sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
36f8f5a068a551a2b928082e94ec040956268a44f323c8c9a2523497c42889e5 | Shell | 366 | 10 | #!/bin/bash
date
for burn in 500 999999999
do
for i in {1..1}
do
(vg mcmc -i 1000 -b $burn -g 100 --vcf-out ./my-output-small/x_small.vcf my-output-small/x_small.mgam ./my-output-small/x_small.vg ./my-output-small/x_small.snarls > ./my-output-small/x_small_paths.vg) 2>&1 | cut -f 1 >> my-output-small/likel... |
99ce5241cd144ce0757587b24dbf82de383b6c2675f6c9766daf692430b80b68 | Shell | 370 | 7 | #!/bin/sh
docker exec -it $((basename $PWD) | tr '[A-Z]' '[a-z]')-jupyterlab-1 sudo pip list --format=freeze > ./tools/requirements_py.txt
docker exec $((basename $PWD) | tr '[A-Z]' '[a-z]')-jupyterlab-1 Rscript ./tools/export_deps.R
grep \
-e sphinx -e numpy -e pand -e matplotlib -e seaborn -e sci -e myst-parser \
./... |
e5be869685c38202ea3ae58e1ca96ba0772472e953a972522ab5d4e06f03fcd1 | Shell | 377 | 7 | blast=$1
SHELL_FOLDER=$(dirname "$0")
source ${SHELL_FOLDER}/config.txt
cat ${blast} | awk '{if($9>$10) print $2"\t"$10-1"\t"$9"\t"$1"\t"$14"\t-" ; if($9<$10) print $2"\t"$9-1"\t"$10"\t"$1"\t"$14"\t+"}' > ${blast}.bed
${bedtools} sort -i ${blast}.bed | ${bedtools} cluster -i stdin -s > ${blast}.bed.cluster
${perl} ${c... |
244ba092c2b0bf83acee1712f7d29beb6873ed98e0e30b5a7a02a43589af05a2 | Shell | 378 | 11 | for f in *_peaks.narrowPeak
do
base=`basename "$f" _peaks.narrowPeak`
sort -r -g -k 5,5 < $base"_peaks.narrowPeak" > $base"_temp.out"
lncnt=$(wc -l < $base"_temp.out")
percent_linecount_infloat=$(echo "$lncnt*.3" | bc)
float2Int=$(printf %.0f "$percent_linecount_infloat")
head -"$float2Int" $base"_temp.out" > ... |
34e9feae8d52132012dbb6ac2c9de9f27d1113fb95cf660e845149bed110faa4 | Shell | 378 | 7 | #!/bin/bash
wget ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE87nnn/GSE87544/suppl/GSE87544_Merged_17samples_14437cells_count.txt.gz
wget ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE87nnn/GSE87544/suppl/GSE87544_1443737Cells.SVM.cluster.identity.renamed.csv.gz
gunzip GSE87544_Merged_17samples_14437cells_count.txt.gz
gunzip ... |
e87cef5bb428cfd89e41a3ab0b16c26b84d4eeb072a46f391dbf8802aa56e6e6 | Shell | 382 | 7 | # initialize and activate new conda environment, assumes working installation of miniconda3
# compatible with TensorFlow 1.15 (https://github.com/tensorflow/models/tree/archive/research/lm_1b)
conda create -n jlstm_env python=3.7 bazel pandas -c conda-forge
# installs TensorFlow from pip
CONDA_BASE=$(conda info --base... |
68c2b891ce2ddc9ce4b9007004ac25cfae075114f8d0678f9be1646763ef382a | Shell | 384 | 11 | #!/bin/bash
# cd /cbica/projects/network_replication/manuscript/code/covbat_harmonization/HBN
# qsub -l h_vmem=64G,s_vmem=64G covbat_edges_HBN.sh
singularity run --cleanenv \
/cbica/projects/network_replication/software/docker/r-packages-for-cubic_0.0.4.sif \
Rscript --save /cbica/projects/network_replicati... |
9e7ad25144117f9091e7d0ff0f3935cf2c775d4c37347dd7b893d7b628abd4ec | Shell | 385 | 22 | #!/bin/bash
home_dir=$(pwd)
rebuild_links()
{
poly_dir="$1/constant/polyMesh"
if [ -d "$poly_dir" ]; then
rm -r "$poly_dir"
ln -s ../../W1/constant/polyMesh "$poly_dir"
fi
}
for dir in $@; do
cd "$dir"
for wd in ./W1[0-9]; do
rebuild_links $wd
done
for wd in ./W[2-9... |
4823eb0f702169327a0d9d89278788176e1ea0d4742b99cd563ca88bb8f30e03 | Shell | 386 | 10 |
dir=$1
sample=$2
n_reads=$3
n_umi=$4
python 4_LARRY_Klein.py $dir/${sample}_whitelist.txt $dir/barcode_reformat.fa $dir/${sample}_h5_bartender_pcr_barcode.csv $dir/${sample}_h5_bartender_pcr_cluster.csv $dir/${sample}_matrix_UMI5 $dir/${sample} $n_reads $n_umi
python 5_cellbc_assign.py $dir/${sample}_matrix_UMI... |
62dc5db111f55d481ab49ee52fdf19c436c0936a75de29226bb1815dcdf7a82e | Shell | 386 | 9 | conda create -n predict_PTMs python=3.7.12
conda activate predict_PTMs
conda install -c conda-forge cudatoolkit=11.2 cudnn=8.1.0
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$CONDA_PREFIX/lib/
pip install --user tensorflow==2.8.1
conda install scikit-learn -c conda-forge
conda install -c conda-forge imbalanced-learn
conda i... |
bfb971aaa3415699584e8a3d3ad2ecb0639cc8fbfea1a4cdd84d4e8120521360 | Shell | 386 | 10 | #!/bin/bash
# cd /cbica/projects/network_replication/manuscript/code/covbat_harmonization/HCPD
# qsub -l h_vmem=64G,s_vmem=64G covbat_edges_HCPD.sh
singularity run --cleanenv \
/cbica/projects/network_replication/software/docker/r-packages-for-cubic_0.0.4.sif \
Rscript --save /cbica/projects/network_replicat... |
78272a4edb26915e258f226ca94ab4928d1d9681dae6dc7b2337e4220583f028 | Shell | 388 | 9 | #!/bin/bash
# download data
wget -O data.txt.gz \
'https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE81608&format=file&file=GSE81608%5Fhuman%5Fislets%5Frpkm%2Etxt%2Egz'
gunzip data.txt.gz
wget https://s3.amazonaws.com/scrnaseq-public-datasets/manual-data/xin/human_gene_annotation.csv
wget https://s3.amazonaws.com/scr... |
164f852f5753b92cd720f5c94147bad39a0f78793ea0452579cd834ab909e21f | Shell | 389 | 9 | # Find firing rate distribution for simulation results.
# This code allows for firing rate results measured after
# rate map smoothing and occupancy normalization.
# This can be run from the command line without the matlab gui.
#
# Settings should be set in gridscore_sim_function.m.
module load matlab # load matlab on ... |
77d05c29c0c30c9dca7469848e0555bdfcd208de6df9951c8bce1fcb7612d11d | Shell | 391 | 10 | mkdir -p data/aggregated/unk;
for unit in "A" "B" "C" "D";
do
python src/aggregate/aggregate_num_unk.py \
--bccwj_eyetrack_path data/BCCWJ-EyeTrack/fpt.csv \
--unit ${unit} \
--lstm_surp_path neural-complexity/outputs/surprisals_1111_${unit}.txt \
--test_path data/bccwj/${unit}.l... |
6bd09ebb7422d67c1168de138b30971732452f66407b75f0db769db4cd1259e1 | Shell | 397 | 10 | #!/bin/bash
# Original works: https://github.com/hemberg-lab/scRNA.seq.datasets/
mkdir -p ./RAW;
cd ./RAW;
wget -O data.csv.gz \
'https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE85241&format=file&file=GSE85241%5Fcellsystems%5Fdataset%5F4donors%5Fupdated%2Ecsv%2Egz'
gunzip data.csv.gz
wget https://s3.amazonaws.com/s... |
c8566a6ef044a8b521c601bbb652ef0687da835a1582705dbfa1b22131318ee2 | Shell | 400 | 20 | #!/bin/sh
#$ -cwd
#$ -l h_rt=24:00:00
#$ -l h_vmem=10G
#$ -pe sharedmem 1
#load the environment modules
. /etc/profile.d/modules.sh
# Load Python
module load anaconda
# activate the virtual environment
source activate myenv
# append the python path
export PYTHONPATH="/home/s1228823/Edmond"
# Run the program
python... |
b8f0494a4fb5cbe712ea13f5f52c529614f6b4fbc8f584e098f84fea2f093381 | Shell | 404 | 7 | #!/bin/bash
# download first 1M reads
wget -qO- https://www.encodeproject.org/files/ENCFF798RSS/@@download/ENCFF798RSS.fastq.gz | gunzip | head -4000000 | gzip > wgbs.1.fq.gz \
&& wget -qO- https://www.encodeproject.org/files/ENCFF113KRQ/@@download/ENCFF113KRQ.fastq.gz | gunzip | head -4000000 | gzip > wgbs.2.fq.gz \
&... |
c6f40c46d68d57be17f2fc1e0f1f2c9e77e0215df08d4e5b9caefbecadd8ec32 | Shell | 406 | 8 | #!/usr/bash
cds=$1
gt="/software/genometools-1.6.1/bin/gt"
${gt} suffixerator -db ${cds} -indexname ${cds} -tis -suf -lcp -des -ssp -sds -dna
${gt} ltrharvest -index ${cds} -gff3 ${cds}.ltr.gff -seqids -out ${cds}.ltr.gff.fa
${gt} gff3 -sort ${cds}.ltr.gff > ${cds}.ltr.sort.gff
${gt} ltrdigest -seqfile ${cds} -hmms /da... |
69b71b3ca2b86768688cb9eccf5e99a47e3ff44b66d15d1ec0dd5486f880ea72 | Shell | 407 | 12 | Input_dir=$1
GRNdir=$2
genome=$3
cd $Input_dir
cat ATAC.txt|cut -f 1 |sed '1d' |sed 's/:/\t/g'| sed 's/-/\t/g' > Region.bed
ml bedtools2/2.26.0-gcc/9.5.0
for i in $(seq 1 22); do
bedtools intersect -a "$GRNdir/${genome}_Peaks_chr$i.bed" -b Region.bed -wa -wb > "Region_overlap_chr$i.bed"
done
i=X
bedtools intersect -a "... |
181903d423b4462eb7bd70d2235bfb260d8646349b812503eaa942cb2c279819 | Shell | 410 | 19 | #!/bin/sh
# Grid Engine options (lines prefixed with #$)
#$ -N hello
#$ -cwd
#$ -l h_rt=00:05:00
#$ -l h_vmem=1G
# These options are:
# job name: -N
# use the current working directory: -cwd
# runtime limit of 5 minutes: -l h_rt
# memory limit of 1 Gbyte: -l h_vmem
# Initialise the environment modules
. /etc/profi... |
92ff282deb4e6490aa96bc08cffc4f9dac652049b69b69b02e00f9cae497fff5 | Shell | 410 | 15 | #!/bin/bash
#SBATCH -A b1042
#SBATCH -p genomics-gpu
#SBATCH -t 16:00:00
#SBATCH -N 1
#SBATCH --gres=gpu:a100:1
#SBATCH --mem=120G
#SBATCH --ntasks-per-node=12
#SBATCH --mail-user=rogangrant2022@u.northwestern.edu
#SBATCH --mail-type=BEGIN,END,FAIL
#SBATCH --job-name='230118_SCVI_integration'
module load R/4.1.1
Rscr... |
e8e10477f1b795452d0eed5d520e5ebabde73310dd100428181097330a7a1201 | Shell | 411 | 17 | #!/bin/bash
if [ $# -lt 2 ]; then
echo "This script is ment to run a command within a python environment"
echo "It needs at least 2 parameters."
echo "The first one must be the environment name."
echo "The rest will be the command"
exit -1
fi
eval "$(conda shell.bash hook)"
env_name=$1
echo "Activ... |
ab5f090718aeebf26af8380f471d983a1adce7bab5e31a3db6e0cd5d13a9ae47 | Shell | 417 | 13 | #!/usr/bin/env bash
# Customise the terminal command prompt
echo "export PROMPT_DIRTRIM=2" >> $HOME/.bashrc
echo "export PS1='\[\e[3;36m\]\w ->\[\e[0m\\] '" >> $HOME/.bashrc
export PROMPT_DIRTRIM=2
export PS1='\[\e[3;36m\]\w ->\[\e[0m\\] '
# Update Nextflow
nextflow self-update
# Update welcome message
echo "Welcome... |
2b75f01f35300062c0728e9c38e54e3232f5ab5d69cb4dfb4e2baa47ae59eeac | Shell | 428 | 12 | # parameter exploration settings
# select params
export run_on_hopper=0 # run from hopper's system
export hopper_run=1 # hopper run number
# Note: set number of vals in for statement {1..<count>} below
p1_v=(7.0 9.0 11.0 13.0 15.01 17.0 19.0 21.0 23.0)
p2_v=(62.0 64.0 66.0 68.0 70.01 72.0 74.0 76.0 78.0)
p1_p="\"VT\"... |
ca144597b71685ae0f976cb5414c6f3842c2e9e2f122dd9b3d0a5005b7bfce69 | Shell | 434 | 16 | #! /bin/bash
args=("$@")
kshrinkDir=${args[0]}
#q1=${args[1]}
#Rscript find_threshold_kernel.R $kshrinkDir/all_maxRatios $q1 | tail -n1 > $kshrinkDir/geneThreshold.$q1.txt
i=1
while [ $i -lt $# ]; do
q=${args[$i]}
for s in $kshrinkDir/sp.*txt; do
Rscript find_threshold_kernel.R $s $q | tail -n1 > $k... |
a6daeec9426b2b05d5b6c4bcdbb4e03271224f89a143dba15b092ec0f4b3960b | Shell | 438 | 14 | #!/bin/bash
ROOT=/cluster/projects/p33/users/alexeas/elleke/pleioprs
CLUMP_DIR=${ROOT}/sumstats/clump
for TRAIT in ADHD; do
for CLUMP_FIELD in PVAL FDR; do
CLUMPED_FILE=${CLUMP_DIR}/${TRAIT}.${CLUMP_FIELD}.clumped
for N in 10 100 1000 10000 50000 100000 150000; do
OUT=${CLUMPED_FILE}.$... |
0128c733ab5844ccb88495485ab0993092b9c247e0ba64e3aad27770aa0a5f9e | Shell | 444 | 17 | #!/bin/bash
# Simulate data for synchrony experiments
#SBATCH -J synchrony
#SBATCH --array=0-2 # how many tasks in the array
#SBATCH -t 47:00:00
#SBATCH --cpus-per-task=6
#SBATCH -o out/an-exp-%a.out
# Load software
# module load Spack
spack load miniconda3@4.10.3 # module load anaconda3
source activate synchrony
#... |
912063ce0c336d5f3426581cb859c615e08b198247a8d254e85426a2789dd5c1 | Shell | 447 | 11 | #!/bin/sh
sh auth.sh docker-compose.yml
docker compose up -d
docker start $((basename $PWD) | tr '[A-Z]' '[a-z]')-jupyterlab-1
docker exec $((basename $PWD) | tr '[A-Z]' '[a-z]')-jupyterlab-1 sudo pip -U pip
sh ./lib.sh
docker exec $((basename $PWD) | tr '[A-Z]' '[a-z]')-jupyterlab-1 sudo pip -U pip
docker exec $((bas... |
bbe3b953d8fa5e2975213696bb69781a75257aaeafd0b300f285eb9ebe42569e | Shell | 448 | 15 | #!/bin/bash
# WIN32 program that does a make all clean and regenerates makefiles from .pro files
for d in utils gui programs/*
do
if [ ! -d $d ]; then continue; fi
if [ $d == "programs/config2" ]; then continue; fi
if [ $d == "programs/us_mpi_analysis" ]; then continue; fi
... |
4762f8ba40d8f695b9c3b918d1e0e74757ac9bcc35d38fa9d50e708a60ded8a5 | Shell | 449 | 16 | #!/bin/bash
# Clean up Xvfb
function cleanXvfb {
kill $XVFB_PID
rm -f ${X_WORK_DIR}/.X${XVFB_PORT}-lock
rm -f ${X_WORK_DIR}/.X11-unix/X${XVFB_PORT}
echo "Cleaned up Xvfb"
}
# Take a screenshot using imagemagick
function screenSnapshot {
# take a screenshot
echo "Taking a screen snapshot -> ${... |
9a318406c524ed6ab6d8f851de23984a5b12d1dd4162e25053170d5c1d78cfc0 | Shell | 449 | 6 | aws dynamodb create-table \
--table-name janelia-neuronbridge-published-dev\
--attribute-definitions AttributeName=itemType,AttributeType=S AttributeName=searchKey,AttributeType=S \
--key-schema AttributeName=itemType,KeyType=HASH AttributeName=searchKey,KeyType=RANGE \
--provisioned-throughput ReadCapa... |
7c6eb0eeb8fe64b0ff9562b41ce342b9db260c2c0e4379208b3d77e4525d2fd8 | Shell | 455 | 17 | #!/bin/bash
# Simulate data for synchrony experiments
#SBATCH -J synchrony
#SBATCH --array=0-2 # how many tasks in the array
#SBATCH -t 47:00:00
#SBATCH --cpus-per-task=6
#SBATCH -o out/sync-exp-%a.out
# Load software
# module load Spack
spack load miniconda3@4.10.3 # module load anaconda3
source activa... |
3422bb0f90940837b230617e931248413745a4565a01e9894eefe2ff84773b6d | Shell | 458 | 8 | wget ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE83nnn/GSE83139/suppl/GSE83139_tbx-v-f-norm-ntv-cpms.csv.gz
wget ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE83nnn/GSE83139/matrix/GSE83139-GPL11154_series_matrix.txt.gz
wget ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE83nnn/GSE83139/matrix/GSE83139-GPL16791_series_matrix.txt.gz
... |
530f82dae02e84c87fcc8de395f9c32b6dad96404e2ceca1dab28fc88d90bbe7 | Shell | 460 | 12 | mkdir -p data/aggregated/concat
python src/aggregate/concat.py \
--bccwj_eyetrack_path data/BCCWJ-EyeTrack/fpt.csv \
--lstm_root data/aggregated/lstm \
--lstm_seeds 1111 1112 1113 \
--rnng_root data/aggregated/rnng \
--rnng_strategies top_down in_order \
--rnng_seeds 3435 3436 3437 \
--rnng... |
fe407067b4426cb769caa9b62cd4cd2c3bf7fea3b8ac682b07067e5e0d5514e0 | Shell | 464 | 17 | #!/usr/bin/bash
set -e
python3.8 -m venv --copies venv
source venv/bin/activate
pip install wheel
pip install -r requirements.txt
python -m ipykernel install --user --name=bluish
pip install pre-commit
pre-commit install
deactivate
# for plotly widget support
pip install --user jupyterlab plotly==4.14.3 "ipywidgets>... |
e3391c307cb29975d5d82a19142a70bbeea9152e5c7509293b22e62fe34fa5da | Shell | 465 | 13 | #!/bin/bash
#source /mnt/software/Modules/current/init/bash
#module load blast/2.6.0+
INPUT=$1
#DB=/pbi/dept/secondary/siv/gconcepcion/db/ncbi/refseq/complete
DB=/pbi/dept/secondary/siv/gconcepcion/db/ncbi/nt
OUTPUT=${INPUT}.blastn
blastn -task megablast -db ${DB} -query ${INPUT} -evalue 0.1 -num_alignments 1 -par... |
137b4eef5c1405b15eaf9350f479816bcddf78d3abca9f399248a27a5dc8f82c | Shell | 468 | 13 | #!/bin/bash
# https://github.com/hemberg-lab/scRNA.seq.datasets/
mkdir -p ./RAW;
cd ./RAW;
# download data
wget -O data.txt.gz \
'https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE81608&format=file&file=GSE81608%5Fhuman%5Fislets%5Frpkm%2Etxt%2Egz'
gunzip data.txt.gz
wget https://s3.amazonaws.com/scrnaseq-public-data... |
48e4b855a824a6eef41ee32b8ffadb1b6e7712730b3eb5079a1aa9d23c366967 | Shell | 469 | 8 | # initialize and activate new conda environment, assumes working installation of miniconda3
# due to frequent updates with both transformers and PyTorch, it may be advisable to install the dependencies manually
# https://huggingface.co/docs/transformers/en/installation
# https://pytorch.org
conda create -n hf_env pytho... |
88e55b0f7772e693b6f4d4717a3c1a51bea1d6a69b42dc40e8599767e7bc3862 | Shell | 470 | 22 | #!/bin/sh
# unquarantine.sh
CDIR=`pwd`
BDIR=`dirname $0`
if [ -z "${BDIR}" -o "{$BDIR}" = "." ]; then
BDIR=${CDIR}
fi
cd ${BDIR}
FILES1=`ls -d us_[a-z]*.app`
FILES2=us.app
for F in ${FILES1} ${FILES2} ; do
STAT=`xattr -d com.apple.quarantine ${F} 2>&1 | grep -c "^No such xattr"`
## echo "STAT=${STAT}"
if [ ${S... |
694225b2d750a5b7532597d3145ffb0b799ae6fb23f8287f41c4d328f56f8295 | Shell | 471 | 20 | if [[ $# -eq 0 ]] ; then
echo "Missing anatomical area argument: use $0 <anatomical_area>"
exit 1
fi
anatomical_area=$1
# Precompute tools location
SCRIPT_DIR=$(dirname ${BASH_SOURCE[0]})
source "${SCRIPT_DIR}/../global-params.sh" ${anatomical_area}
source "${SCRIPT_DIR}/cds-params.sh"
source "${SCRIPT_DIR}/... |
6f7ce6a1356601205d2af174741b2fe4805619de76c059ac30bace00d3675a24 | Shell | 474 | 25 | #!/bin/bash
# Run Freesurfer recon-all on subjects.
# Values
megID="$1"
T1seq="$2"
## Warnings
if [[ -z "$2" ]]; then
echo "Warning: missing sequence number"
exit 1
fi
## Setup Freesurfer
export FREESURFER_HOME=/opt/freesurfer
source /home/mikkel/PD_long/scripts/mri_processing/setUpFreesurfer.sh
## Paths
export S... |
2faf298bd08b334a0357413eb0320492c19d561ee265b585b8f4b64bb1b9ee24 | Shell | 476 | 11 | #!/bin/bash
SCRIPT_DIR=$(dirname ${BASH_SOURCE[0]})
sh ${SCRIPT_DIR}/submit-export.sh brain+vnc EM_MIPS
sh ${SCRIPT_DIR}/submit-export.sh brain+vnc LM_MIPS
sh ${SCRIPT_DIR}/submit-export.sh brain EM_CD_MATCHES
sh ${SCRIPT_DIR}/submit-export.sh brain LM_CD_MATCHES
sh ${SCRIPT_DIR}/submit-export.sh brain EM_PPP_MATCHES
... |
7f00182dd3ce4a9b52a9a48c7a2611ac5937bf5361fe20bf53f9e1a79bce00b7 | Shell | 477 | 11 | #!/bin/bash
SCRIPT_DIR=$(dirname ${BASH_SOURCE[0]})
sh ${SCRIPT_DIR}/submit-upload.sh brain+vnc EM_MIPS
sh ${SCRIPT_DIR}/submit-upload.sh brain+vnc LM_MIPS
sh ${SCRIPT_DIR}/submit-upload.sh brain EM_CD_MATCHES
sh ${SCRIPT_DIR}/submit-upload.sh brain LM_CD_MATCHES
sh ${SCRIPT_DIR}/submit-upload.sh brain EM_PPP_MATCHES
... |
864343c3b29989fe5bd29074c0485306028e2ce51ff773c4a945bbc1f520a03d | Shell | 478 | 12 | #!/bin/bash
mkdir -p ./RAW;
cd ./RAW;
wget ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE87nnn/GSE87544/suppl/GSE87544_Merged_17samples_14437cells_count.txt.gz
wget ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE87nnn/GSE87544/suppl/GSE87544_1443737Cells.SVM.cluster.identity.renamed.csv.gz
gunzip GSE87544_Merged_17samples_1443... |
ccfc7a27702d066e2aa6f1641667bbd800265b193215283f20ba8b59301bdeaf | Shell | 482 | 12 | # parameter exploration settings
# select params
export run_on_hopper=0 # run from hopper's system
export hopper_run=1 # hopper run number
# Note: set number of vals in for statement {1..<count>} below
p1_v=(30.0000 47.5000 65.0000 82.5000 100.0000 118.0000 135.0000 152.5000 170.0000)
p2_v=(1.7800 4.1238 6.4675 9.010... |
9d05a0d289adc05424652afbae0fe406f09ad778620f8191b616dd7e728f78ef | Shell | 484 | 20 | #!/bin/bash
#SBATCH --job-name=subsetBfiles
#SBATCH --account=p33
#SBATCH --time=48:00:00
#SBATCH --cpus-per-task=32
#SBATCH --mem-per-cpu=8GB
source ~/.bashrc
module purge
module load plink2/2.00a2LM
set -o errexit
plink2 --bfile ${ukb}/genetics/UKB42k_160320/UKB42k_QCed_160320 \
--king-cutoff 0.05 \
--keep ${mu... |
7ca194219056aca5282bdfaa316f4a886e9f0ec60c75867de9f16e32395c3ba4 | Shell | 485 | 13 | mkdir -p data/aggregated/lstm
for seed in 1111 1112 1113;
do
for unit in "A" "B" "C" "D";
do
python src/aggregate/aggregate_surp_lstm.py \
--bccwj_eyetrack_path data/BCCWJ-EyeTrack/fpt.csv \
--unit ${unit} \
--lstm_surp_path neural-complexity/outputs/surprisal... |
886852df91735fce63b5923ac27041238b462aa840024d522d641d0fc69aa9bb | Shell | 493 | 24 | #!/bin/bash
# Based on https://github.com/openai/gym/blob/master/bin/docker_entrypoint
set -ex
# Set up display; otherwise rendering will fail
Xvfb -screen 0 1024x768x24 &
export DISPLAY=:0
# Wait for the file to come up
display=0
file="/tmp/.X11-unix/X$display"
for i in $(seq 1 10); do
if [ -e "$file" ]; then
... |
01fe49a3020e6c6800420ce86e0a3b4f9856bac7955e0ff6461365f853e6f23d | Shell | 494 | 6 | # python ./bin/plot_correlation.py -p ./data/current-pulses/correlation_data.csv -c "1 2" -l "V(mV) TemperatureºC" -sv y -sh n -scx -1000 -sf pdf
# python ./bin/laser_pulse.py -p './data/current-pulses/pipette_pulse_recording.asc' -slope 1.1931 -sf pdf
python ./bin/plot_correlation.py -p ./data/current-pulses/correlat... |
c9bd68b6625723c99603bed0cc65ab3924282feed17faafa5f3bf094ac619a9f | Shell | 501 | 9 | #!/bin/bash
module add miniconda3-4.5.11-gcc-8.2.0-oqs2mbg
conda create -p /home/data/nbc/misc-projects/Peraza_GradientDecoding/env/conda_env pip python=3.9 -y
conda config --append envs_dirs /home/data/nbc/misc-projects/Peraza_GradientDecoding/env
source activate /home/data/nbc/misc-projects/Peraza_GradientDecoding/... |
7924a8b2a0168bbe84e9f01f7613e3a6cf9c24817e399c3dd6bf514ba51b55ae | Shell | 520 | 20 | #!/bin/bash
#SBATCH --mail-type=ALL
#SBATCH --mail-user=jfisher7@uab.edu
#SBATCH --job-name=tau_test
#SBATCH -n 1
#SBATCH --mem-per-cpu=25000
#SBATCH --nodes=1
#SBATCH --time=0-12:00:00
#SBATCH --share
#SBATCH --partition=short
#SBATCH --error=%j.%N.err.txt
#SBATCH --output=%j.%N.out.txt
cd /data/project/lasse... |
3a7b69d51d4e75a1437e54d91081147f7be69706819fa32f776f339fba5e1463 | Shell | 521 | 20 | #!/bin/bash
CONTAINER_PATH="/lustre03/project/6003287/containers"
VERSION=("20.2.1" "20.2.5")
module load singularity/3.8
echo "Check signularity containers"
for v in ${VERSION[*]}; do
echo "fmriprep-${v}"
current_container=${CONTAINER_PATH}/fmriprep-${v}lts.sif
if [ -f "${current_container}" ]; then
... |
4e0ed1261fc38fd72de1d790ee9f9d111389c54363a3c4287e358411e00f9c3b | Shell | 525 | 21 | #!/bin/bash
#SBATCH --mail-type=ALL
#SBATCH --mail-user=jfisher7@uab.edu
#SBATCH --job-name=tau_combine
#SBATCH -n 1
#SBATCH --mem-per-cpu=20000
#SBATCH --nodes=1
#SBATCH --time=0-02:00:00
#SBATCH --share
#SBATCH --partition=express
#SBATCH --error=%j.%N.err.txt
#SBATCH --output=%j.%N.out.txt
cd /data/project/... |
01a35fe7ae3ca0578520c7d4583def2165b78358b106b3d35ef55607cea94f6a | Shell | 527 | 25 | #!/bin/sh
# Exit after any error
set -o errexit
RELEASE_VER=$1
if [ "$RELEASE_VER" == "" ]; then
echo "Usage: release.sh <version>"
exit 1
fi
echo "Changing version numbers to ${RELEASE_VER}"
./mvnw versions:set -DnewVersion=${RELEASE_VER} -DgenerateBackupPoms=false
git commit -a -m "Updated version to ${RE... |
9c37def6fd7970f5510f298a38eae6f6d70ce29377ad98993fe0bf8764c49175 | Shell | 529 | 32 | #!/bin/bash
set -e
for dir in $(ls inputs)
#for dir in simple
do
echo
echo --------------------------
echo $dir
echo --------------------------
echo
(
cd inputs/$dir
rm -rf bids
rm -f output
../../../../hooks/bl2bids
[ -f check.sh ] && ./check.sh
tree bids | tee output
dif... |
829e4c01b4bad5675b1eede669cc7570a76648af88d2a4b1e3032af11fad0e90 | Shell | 534 | 16 | mkdir -p neural-complexity/outputs;
for seed in 1111 1112 1113;
do
for unit in "A" "B" "C" "D";
do
python neural-complexity/main.py \
--model_file neural-complexity/models/${seed}.pt \
--vocab_file neural-complexity/data/npcmj-vocab.txt \
--data_dir data/b... |
a7342a030b0d2e405a62cb03f9e41f0ec78bccf188ce97225a0a0158460538be | Shell | 535 | 21 | #!/bin/bash
#SBATCH --mail-type=ALL
#SBATCH --mail-user=jfisher7@uab.edu
#SBATCH --job-name=tau_combine
#SBATCH -n 1
#SBATCH --mem-per-cpu=20000
#SBATCH --nodes=1
#SBATCH --time=0-02:00:00
#SBATCH --share
#SBATCH --partition=express
#SBATCH --error=%j.%N.err.txt
#SBATCH --output=%j.%N.out.txt
cd /data/project/... |
4801cdb1304ae15a62b7d54d83e3cd57ca26dbe3c3b307f88837b17abee2a90a | Shell | 536 | 11 | #!/bin/bash
# dowload data
wget -O bipolar_data_Cell2016.Rdata.gz \
'https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE81904&format=file&file=GSE81904%5Fbipolar%5Fdata%5FCell2016%2ERdata%2Egz'
# unzip data
gunzip bipolar_data_Cell2016.Rdata.gz
# download additional data
# downloaded from single cell portal on 02-02-1... |
f1e16bb5dfa1cab8d7af38ad2bfe74d8ae4c8dcf0dc872f258a3d3fa1fff13c1 | Shell | 541 | 13 | # izhikevich model firing pattern parameter exploration parameters
# This is for K and A params
# select params
export run_on_hopper=0 # run from hopper's system
export hopper_run=1 # hopper run number
# Note: set number of vals in for statement {1..<count>} below
p1_v=(-20.0000 -14.7292 -9.4583 -4.1875 1.0833 6.3542... |
57d7faa3182ca3e85b6057529a049d7aedca78c49d5e9915091165c4391e6994 | Shell | 545 | 23 | #! /bin/bash
# randomly prune the second trees to match the number of leaves in the first trees
fulltrees=$1
inducedtrees=$2
taxafile=`mktemp`
while read tree1 && read -u 3 tree2; do
echo $tree1 | nw_labels -I - > $taxafile
n1=`echo $tree1 | nw_stats -fl - | awk '{print $3;}'`
n2=`echo $tree2 | nw_stats... |
7c2f4c7995267f39ba761759ef80010f08003289bddca604f07897b7a18b7864 | Shell | 545 | 21 | #!/bin/bash
#SBATCH --mail-type=ALL
#SBATCH --mail-user=jfisher7@uab.edu
#SBATCH --job-name=conda_packages
#SBATCH -n 1
#SBATCH --mem-per-cpu=20000
#SBATCH --nodes=1
#SBATCH --time=0-02:00:00
#SBATCH --share
#SBATCH --partition=express
#SBATCH --error=%j.%N.err.txt
#SBATCH --output=%j.%N.conda.packages.out.txt
... |
43e54f7f99d768cbab1f8c9e7e31a0feeb763327d4cdd7626bcc1292023da33e | Shell | 546 | 29 | #!/bin/bash
set -euo pipefail
# Install bcl2fastq per illumina docs
BASE=${PWD}
SOURCE=${BASE}/bcl2fastq
BUILD=${BASE}/bcl2fastq2-build
INSTALL_DIR=/usr/local
# cmake won't find libraries without this
export C_INCLUDE_PATH=/usr/include/x86_64-linux-gnu
tar -xzf bcl2fastq2.tar.gz
mkdir -p ${BUILD}
cd ${BUILD}
chmod... |
a72081ffe35f157668c5c0578c0c33604710490349165ec3a061bc9cacf0beb1 | Shell | 547 | 6 | #!/bin/sh
python3 Code_data/main_digit_create.py --n_letters 5 --offset random_occluded --n_samples_train 110000 --FILENAME _data/digitclutter5
python3 Code_data/main_digit_create.py --n_letters 4 --offset random_occluded --n_samples_train 110000 --FILENAME _data/digitclutter4
python3 Code_data/main_digit_create.py --... |
40795c5e1d9a11b172d3e625cafb9897feca2767b54a1ea19eaca19e11cbfdcd | Shell | 551 | 16 | #!/usr/bin/env bash
# conda install go-shfmt shellcheck ruby
# gem install bashcov codecov
echo "formatting code with shfmt"
shfmt --binary-next-line --func-next-line --indent 4 --write genome_updater.sh
shfmt --binary-next-line --func-next-line --language-dialect bats --indent 4 --write tests/*.bats
if shellcheck ge... |
4a8f0dcc4987e4e895d84996c898e59c9774ce91764f00b611bc831e6a3ca400 | Shell | 554 | 18 | #!/bin/bash
################################################
# variables graphs and sites
################################################
BRAND_BASE_DIR=$(pwd)
BRAND_MOD_DIR=$BRAND_BASE_DIR/../brand-modules/
export BRAND_BASE_DIR # save brand base dir to the environment
# Activate the rt environment to get to work
... |
462e41c5fc50996853fd567bcaf99b882ae6339e3af60097244babe235a5ff87 | Shell | 555 | 12 | #!/bin/bash
wget ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE67nnn/GSE67835/matrix/GSE67835-GPL15520_series_matrix.txt.gz
wget ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE67nnn/GSE67835/matrix/GSE67835-GPL18573_series_matrix.txt.gz
gunzip GSE67835-GPL15520_series_matrix.txt.gz
gunzip GSE67835-GPL18573_series_matrix.txt.gz
... |
a2b8a7ea3f67db372a26b3addfa84efc99ace809bff31768701f8f97df8bd9fd | Shell | 557 | 18 | #!/bin/bash
# Mac-compatible version of setup.sh
# Differences from Linux version:
# - No sudo (real-time scheduling is skipped on macOS)
BRAND_BASE_DIR=$(pwd)
BRAND_MOD_DIR=$BRAND_BASE_DIR/../brand-modules/
export BRAND_BASE_DIR
conda activate rt
# Use /tmp/redis.sock instead of /var/run/redis.sock — the latter ... |
3590ef1401230e8d7dd29e5b323a3c61ed9581489cf492d534cff39144f2da3c | Shell | 561 | 21 | #!/bin/bash
#SBATCH --mail-type=ALL
#SBATCH --mail-user=jfisher7@uab.edu
#SBATCH --job-name=tau_A549
#SBATCH -n 1
#SBATCH --mem-per-cpu=20000
#SBATCH --nodes=1
#SBATCH --time=0-02:00:00
#SBATCH --share
#SBATCH --partition=express
#SBATCH --error=%j.%N.err.txt
#SBATCH --output=%j.%N.out.txt
cd /data/project/las... |
6f03324ec9e14195d65d86d055763883a71a4e64fb790e9b4079058227c350f9 | Shell | 561 | 21 | #!/bin/bash
#SBATCH --mail-type=ALL
#SBATCH --mail-user=jfisher7@uab.edu
#SBATCH --job-name=tau_HA1E
#SBATCH -n 1
#SBATCH --mem-per-cpu=20000
#SBATCH --nodes=1
#SBATCH --time=0-02:00:00
#SBATCH --share
#SBATCH --partition=express
#SBATCH --error=%j.%N.err.txt
#SBATCH --output=%j.%N.out.txt
cd /data/project/las... |
71120477516597236caf7ea35e0081fdcaa8a129447a8ea6dc3ee56f503c8885 | Shell | 561 | 21 | #!/bin/bash
#SBATCH --mail-type=ALL
#SBATCH --mail-user=jfisher7@uab.edu
#SBATCH --job-name=tau_1HAE
#SBATCH -n 1
#SBATCH --mem-per-cpu=20000
#SBATCH --nodes=1
#SBATCH --time=0-02:00:00
#SBATCH --share
#SBATCH --partition=express
#SBATCH --error=%j.%N.err.txt
#SBATCH --output=%j.%N.out.txt
cd /data/project/las... |
7c9efbf305732412dec09731d5a79a0cd8de8681995a8e0846382aaa0c47d045 | Shell | 561 | 21 | #!/bin/bash
#SBATCH --mail-type=ALL
#SBATCH --mail-user=jfisher7@uab.edu
#SBATCH --job-name=tau_YAPC
#SBATCH -n 1
#SBATCH --mem-per-cpu=20000
#SBATCH --nodes=1
#SBATCH --time=0-02:00:00
#SBATCH --share
#SBATCH --partition=express
#SBATCH --error=%j.%N.err.txt
#SBATCH --output=%j.%N.out.txt
cd /data/project/las... |
10586721dc89953ce525e1c8ba87af15c4cf5811a02426afeaa5436af6e20824 | Shell | 563 | 19 | #!/bin/bash
#SBATCH --job-name=permute_bfile
#SBATCH --account=p33_norment
#SBATCH --time=60:00:00
#SBATCH --mem-per-cpu=8GB
#SBATCH --cpus-per-task=4
source /cluster/bin/jobsetup
module purge
module load Python/3.7.4-GCCcore-8.3.0
source /cluster/projects/p33/users/elizabept/software/py3/bin/activate
module list
... |
2a5cdf031a32ec391a0cd4f64196f74b00fca943df2c2e9722b1f2d1b88d74d2 | Shell | 563 | 21 | #!/bin/bash
#SBATCH --mail-type=ALL
#SBATCH --mail-user=jfisher7@uab.edu
#SBATCH --job-name=tau_HEPG2
#SBATCH -n 1
#SBATCH --mem-per-cpu=20000
#SBATCH --nodes=1
#SBATCH --time=0-02:00:00
#SBATCH --share
#SBATCH --partition=express
#SBATCH --error=%j.%N.err.txt
#SBATCH --output=%j.%N.out.txt
cd /data/project/la... |
20e8ab71fec79bd64c65c11ffbb48c8b90489c008c1c36be4cac031c67d76f5e | Shell | 572 | 21 | #!/bin/bash
#SBATCH --mail-type=ALL
#SBATCH --mail-user=jfisher7@uab.edu
#SBATCH --job-name=tau_array
#SBATCH -n 1
#SBATCH --mem-per-cpu=20000
#SBATCH --nodes=1
#SBATCH --time=0-02:00:00
#SBATCH --share
#SBATCH --partition=express
#SBATCH --error=%j.%N.err.txt
#SBATCH --output=%j.%N.out.txt
cd /data/project/la... |
def275f19f4820f113752e45a368946913d006ff1eafe44faa708f8cebcd346f | Shell | 575 | 9 | # mouse juvenile & adult oligodendrocytes
# Marques et al. (2016) Oligodendrocyte heterogeneity in the mouse juvenile and adult central nervous system. 352(6291) 1326-1329 DOI: 10.1126/science.aaf6463
wget ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE75nnn/GSE75330/suppl/GSE75330_Marques_et_al_mol_counts2.tab.gz
gunzip GS... |
048719a64aaaaa26acf1a632dad2a7066f59d26dbae772df41de0afbd65651f6 | Shell | 576 | 20 | #!/bin/bash
# make connectivity matrices - main analysis
datasets=("PNC" "NKI" "HCPD" "HBN")
script_dir="/cbica/projects/network_replication/manuscript/code/connectivity_matrices"
outputs_dir_logs="/cbica/projects/network_replication/manuscript/logs"
# Loop through each dataset
for dataset in "${datasets[@]}"; do
... |
97f4626bbe59b3bab27c3a6c9a7c3303c62e78ae48f9eca730710cf032b6ec14 | Shell | 578 | 16 | #!/usr/bin/bash
fai=$1
best=$2
SHELL_FOLDER=$(dirname "$0")
source ${SHELL_FOLDER}/config.txt
awk '$2 >= 10000' ${fai} > ${fai}.10k
awk '$2 >= 15000' ${fai} > ${fai}.15k
awk '$2 >= 20000' ${fai} > ${fai}.20k
${perl} ${fishInWinter} -bf table -ff table -bc 1 -fc 1 ${fai}.10k ${best} > ${best}.10k
${perl} ${fishInWinte... |
03721d1843f68681819e1b0b0fced16bec3aaf83d4e58c85e929c301251e70fe | Shell | 580 | 17 | #!/bin/sh
# This script is for the author to protect docs and analysis outputs private before acceptance
# We will move docs in a privae repository tentatively during revision
NB_NAME="$(basename $1)"
HGF_DIR=$PWD
mv $1 ~/Desktop/hgf_manuscript/hgf_docs
cd ~/Desktop/hgf_manuscript/hgf_docs
git add ~/Desktop/hgf_manu... |
057cfacfa92b57aa88f2ef558090b4b3df66b877d372efccc4fc44051705474d | Shell | 582 | 21 | #!/bin/bash
source ${HOME}/.profile
which plink
FIRST_CHUNK_I=0
LAST_CHUNK_I=906
DIR=/cluster/projects/p33/users/alexeas/elleke/data
BFILE_CHUNKS_DIR=${DIR}/bfile_chunks
MAX_PADDING=3
MERGE_LIST=${DIR}/bfile_chunks_list.txt
BFILE_MERGED=${DIR}/UKB34886_T1_QCed_230222.perm
rm -rf ${MERGE_LIST}
for i in $(seq ${FIRST_... |
ee4de1efd076d52f84a32861f993fd86a451faed59fab91f0f9c1b919f7a2485 | Shell | 587 | 21 | if [[ $FB_MODE =~ "xvfb" ]]; then
echo "initialize virtual framebuffer"
START_PORT=`shuf -i 5000-6000 -n 1`
XVFB_WORKING_DIR=${WORKING_DIR}/xvfb_temp
mkdir -p ${XVFB_WORKING_DIR}
source ${XVFB_HELPER_SCRIPTS_DIR}/init_xvfb.sh ${START_PORT} ${XVFB_WORKING_DIR}
function exitXvfb {
echo "Ex... |
37aa473e7967f3fb04de598032386f88c7ded1870f621b9915d2bc2843914874 | Shell | 588 | 28 | #!/bin/sh
# make-somodoc.sh
TFILE=~/ultrascan3/somo/arc/somodoc.tgz
SRCDIR=~/ultrascan2
cd ${SRCDIR}
TARGS="\
doc/manual/Deb* \
doc/manual/lic* \
doc/manual/somo* \
doc/manual/ultra* \
doc/manual/us_* \
doc/manual/version* \
"
echo "=== Creating a somo doc archive ==="
tar -cvf - $TARGS | gzip --stdout > ${... |
e47edfa5e81655d455423d99148d4e4a2d0b01575ee1002f55c7d38aee66700e | Shell | 589 | 30 | #!/bin/bash
SCRIPT_DIR=$(dirname ${BASH_SOURCE[0]})
if [ "$#" -ge 1 ]; then
AREA=$1
shift
else
echo "Anatomical area must be specified: submit_import.sh <anatomical_area> <libname>"
echo "Valid values: {brain | vnc}"
exit 1
fi
if [ "$#" -ge 1 ]; then
LIBNAME=$1
shift
else
echo "Librar... |
ec0827d59dae9a2078e5964f6f201e5b1c58db2560005f693390ec33cf1b0997 | Shell | 590 | 5 | # python ./bin/plot_correlation.py -p ./data/continuous-current/example_from24/correlation_data.asc -c "0 2" -l "V(mV) Temperature ºC" -sv y -sh n -scx 1000 -my 24 -sf pdf -dw y
# python ./bin/laser_pulse.py -p './data/continuous-current/example_from24/pipette_pulse_recording.asc' -slope 2.073 -sf pdf
python ./bin/plo... |
5f8e78cf4300a626fbaaf92799bb4267254833167ef175ca4050f664708a40ba | Shell | 593 | 17 | #!/bin/bash
# Usage: docker2singularity.sh <docker2singularity container name> <remote host> <remote host dir>
D2S=$1
REMOTE_HOST=$2
REMOTE_DIR=$3
while read -r container
do
echo "Transferring $container to ${REMOTE_HOST}:${REMOTE_DIR}" \
&& name=`basename $container` \
&& file="${name}.img" \
&& docker run \
-v ... |
585508115e9307aeaa3a78b2f281d2212b0bfa2aac1d963cbc68f568587e9d05 | Shell | 595 | 14 | BASE_EXPORT_FOLDER=${BASE_EXPORT_FOLDER:=/nrs/neuronbridge}
DATA_VERSION=${DATA_VERSION:=v3.0.0}
export EXPORT_DIR=${EXPORT_DIR:="${BASE_EXPORT_FOLDER}/${DATA_VERSION}"}
export JACS_URL=${JACS_URL:="http://host/api/rest-v2"}
export JACS_AUTH_TYPE=${JACS_AUTH_TYPE:="APIKEY"}
export JACS_AUTH_TOKEN=${JACS_AUTH_TOKEN:="t... |
3c52bacb958683c26f40ae624039e6cedaffc437ed1f270ce71750f1a5536399 | Shell | 597 | 21 | #!/bin/bash
which plink2
which plink
ROOT=/cluster/projects/p33/users/alexeas/elleke/pleioprs/geno
GENO_DIR=/cluster/projects/p33/groups/biostat/genetics/imputed/cur/stage1
BATCHES="norment_i_a0807b norment_ii_fe2200 norment_iii_0c942c"
MERGE_LIST=${ROOT}/merge_list.txt
rm -f ${MERGE_LIST}
for BATCH in ${BATCHES}; d... |
ece1ec26c61335699c7eae96d6221b9fa5992bef180b2dee27ab13cddcea6ed5 | Shell | 597 | 22 | #!/bin/bash -l
#SBATCH --job-name="ebc_simulation"
#SBATCH --mail-type=ALL
#SBATCH --mail-user=alice.geminiani@unipv.it
#SBATCH --time=00:10:00
#SBATCH --nodes=1
#SBATCH --ntasks-per-core=1
#SBATCH --ntasks-per-node=4
#SBATCH --cpus-per-task=1
#SBATCH --partition=normal
#SBATCH --constraint=mc
#SBATCH --hint... |
730be587bb9ccecb338cc58ea62b9008f3c8519e62e447a3d80fc679173adfff | Shell | 598 | 18 | #! /bin/sh
python main_digit_create.py \
--n_samples_train 1 --n_samples_gnrl 0 \
--n_letters 2 --offset random_occluded --digit_colour_type b_w_e --linewidth 20 \
--fontsize 180 --FILENAME /media/aiswarya/Depth_inverting_autoencoders/Dataset/Code_data \
# python -W ignore main_digit_create.py... |
0429e19ffcaf3ff73207bd893f36319dc3722a4f3c59a93404d16d9beef902de | Shell | 599 | 18 | #!/bin/bash
which plink
ROOT=/cluster/projects/p33/users/alexeas/elleke/pleioprs
BFILE=${ROOT}/geno/all_qc
SUMSTATS_DIR=${ROOT}/sumstats
for TRAIT in ADHD; do
SUMSTATS=${SUMSTATS_DIR}/${TRAIT}.sumstats.prs.id.txt
for CLUMP_FIELD in PVAL FDR; do
echo ${TRAIT} ${CLUMP_FIELD}
OUT=${ROOT}/sumstat... |
263c81a75b3180ed2c9c1e9bdc29fcbe09a15236ec967066f506b41f901f0853 | Shell | 610 | 20 | #!/bin/bash
#SBATCH -p fat
#SBATCH -N 1
#SBATCH -n 15
#SBATCH -t 48:00:00
#SBATCH --job-name pre4
#SBATCH -o %j.out
#SBATCH -e %j.err
module load bbmap
module load samtools
module load anaconda3
module load openjdk
source ~/.bashrc
conda activate /usr/users/mmnb1ngs/collab_work/workspace/lineage_analysis/conda_linea... |
e7cdf92fc0510936b6f8dd721c1e396a5c99627c2da844230d00a322d1c5ba64 | Shell | 610 | 20 | #!/bin/bash
#SBATCH -p fat
#SBATCH -N 1
#SBATCH -n 15
#SBATCH -t 48:00:00
#SBATCH --job-name pre1
#SBATCH -o %j.out
#SBATCH -e %j.err
module load bbmap
module load samtools
module load anaconda3
module load openjdk
source ~/.bashrc
conda activate /usr/users/mmnb1ngs/collab_work/workspace/lineage_analysis/conda_linea... |
f27634f1a2b641a09e518de7466cd0a39c37daa38e9395b98417803e124aae2b | Shell | 610 | 20 | #!/bin/bash
#SBATCH -p fat
#SBATCH -N 1
#SBATCH -n 15
#SBATCH -t 48:00:00
#SBATCH --job-name pre2
#SBATCH -o %j.out
#SBATCH -e %j.err
module load bbmap
module load samtools
module load anaconda3
module load openjdk
source ~/.bashrc
conda activate /usr/users/mmnb1ngs/collab_work/workspace/lineage_analysis/conda_linea... |
ff83b351be59eae4831feea1e803446c197c9d5cabcd2c8ec24262725d7c6cda | Shell | 610 | 20 | #!/bin/bash
#SBATCH -p fat
#SBATCH -N 1
#SBATCH -n 15
#SBATCH -t 48:00:00
#SBATCH --job-name pre3
#SBATCH -o %j.out
#SBATCH -e %j.err
module load bbmap
module load samtools
module load anaconda3
module load openjdk
source ~/.bashrc
conda activate /usr/users/mmnb1ngs/collab_work/workspace/lineage_analysis/conda_linea... |
002cf4d8ec82f6013d96d0486ea3067566a511805d80e6cab6c6403f79a8242a | Shell | 613 | 16 | #!/bin/bash
# Original works: https://github.com/hemberg-lab/scRNA.seq.datasets/
mkdir -p ./RAW;
cd ./RAW;
# get data
wget https://www.ebi.ac.uk/arrayexpress/files/E-MTAB-5061/E-MTAB-5061.processed.1.zip
unzip E-MTAB-5061.processed.1.zip
head -n 1 pancreas_refseq_rpkms_counts_3514sc.txt > labels.txt
sed -i '1s/#sampl... |
0b6bb9c42ad261ea03a43670079c258d599224b69931e7e45966e85b2ab73044 | Shell | 618 | 24 | #!/bin/bash
#SBATCH --job-name=munge_sumstats
#SBATCH --account=p33_norment
#SBATCH --time=24:00:00
#SBATCH --cpus-per-task=32
#SBATCH --mem-per-cpu=8GB
#SBATCH --array=0-400
set -o errexit
source ../settings.sh
source ${SOFTWARE}/ldsr/bin/activate
which python
LDSR_SRC=${DATA}/ldsc
LDSR_OUT=${OUT}/h2
LDSR_IN=${OUT... |
9dc98ad6b061ff30b26921616cc8bbfd843ad5afc2a139abd8a4a7f3935f73d1 | Shell | 622 | 22 | #!/bin/bash
# Original works: https://github.com/hemberg-lab/scRNA.seq.datasets/
mkdir -p ./RAW;
cd ./RAW;
# download data
wget -O FACS.zip \
'https://figshare.com/ndownloader/files/10700143'
unzip FACS.zip
wget -O metadata_FACS.csv 'https://figshare.com/ndownloader/files/10842785'
wget -O annotations_FACS.csv 'https... |
fc9a06ec3db4c5770f217c7563438c4133460cb8092026d9a30bad323d62e945 | Shell | 623 | 14 | #!/bin/bash
wget -O data.txt.gz \
'https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE63472&format=file&file=GSE63472%5FP14Retina%5Fmerged%5Fdigital%5Fexpression%2Etxt%2Egz'
gunzip data.txt.gz
# download proper gene names
# downloaded from Ensembl Biomart on 1-3-17
wget https://s3.amazonaws.com/scrnaseq-public-dataset... |
21a9d7589bd3c7e9fa0627071ed42a56ee3a7934151349cd79bb0166454015fb | Shell | 624 | 15 | #!/bin/bash
# Warning, this script will take a long time to run
# It is merely meant as an example of all the different parameter combinations that we ran
python 1_predict_gf.py 0.01 pos Repeated10Fold
python 1_predict_gf.py 0.05 pos Repeated10Fold
python 1_predict_gf.py 0.10 pos Repeated10Fold
python 1_predict_gf.py... |
c31996aaad682b8bb3db2a021ec5ad13a133aaeea354c98548430dd4a3b6140a | Shell | 629 | 29 | #!/bin/sh
NUM_TREES=$1
NUM_CONCURRENT=2 # constant
readarray -d ',' -t RECOS < $2
IFS=',' read -ra PARAMS <<< $3
OUTFOLDER=$4
PREFIX=$5
SLIM_FILE=$6
SELECTION_STRENGTH=$7
function run_slim(){
nohup slim -d reco=${RECOS[i]} -d N1=${PARAMS[0]} -d N2=${PARAMS[1]} \
-d growth=${PARAMS[2]} -d T1=${PARAMS[3]}... |
f11f8956dc2508da9fb217dd7062688a5bc347b725f03575be2aaf2496e1874c | Shell | 640 | 13 | # http://genome-tech.ucsd.edu/ZhangLab/index.php/data/epigenomics-and-transcriptomics/sns/
# Lake et al. (2016) Neuronal subtypes and diversity revealed by single-nucleus RNA sequencing of the human brain. Science. 352 (6293): 1586-1590
#Prefrontal cortex - BA10
#Frontal cortex (eye fields) - BA8
#Auditory cortex (spe... |
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