunits
R package to support Transcription Unit inference
|
568ef4c8a2f219a3a1fdb5ee831924e947ac183be87a7a6d47446c2da5305947 | Text | 65 | 3 | # Anorexia-Nervosa-Food-and-IAPS-experiment
EEG dataset (AN/AAN) |
5eef20ddfb7cb2dec4ac07ef1998249eb0270e2b16a3c8eac152ff45c2828b1a | Text | 67 | 2 | # brainage-in-adolescent-alcohol-initiation
BrainAGE analysis code
|
6af895ec996465e1ef945b66f0301208c15b3ebf30fed4e841851313aa581cb2 | Text | 69 | 2 | # songfamiliarity
Analysis scripts for the Song Familiarity project.
|
d76e5be03d7b653d84021b70da50334079342a3e947f437b24b92479e40cca62 | Text | 70 | 1 | Codes to perform the basic analysis for the CRITICAL ROAMING project.
|
13d1a2c918b5d92c232071c0eb8d71340e32a1442050e5399ae846614ef6a35e | Text | 112 | 3 | # AstroNet
AstroNet toolbox for astrocyte detection and functional network reconstruction from calcium imaging
|
4ba8d93c9a2520f3a6f4d090499b09cb5734bd7527a589215a111edff2f19e36 | Text | 120 | 3 | # 247-encoding
Contains python scripts for performing encoding on 247 (tfs) data.
*tfs* stands for (T)wo (F)our (S)even
|
3904c18f94c0beb22b4c181937c2b33ea77231e55d4d15fac0bab46af88b60a9 | Text | 137 | 2 | # physiocorr
Creation of physiological noise regressors from BIDS compatible pulse and/or respiratory data traces and BrainVoyager's FMR
|
9d523bd56bb0171989bafc1f24cfdec3e878edbfb22786a1f52c0f34f5840615 | Text | 269 | 7 | # Calcium event classifier
[](https://handle.test.datacite.org/10.5072/zenodo.518966)
## Description
Supervised binary classifier of discrete zscore and dF/F0 traces to detect the
presence of calcium transients.
|
8ae96129df843c47f01a990ae248a90971a18fa47f58aa00159144c67dd58f95 | Text | 275 | 5 | # Network Level Analysis (NLA) Toolbox
NLA is an extensible MATLAB-based software package for the analysis of behavioral associations with brain connectivity data.
Documentation is located at [read the docs](https://network-level-analysis-toolbox.readthedocs.io/en/latest) |
fa20b28fa13a8fd124d10a698d505ad03f0193040f6021b188a7739813dccd3f | Text | 293 | 9 | # REMHFOs
Code accompanying the paper: Shin, J. D. et al. (2026). REM sleep prefrontal high-frequency oscillation chains mediate distinct cortical – hippocampal reactivation patterns compared to NREM sleep
https://doi.org/10.7554/eLife.110795.2
eLife
Codes were created in MATLAB 2022a.
|
c8e9c73d1e699341b3b6550cae362d9e7737d3dcd5cc5e670347d55c3d4cd009 | Text | 306 | 3 | # adni-glial-vascular-axis
This repository contains only analysis code. ADNI participant-level data are not included and cannot be redistributed. Users who wish to reproduce the analysis must obtain ADNI data directly through the official ADNI/LONI access system and agree to the ADNI Data Use Agreement.
|
313a8be62298481f5eb625328a1846f36bad899196a95a9fb8a2bdfdec56da36 | Text | 340 | 3 | The two images here were used to create the far-field shown in white in the 3D visualisation:
* `full_shoulder.png` - slit-scan data (obtained by scanning the image across a spectrometer slit) summed along the wavelength axis
* `comp_farfield_shoulder.png` - a separate far-field image used to fill in the gap where the ... |
1d74ce7cb746bcd1a00af1b7fac3c057da4c65fc9be348a502784facae412f08 | Text | 348 | 7 | # Belki
A desktop application for visual exploration of multi-dimensional proteomics data.
Belki runs on **MacOS**, **Windows**, and **GNU/Linux** systems. It is **free software** under the GNU General Public License, version 3.
Please see the [Wiki](https://github.com/phys2/belki/wiki) for instructions on how to in... |
1c43a01150e71b19977490bb8dc9e9dd0241f1ece0f224887de6a9444c60fb9c | Text | 360 | 5 | # Home for Amii Applied Research in the Cellular Agriculture domain.
Two public projects to date:
1) Code used in the development of the public protein thermostability dataset (**protein-thermostability-data-tools** directory)
2) Code used in the active learning analysis applied to cell media optimization (**activ... |
90f402117d037546dc173eaa2c525d88f045e91ccd53c7c0337eda647b6fbd1b | Text | 362 | 6 | # ECG 1f memory
This code relates to this paper https://doi.org/10.7554/eLife.100605.3
This repository is for analysing the effect of different working memory load conditions on the ECG.
The data that is analysed is from this study https://www.nature.com/articles/s41597-022-01414-2 and can be found here https://openn... |
cb2d6923f1078bc45c308a14b97b883d3652079bee058aad977bd49d2b05fd8f | Text | 448 | 16 | # Cardiac 1/f
This code relates to this paper https://doi.org/10.7554/eLife.100605.3
Most of the data used in this project comes from open repositories.
The ECG only analysis is done using the Autonomic aging dataset from physionet
https://physionet.org/content/autonomic-aging-cardiovascular/1.0.0/
The MEG analys... |
df6f9b168819268c5e06bc3ece9c7b062f61984b8ea7b079df603ce28c93c467 | Text | 520 | 12 | ## functional_resilience_ftd
Code supporting Tsvetanov et al, "Cellular signatures underlying functional resilience in presymptomatic frontotemporal dementia".
### Background
### Dependencies
Dependencies can be accessed at my [external](https://github.com/kamentsvetanov/CommonalityAnalysis/tree/main/code/external... |
a7371a6635d134c9e315b934d36a064d56a30f6244190585df815c7f954740b0 | Text | 545 | 15 | # TB Portal FQ-R Modeling Code
This repository contains the author-written code used for the manuscript
analyses of fluoroquinolone resistance prediction among rifampicin-resistant
tuberculosis patients.
## Data Availability
The data underlying the analyses are available from the TB Portals website
(https://tbporta... |
cfcc4ddbc5d56d5d46092abf48d6e9845a7bddecf0ca548641c781c50ff6ff88 | Text | 547 | 13 | # Environment Setup
Install [Mamba](https://mamba.readthedocs.io/en/latest/installation/mamba-installation.html) to manage environments.
Setup environments:
```
mamba create -f nemo.yaml
mamba create -f nemo_cpu.yaml
mamba create -f prep.yaml
```
# Reference
Kevin C Rockenbach, Silvia F Zanini, Richard J Morris... |
a04d22e84db243d109b7898ab98c3d0100efb9038e8e537d9035be9340906f10 | Text | 555 | 16 | # Bio Image U-Net
Implementations of U-Net, Siam U-Net and 3D U-Net for biological image segmentation
## Installation
### PyPI
``pip install bio-image-unet``
### GitHub
``pip install git+https://github.com/danihae/bio-image-unet``
## Usage example
Import package with ``import bio_image_unet``
[iPython Notebook for... |
e214e2a2522c72504e8b4e497934617b68146696fce587359762d71c574b3166 | Text | 559 | 13 | # aedes_public
This repository is for materials, data, and code related to "Recurrent synapses between CO2-sensitive olfactory sensory neurons necessary for robust CO2 detection in <i>Aedes aegypti</i> mosquitoes".
## EM dataset
Image data can be accessed through [CATMAID](https://radagast.hms.harvard.edu/catmaida... |
e19a2872fe81524ca4623bc6c5209b1ca5473cf8191785011c8ce3eb7e5559be | Text | 657 | 5 | Cell Ranger is a set of analysis pipelines that perform sample demultiplexing, barcode processing, single cell 3' and 5' gene counting, V(D)J transcript sequence assembly and annotation, and Feature Barcode analysis from 10x Genomics Chromium Single Cell data.
Please note that this source code is made available only f... |
69fb23b7bdba3528436516a9b3d34f3fe1304d711dfb66cf1f787799077116d3 | Text | 775 | 9 | Workflow and Scripts for analysis of RNA-Seq data to identify transcriptional responses underlying mutualistic association between anemone and anemonefish.
1. RNA-Seq_data_QC_and_trnascriptome_assembly has all the scripts for the initial QC of the RNA-seq data, mapping the reads to the A. clarkii reference genome, con... |
66e39179d41fb14f109495eb5bd921c0330bdfd43f774a6a3955ff4abe3aefb3 | Text | 904 | 19 | # Szczepankiewicz_NMRBiomed_2026
Paper repository for Restriction-weighted q-space trajectory imaging (ResQ): Toward mapping diffusion time effects with tensor-valued diffusion encoding in human prostate cancer xenografts
### Citation
If you use this work, please cite:
> **Restriction-weighted q-space trajectory imag... |
c0c02969ccbfa9a3d3692584d0b7083dafd44d5d18a5a4b625c41c3cd33d8331 | Text | 905 | 21 | # Project Title: Evaluating the Generalisability of LiSep LSTM for Early Prediction of Septic Shock Across US and European Cohorts
----------------
Public repository containing research code for th e project Evaluating the Generalisability of LiSep LSTM for Early Prediction of Septic Shock Across US and European Cohor... |
278d567f0fa19cc3cb50542885fdc8a9c455242ac32d5fde51be08f3c6150ff0 | Text | 909 | 16 | # SmartERD
Codes and data for pipeline SmartERD
Scripts and data for the pipeline SmartERD;
launch_SmartERD.m script to load the ERDgrams and apply SmartERD;
TFfindRespFreq2_scirep.m core script of SmartERD: searches for peaks, selects the earlier peak within the boundary and estimates the AEP, the SmartERD peak a... |
f8d7678f18936c5a6985470019d94532d6315bae6a6fd972096564131a5d44d6 | Text | 929 | 13 | # Bioprotocol
This repository contains FIJI scripts (.ijm and .py), as well as CellProfiler pipelines (.cppipe) from the protocol paper "Quantitative Analysis of Axonal Degeneration and TDP-43 Aggregation in Compartmentalized Human iPSC-Derived Motor Neuron–Myotube Co-cultures" (DOI: 10.21769/BioProtoc.5801)
# Install... |
9dcf8ee221288070e62e817d37efd72e3ef1690c2e2e1a94a99f0cdc3f8d6ea3 | Text | 932 | 22 | # Spatial Isoform Finder (Spl-IsoFind)
Spl-IsoFind can be used to detect spatially variable isoforms in long-read spatial transcriptomics data.
### Installation
Spl-IsoFind requires Python 3.9 or higher. The easiest way to install is through the following command:
```
pip install SplIsoFind
```
Installation norma... |
00253f3ce3ffeeeaca5ed165ea1f2a0bcf91fa6507815ec89304e38905aeb6a7 | Text | 940 | 15 | # OPM-CFA-correction
Cardiac field artefact correction for OP-MEG
This repository contains the code related to the paper "Model-Based Cardiac Field Artefact Correction for OP-MEG". This repository is under developement, while and archived version of the code along with the corresponding dataset can be accessed via Zen... |
4d86e8b5bad55716af0f72754f5e30aafe57e039f6b0043981c1f5c5063af779 | Text | 959 | 21 | # IDEA
## Integrated Differential Expression and Annotation
<p align="center">
<img src="https://github.com/noamteyssier/idea/blob/main/assets/logo.png?raw=true" width="50%" />
</p>
This is a python module to perform GO analysis using [Enrichr](https://maayanlab.cloud/Enrichr/)
and visualize the [bipartite graph... |
b89a328beebaefb62b598537884386a32389acd10546bc60ce4310fa5a7c6cef | Text | 959 | 27 | # SIMLINK
# 1. Description
SIMLINK (Simultaneous Modeling of Linear and Nonlinear Components of Knowledge Graph) is a method using a knowledge graph–based framework to model gene–variant–feature associations while integrating a linear model to isolate the linear component of variant pathogenicity.
## 2. Requirements
... |
7872b565f064d20ce4c4bd56690dd8947de13df6a3b78a4793fc84d7dbcfb306 | Text | 973 | 19 | # actin_cortex_analysis
Analysis of the actin cortex based on cryo-ET data
# Publication
If you use this code please cite the the [BioRxiv](https://www.biorxiv.org/content/10.1101/2023.01.31.526409v1) preprint for which this code was developed:
```
@article {Lembo2023.01.31.526409,
author = {Sergio Lembo and L{\'e}... |
e49c475370ebbfec2becf88ccf64f297903f53951d247817883364ccc7e17085 | Text | 1,023 | 9 | This README document contains the code and de-identified human testing data for the Spatial-Temporal-Spectral Source Imaging (STSI) algorithm.
The source code and testing data are provided as a service to the scientific community and may be used for any non-commercial purposes under a CC-BY-NC-SA-4.0 license. Users sh... |
aec42b6b261b50d15fd163fd054b9e6773859fa634798570a1e88331b8621b76 | Text | 1,034 | 42 | # Yamashiro-eLife-2024
Analysis code for Yamashiro et al., eLife, 2024: "Enhanced Tactile Coding in Rat Neocortex Under Darkness".
## Prerequisites
Before running the project, make sure you have the following installed:
- Python 3.8+
- pip
- virtualenv (recommended)
Then, create a virtual environment and install th... |
a10f894c493a529313de7336361bd19e0b32d6a38cbdd6777694bfa4e04da889 | Text | 1,048 | 22 | # RGS14 repository
Scripts for "Increased cortical plasticity leads to memory interference and enhanced hippocampal-cortical interactions."
doi: https://doi.org/10.7554/eLife.84911
_Dependencies:_ Some scripts in the "nonrem_oscillations" folder will require the [CorticoHippocampal](https://github.com/Aleman-Z/Cortic... |
595f5ae024a04143eb18e9aad4c3b1cd273e781052331f01a8ae0fe61ac0b36e | Text | 1,050 | 23 | # IDEA
[](https://doi.org/10.5281/zenodo.20736466)
## Integrated Differential Expression and Annotation
<p align="center">
<img src="https://github.com/noamteyssier/idea/blob/main/assets/logo.png?raw=true" width="50%" />
</p>
This is a python module to perform GO an... |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.