sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
3bcf25a5727366750efa7fc2a01aa56a5ef134fc7fecb73aa08bd4a314ce0f15 | Shell | 18,703 | 427 | #!/bin/bash
set -e
# Requirements for this script
# installed versions of: FSL (version 5.0.6), FreeSurfer (version 5.3.0-HCP) , gradunwarp (HCP version 1.0.2)
# environment: use SetUpHCPPipeline.sh (or individually set FSLDIR, FREESURFER_HOME, HCPPIPEDIR, PATH - for gradient_unwarp.py)
#########################... |
5c1d3cee1d445c580d6201f4349a41bcc750858ebcb2a45e8f44a690dbe3dc49 | Shell | 18,753 | 279 | #!/usr/bin/env bash
set -e
#echo -e "\n START: FreeSurferHighResPial"
#START200310
echo -e "\nSTART: $0"
SubjectID="$1"
SubjectDIR="$2"
T1wImage="$3" #T1w FreeSurfer Input (Full Resolution)
T2wImage="$4" #T2w FreeSurfer Input (Full Resolution)
echo " T2wImage = $T2wImage"
##START200309
#if [ ! -f "$T2wImage" ];... |
15251f9f019a5e3118f3243d275fea51e30deceb794dab4627281d388ed19ad7 | Shell | 18,795 | 214 | #!/bin/bash
set -e
echo -e "\n START: FS2CaretConvertRegisterNonlinear_1res"
StudyFolder="$1"
Subject="$2"
T1wFolder="$3"
AtlasSpaceFolder="$4"
NativeFolder="$5"
FreeSurferFolder="$6"
FreeSurferInput="$7"
T1wImage="$8"
T2wImage="$9"
SurfaceAtlasDIR="${10}"
HighResMesh="${11}"
LowResMeshes="${12}"
AtlasTransform="${13}... |
0303295fb2a646ccade8bc3665bb13fc110f6b2991e670842a9abc9617c57ba6 | Shell | 19,230 | 187 | #!/bin/bash
set -e
echo -e "\n START: CreateMyelinMaps"
StudyFolder="$1"
Subject="$2"
AtlasSpaceFolder="$3"
NativeFolder="$4"
T1wFolder="$5"
HighResMesh="$6"
LowResMeshes="$7"
OrginalT1wImage="$8"
OrginalT2wImage="$9"
T1wImageBrain="${10}"
InitialT1wTransform="${11}"
dcT1wTransform="${12}"
InitialT2wTransform="${13}"
... |
44a0166e0be37b47f97f8e458cf3b9966324e1914d703e39d080d3bf3ba2c04e | Shell | 19,597 | 434 | platform='unknown'
unamestr=`uname`
if [[ "$unamestr" == 'Linux' ]]; then
platform='linux'
elif [[ "$unamestr" == 'Darwin' ]]; then
platform='darwin'
fi
# 1-100: g3.4
# 101-200: p2
# AMI="ami-660ae31e"
AMI="ami-55c2792d" #extract
#AMI="ami-7428ff0c" #extract
#INSTANCE_TYPE="g3.4xlarge"
#INSTANCE_TYPE="p2.xlarge... |
5a65e04c2d947137e1ce9bdd036e0def1b55481a0c6f1acd51dc3d49c8fc1701 | Shell | 19,806 | 535 | #!/bin/bash
# ------------------------------------------------------------------------------
# Code Start
# ------------------------------------------------------------------------------
# If any commands exit with non-zero value, this script exits
set -e
g_script_name=$(basename "${0}")
# -------------------------... |
d0ed7e04c698bef060bac4e1fb8dd7137c8879c4fb529ba69076ba3f2330560e | Shell | 20,798 | 402 | platform='unknown'
unamestr=`uname`
if [[ "$unamestr" == 'Linux' ]]; then
platform='linux'
elif [[ "$unamestr" == 'Darwin' ]]; then
platform='darwin'
fi
# 1-100: g3.4
# 101-200: p2
# AMI="ami-660ae31e"
AMI="ami-55c2792d" #extract
#AMI="ami-7428ff0c" #extract
#INSTANCE_TYPE="g3.4xlarge"
#INSTANCE_TYPE="p2.xlarge... |
b2f4518b0cc8901d3cb1624430d527cb6108a7c3081dfa07367648d733c4db56 | Shell | 20,889 | 609 | #!/bin/bash
#~ND~FORMAT~MARKDOWN~
#~ND~START~
#
# # MSMAllPipeline.sh
#
# ## Copyright Notice
#
# Copyright (C) 2015-2017 The Human Connectome Project
#
# * Washington University in St. Louis
# * University of Minnesota
# * Oxford University
#
# ## Author(s)
#
# * Matthew F. Glasser, Department of Anatomy and Neurobio... |
fff0fae9f69da9fc1dd07adfdd42b161bbba520a51ba3195a047cb0d9e3601cf | Shell | 20,921 | 216 | #!/usr/bin/env bash
set -e
echo -e "\n START: $0"
StudyFolder="$1"
Subject="$2"
AtlasSpaceFolder="$3"
NativeFolder="$4"
T1wFolder="$5"
HighResMesh="$6"
LowResMeshes="$7"
OrginalT1wImage="$8"
OrginalT2wImage="$9"
T1wImageBrain="${10}"
InitialT1wTransform="${11}"
dcT1wTransform="${12}"
InitialT2wTransform="${13}"
dcT2wT... |
ac7ace2831c64ab6d950d0a1a48f3a973b90f7dd37dcbabc23ccd4510cf19a30 | Shell | 21,058 | 458 | platform='unknown'
unamestr=`uname`
if [[ "$unamestr" == 'Linux' ]]; then
platform='linux'
elif [[ "$unamestr" == 'Darwin' ]]; then
platform='darwin'
fi
# 1-100: g3.4
# 101-200: p2
# AMI="ami-660ae31e"
AMI="ami-d0a16fa8" #extract
INSTANCE_TYPE="g3.4xlarge"
# INSTANCE_TYPE="g3.4xlarge"
# INSTANCE_TYPE="p3.2xlarg... |
628f123cb7e7aa924b4a0c4fa6fb5cdf7cace8c15a7dee3d473e71e86c236349 | Shell | 22,185 | 364 | #!/bin/bash
# Pre processing pipeline for T1w and DWI images
# Requirements: ANTs, FSL, Anima, MRtrix3, Python3 with the environment_preprocessing_and_metrics.yaml environment
#import Anima bins
Anima_dir=/path_to_anima_folder/.anima/
export PATH=$PATH:/${Anima_dir}/Anima-Binaries-4.2/
export PATH=$PATH:/${Anima_dir}/A... |
929256abdf2e77c0ec09c25f1841cfc80c558cfb8acc71df5d444d1c56682e35 | Shell | 22,633 | 646 | #===============step1==============
GATK=/home/Mpzhang/bin/gatk-4.2.2.0
REF=/home/Mpzhang/goldref/DRCv10.fa
INP=/work01/Mpzhang/bamfiles
OUTPUT=/work01/Mpzhang/1.Russia_pigs/2.SNPs_calling
SAMP=A18375_mkdup_realn.bam
NAME=`echo ${SAMP}|awk -F"_mkd" '{print $1}'
for i in `seq 1 18` X Y MT;do
$GATK --java-options "-Xm... |
8de2379754e2dc9eeb02eb8cb4cd690ab64f490901d04e6e04a09bb546237230 | Shell | 23,548 | 574 | #!/usr/bin/env bash
set -e
echo "****** START $0 ******"
P0=${OGREDIR}/lib/OGREDistortionCorrectionAndEPIToT1wReg_FLIRTBBRAndFreeSurferBBRbased.sh
P1=${OGREDIR}/lib/OGREOneStepResampling.sh
P2=${OGREDIR}/lib/OGREIntensityNormalization.sh
P3=${OGREDIR}/lib/OGREMotionCorrection.sh
do_GradientDistortionCorrection=1
d... |
6853f956b72842961df95f978f5e28cd33a0def8eb891ed7bf159d8b038dad34 | Shell | 24,719 | 423 | #!/bin/bash
set -e
# Must first source SetUpHCPPipeline.sh to set up pipeline environment variables and software
# Requirements for this script
# installed versions of FSL 5.0.7 or greater
# environment: FSLDIR , HCPPIPEDIR , CARET7DIR
########################################## PREPARE FUNCTIONS #################... |
3abf8bf7e382701e91ebc4589477d365c9af9429ebef1b5ebe75ad31dd7fdce3 | Shell | 25,250 | 636 | #!/usr/bin/env bash
P0=${OGREDIR}/lib/OGREGenericfMRIVolumeProcessingPipeline.sh
echo "**** Running $0 ****"
get_batch_options() {
local arguments=("$@")
unset command_line_specified_study_folder
unset command_line_specified_subj
unset command_line_specified_run_local
unset command_line_specifi... |
958dcd71bc71328b107ba8d19161f28d13719a9b115cde52d1e9b40b21f5798f | Shell | 27,029 | 654 | #!/bin/bash
#~ND~FORMAT~MARKDOWN~
#~ND~START~
#
# # PreFreeSurferPipeline.sh
#
# ## Copyright Notice
#
# Copyright (C) 2013-2014 The Human Connectome Project
#
# * Washington University in St. Louis
# * University of Minnesota
# * Oxford University
#
# ## Author(s)
#
# * Matthew F. Glasser, Department of Anatomy and... |
2d3e5cddf942c934f01608a43feaf33734bcb811437a97055b2b1856fe6c1620 | Shell | 28,394 | 463 | platform='unknown'
unamestr=`uname`
if [[ "$unamestr" == 'Linux' ]]; then
platform='linux'
elif [[ "$unamestr" == 'Darwin' ]]; then
platform='darwin'
fi
# 1-100: g3.4
# 101-200: p2
# AMI="ami-660ae31e"
AMI="ami-d0a16fa8" #extract
AMI="ami-7428ff0c" #extract
#INSTANCE_TYPE="g3.4xlarge"
#INSTANCE_TYPE="p2.xlarge"... |
fc676b51ec033678457575a857fda4e18f480bf81daaa14cf2b6e5036a65ba2c | Shell | 30,262 | 775 | #!/usr/bin/env bash
P0=${OGREDIR}/lib/OGREPreFreeSurferPipeline.sh
echo "**** Running $0 ****"
set -e
#~ND~FORMAT~MARKDOWN~
#~ND~START~
#
# # PreFreeSurferPipelineBatch.sh
#
# ## Copyright Notice
#
# Copyright (C) 2013-2018 The Human Connectome Project
#
# * Washington University in St. Louis
# * University of Minne... |
f3edff3ade88ac539edf1855f9f2bde47ec9f9b0e109c7304523223736b339c0 | Shell | 30,654 | 764 | #!/usr/bin/env bash
#~ND~FORMAT~MARKDOWN~
#~ND~START~
P0=${OGREDIR}/lib/OGRET2wToT1wReg.sh
P1=${OGREDIR}/lib/OGREBiasFieldCorrection_sqrtT1wXT1w.sh
P2=${OGREDIR}/lib/OGREAtlasRegistrationToMNI152_FLIRTandFNIRT.sh
echo " **** Running $0 ****"
# Setup this script such that if any command exits with a non-zero valu... |
c15e5c4fe38567819c22f3f9264311b1e6b3d3da2d281ed3087fb9fef54a889b | Shell | 34,093 | 553 | platform='unknown'
unamestr=`uname`
if [[ "$unamestr" == 'Linux' ]]; then
platform='linux'
elif [[ "$unamestr" == 'Darwin' ]]; then
platform='darwin'
fi
# 1-100: g3.4
# 101-200: p2
# AMI="ami-660ae31e"
AMI="ami-55c2792d" #extract
#AMI="ami-7428ff0c" #extract
#INSTANCE_TYPE="g3.4xlarge"
#INSTANCE_TYPE="p2.xlarge... |
86e3f2cbe2851ac96c47f8f7fe0b023b59bf830341feb0565645febe3e73092e | Shell | 34,264 | 650 | #!/bin/bash
set -e
# Requirements for this script
# installed versions of: FSL (version 5.0.6) and FreeSurfer (version 5.3.0-HCP)
# environment: FSLDIR, FREESURFER_HOME + others
# ---------------------------------------------------------------------
# Constants for specification of Readout Distortion Correction M... |
3e540707ad21f6202476a12912b84a3a81e67046efd0ef9f43381c70d7ceebb3 | Shell | 36,151 | 331 | #!/bin/bash
# The script generetes the structural connectomes using MRtrix3
# Requirements: ANTs, FSL, Anima, MRtrix3, Python3 with the environment_preprocessing_and_metrics.yaml environment
#import Anima bins
Anima_dir=/path_to_anima_folder/.anima/
export PATH=$PATH:/${Anima_dir}/Anima-Binaries-4.2/
export PATH=$PATH:... |
88a43390a33ba9732e9ddda31155d9cca6383bf5cc9dd366ad2e6e1ebad8f80d | Shell | 37,484 | 653 | #!/usr/bin/env bash
set -e
echo " **** Running $0 ****"
P0=${OGREDIR}/lib/OGREFreeSurferHiresWhite.sh
P1=${OGREDIR}/lib/OGREFreeSurferHiresPial.sh
# Requirements for this script
# installed versions of: FSL (version 5.0.6), FreeSurfer (version 5.3.0-HCP)
# environment: FSLDIR , FREESURFER_HOME , HCPPIPEDIR , C... |
5c66337b3519ddaf654e2bad05ed8c12228e6ff52e669f2ef6babd5f2725ac28 | Shell | 38,467 | 726 | #!/usr/bin/env bash
set -e
echo -e "\n***** START $0 *****"
# Requirements for this script
# installed versions of: FSL (version 5.0.6) and FreeSurfer (version 5.3.0-HCP)
# environment: FSLDIR, FeEESURFER_HOME + others
# ---------------------------------------------------------------------
# Constants for specif... |
4adf6841d1d3b0af3a2408da5fdcca3692f19e58fef7167a89a945a9539dd0ef | Shell | 39,498 | 1,138 | #!/bin/bash
#~ND~FORMAT~MARKDOWN~
#~ND~START~
#
# # RestingStateStats.sh
#
# ## Copyright Notice
#
# Copyright (C) 2015-2016 The Human Connectome Project
#
# * Washington University in St. Louis
# * University of Minnesota
# * Oxford University
#
# ## Author(s)
#
# * Matthew F. Glasser, Department of Anatomy and Neuro... |
730ac1827bd2812cb0e281b24fcd78812f0d767112a2568f1d59b19548224489 | Shell | 40,860 | 550 | #!/usr/bin/bash
set -e
MYDIR=`dirname $0`
Creating_conf(){
local genome_build_version=$1
local organism=$2
local annotation_path=$3
local genome_fasta=$4
local gencode_gff3=$5
local hisat2_index=$6
local dbSNP_all=$7
local rmsk=$8
local ERCC=$9
local hisat2_index_s=true
... |
ae88e64e0e4f40a3b87ad9620480d6e36533ee78d260baf78f7f961ee41306ff | Shell | 41,339 | 830 | #!/bin/bash
#
# # DeDriftAndResamplePipeline.sh
#
# ## Copyright Notice
#
# Copyright (C) 2015-2017 The Human Connectome Project
#
# * Washington University in St. Louis
# * University of Minnesota
# * Oxford University
#
# ## Author(s)
#
# * Matthew F. Glasser, Department of Anatomy and Neurobiology, Washington Unive... |
8c813695b80a74a3fd16df5b58541097a7c2567cb9ea9605e3db38430685ed52 | Shell | 43,792 | 1,092 | #!/bin/bash
#
# # MakeAverageDataset.sh
#
# ## Copyright Notice
#
# Copyright (C) 2014-2017 The Human Connectome Project/Connectome Coordination Facility
#
# * Washington University in St. Louis
# * University of Minnesota
# * Oxford University
#
# ## Author(s)
#
# * Matthew F. Glasser, Department of Anatomy and Neuro... |
2ae26a70b6f55504673fd2c75d95521ee35f682b0b624c6eb72583a5670bd14a | Shell | 46,173 | 1,159 | #!/usr/bin/env bash
shebang="#!/usr/bin/env bash"
#Hard coded HCP batch scripts
PRE=OGREPreFreeSurferPipelineBatch.sh
FREE=OGREFreeSurferPipelineBatch.sh
POST=OGREPostFreeSurferPipelineBatch.sh
SETUP=OGRESetUpHCPPipeline.sh
MASKS=OGRESplitFreeSurferMasks.sh
MASKSLOW=OGREMasksLow.sh
#Resolution. MNI152 options: 1, 0... |
c1c154c0ca342e7660dbc6480de45c67b9d14cfbdcf7ff7a723c916981f220bd | Shell | 65,081 | 609 | #!/bin/bash
set -e # If any commands exit with non-zero value, this script exits
# ------------------------------------------------------------------------------
# Verify HCPPIPEDIR environment variable is set
# ------------------------------------------------------------------------------
if [ -z "${HCPPIPEDIR}" ]... |
64faf3b74e1ca7482b7b4b02d772aed3ad0a3ffce03fa7c6097730c8a962d56a | Shell | 69,749 | 715 | #!/usr/bin/env bash
set -e # If any commands exit with non-zero value, this script exits
echo "START: $0"
# ------------------------------------------------------------------------------
# Verify HCPPIPEDIR environment variable is set
# ------------------------------------------------------------------------------
... |
5b76d863b9bca8d5c2e4077cf2711712d83b0c6289de320067c577fb68ede5c6 | Shell | 72,703 | 1,415 |
cat << 'EOF' >gather_sumstats.R
#load in packages
library(data.table)
library(tidyverse)
library(GenomicSEM)
library(bigsnpr)
########## CHILDHOOD OBESITY
# http://egg-consortium.org/childhood-obesity-2019.html
# wget http://egg-consortium.org/Childhood_Obesity_2019/CHILDHOOD_OBESITY.TRANS_ANCESTRAL.RESULTS.txt.gz
... |
8dbebf73c9e4d38511cd38217905f0a1ffd21c2bbd46377207fc11215865f66b | Shell | 81,303 | 1,938 | #!/bin/bash
TRANSFER_COMMAND_FILE=/tmp/run_all_transfers.txt
rm $TRANSFER_COMMAND_FILE
touch $TRANSFER_COMMAND_FILE
echo "Generating config files..."
###################
# RESNET26 Task #
###################
SRC_TASKS="denoise_25 rgb2sfnorm_25 random \
class_places_25 room_layout_25"
TASKS="denoise_25 rgb2sfnorm_25... |
9585d095e52d6d3d4e5a7a403b557fde673057d07445df0d8c3745d38b91663b | Shell | 86,692 | 1,422 | #!/bin/bash
#~ND~FORMAT~MARKDOWN~
#~ND~START~
#
# # MSMAll.sh
#
# ## Copyright Notice
#
# Copyright (C) 2015-2017 The Human Connectome Project
#
# * Washington University in St. Louis
# * University of Minnesota
# * Oxford University
#
# ## Author(s)
#
# * Matthew F. Glasser, Department of Anatomy and Neurobiology, Wa... |
47aa77a7b24064f2f74eba5315252c5922fa2863abee2d32791f550622427130 | Shell | 200,000 | 1,302 | #!/bin/bash
#$ -cwd
#$ -j y
#$ -l mem_free=8G
#$ -l h_vmem=8G
#$ -l cancergen
module load aws/2.0.54
cd /dcs05/scharpf/data/annapragada/mced_paper/Biology/PCAWG
# ICGC PDC Script Manifest
#
# Script to download ICGC files in PDC. Generated from https://dcc.icgc.org/repositories.
# Requires AWS CLI to be installed:
#... |
75b5713ec4ac6b2c3e7c674b110acb380fa4d54e7a881a5e2c8eef757ae87e02 | Stan | 3,557 | 197 | data {
int nn;
int nt;
int ns;
matrix[nt, ns] Obs;
matrix [nn, nn] SC;
matrix[ns, nn] gain;
matrix[nn,nn] eig;
}
transformed data {
real dt;
real tau0;
real I1;
real Ks;
vector[nt*ns] xs;
matrix[nt,ns] wtm;
vector[nt*ns] wt;
vector[nn] x_init;
for(i in 1:nn){
x_init[i]=-1.9... |
148aa09545d88f1863f933641aa81ec94338333167f8d1ff25963a3f0a8e2375 | Stan | 7,581 | 338 | functions {
matrix correct_baseline(matrix Seeg, int n_bsl) {
int nt = rows(Seeg);
int ns = cols(Seeg);
matrix[nt, ns] output;
real bsl_value;
if (n_bsl==0)
return Seeg;
for (s in 1:ns) {
bsl_value = mean(sub_col(Seeg, 1, s, n_bsl));
outp... |
164d8ce6137906712714163f3505d9d5ffb285018d74504e5e37926d093be413 | Text | 17 | 1 | # Rosas-Vidal2025 |
e250453ecd8018c9fe5339675b91ce3b425ccffb32a4611e48837fbf0dc7b23f | Text | 41 | 3 | # install custom layers
bash install.sh
|
33681700885f981cce5ebbf6c53c4527edb133faf6dfc8acbdcdb680c8b6b253 | Text | 52 | 2 | # halobenzenes
MDCM study of series of halobenzenes
|
05d901adf4cfe98a82ffc987f66176514764c32506b23a6ff69474a9beaf54d5 | Text | 73 | 3 | # GSF3874-EMS-pilot
Sequencing M1,M2,M3 and NM1,NM2,NM3 of candidate A5
|
702c99eff1b7f8f3e92bad8b5af3ef600b52a9d08983ade1b3f98888e691f98b | Text | 83 | 3 | # Fuel_Cell_Diagnosis
Data can be found at: https://doi.org/10.17632/pn95bsbhv9.1
|
58ddb48d9125b3c79dfcb309a2c5ec15bb849a8dd6691a3789d39aa6d97567a8 | Text | 132 | 4 | # DSN
Python implementation of Diffusion Similarity Networks
Preprint: https://www.biorxiv.org/content/10.1101/2025.03.29.646134v1
|
d65708fc272c436f4a27e9ab62d05267241520f20cd83b746cd60c567935039a | Text | 148 | 3 | # TD-modulation-model
this is the code for generating the model analysis in paper: eLife2025;13:RP96402 DOI: https://doi.org/10.7554/eLife.96402.3
|
b199db50bc86855acec6c96c3fff9ad9539b29059027343c9ad61822f7bf5aae | Text | 155 | 2 | # MusicianshipEEG
Analysis code for "Large-scale multi-site study shows no association between musical training and early auditory neural sound encoding".
|
4d6dc77fb3adce65063c77ca2a1cc7b8af8e60aeafb7a7b3e9b813c4a76154c9 | Text | 179 | 1 | This repository holds the code for producing the deep learning solution and running the inference task. The code execution was carried out in Microsoft AzureML during the study.
|
f4d8a9f283ded749c795bd11e37786e443b8aa004303ed14086f1dc80ceab973 | Text | 227 | 4 | ---copy: reproduction characters
---model:reference characters
---copyData.xlsx: contains the correnspondinag reproduction skill scores and writers' train EI questionnaire z-scores
---split_data.py: split dataset python code |
84e01a32e459cf55780f42d82ab34993ad9acad3b0fb85bb12e998936f29a5ff | Text | 232 | 4 | 'column_arrangement.mlapp' is a MATLAB app code
'bfmatlab' is necessary to import Zeiss lsm format image files.
https://docs.openmicroscopy.org/bio-formats/5.3.4/users/matlab/index.html
Add 'bfmatlab' folder to your MATLAB path.
|
72889edf94cbf91aafa0011fe264cf4b4413a6ff296d62dcefb30d5b72c3697f | Text | 234 | 4 | # Kang2025CommunBiol
Custom MATLAB script for Kang et al., 2025, Communications Biology.
Codes for representational similarity analysis (RSA), support vector regression (SVR), and representational connectivity analysis are included.
|
1ac03112c3e05fd2dae1938fa88742bec32bd902756f4ddf7e527c86ad5a932a | Text | 236 | 6 | # cued_action_selection
Stimulus code for Bonaiuto, et al "Laminar-specific cortical dynamics in human visual and sensorimotor cortices"
https://www.biorxiv.org/content/early/2017/11/30/226274
https://elifesciences.org/articles/33977
|
fa3e9192663383a7fca8a21b2ffadc701f9502994fc40076826698c36cb6119f | Text | 249 | 5 | # Computational examples of software from the tractometry.org ecosystem
For explanations and more details, please refer to https://tractometry.org
The examples can be run interactively through Code Ocean at https://doi.org/10.24433/CO.1278808.v2
|
eb77d7762887a27d8f069864a0a41b29f20a67cc7024bef63b039fdac369f518 | Text | 252 | 10 | # mglia-nat25
Code for `Extended Data Fig 6e`
This is the code for processing and visualization of several mglia data sets.
* `bin/mglia-natrev-proc.py` - aggregation and processing
* `bin/mglia-natrev-viz.py` - visualization from the full matrix
|
5aee1551893d1a9296029f06d1da45d560999baaa8873290f08075c6a1a84b01 | Text | 253 | 3 | # core-multi
code to accompany Vriend et al. 2025: Treatment outcome is associated with pre-treatment connectome measures across psychiatric disorders - evidence for connectomic reserve? NeuroImage: Clinical https://doi.org/10.1016/j.nicl.2025.103870
|
c391635722ad9860547a2729b8ca37160afff7e93babb2a664d7b779d59e7282 | Text | 258 | 7 | <a href="https://ccs.how/">
<img src="docs/img/ccs2022.png" alt="CCS logo" width="200px" align="right"/>
</a>
<h1 align="center">CCS - Generate PacBio HiFi data</h1>
<p align="center">Latest documentation on <a href="https://ccs.how/">ccs.how</a></p>
***
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a61b616240b5abb293106b27807f7e0a0823cc1fb0185f05e55e9950d64f6cd7 | Text | 268 | 5 | Code for reproducing results and figures in "Oxygen-induced stress reveals context-specific gene regulatory effects in human brain organoids" (Genome Research; doi: 10.1101/gr.280219.124).
A [workflowr][] project.
[workflowr]: https://github.com/workflowr/workflowr
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6a53eef3506f9e4f1b8ec216a97f90931dfb67d812d63134fda1244f044614ea | Text | 285 | 6 | # Memory Transformation Differentiable Neural Computer
Run the start_training.py file directly.
Note:
By default, only the first babi task is trained. You can modify the task_selection parameter in the config.yaml configuration file to 'all' to train the joint 20 babi tasks.
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915375f2dc37bffd074dbdd18c0d0c577f847b41d2af3443252aed711344f0a3 | Text | 302 | 14 | # vEpiNetV2
## Create a virtual environment with conda
```python
conda create -n vepinetv2 python=3.9
conda activate vepinetv2
pip install -r requirements.txt
```
## How to run
1.`vim train_config.py`
2.`python train.py`
3.`python eval.py --test_path test_set_csv_file_path --weight model_file_path` |
44c5948f6e2cf0cfafb3d72a9e6e1a8b07e34fad19d93964605a345482ad1526 | Text | 323 | 10 | The mat-files contains 4 datasets:
1st behavioral experiment:
threshold_ipd_m: threshold ipd for 3 runs per each subject
threshold_ipd_v: geomean threshold per subject
2nd behavioral experiment:
n_subs_m: number of presentations for 4 conditions per subject
k_subs_m: number of correct answers per condition per subjec... |
0c4d06c2f7ef07f99c9172cb6c433e7da061d94d048c768da58810c2e17b651b | Text | 324 | 4 | # Park_npjSoL_2025
Park, Y., Zhang, Y., Schwartz, F., Iuculano, T., Chang, H., & Menon, V. (2025). Distinct neural representational changes following cross-format number sense tutoring in children with mathematical difficulties.
Behavioral and individual-level statistical data are available at https://osf.io/29ju... |
5926725e937383de75da0b48bb9cdc3df533f427d3a24a4b3500d1fa721f66e6 | Text | 347 | 4 | # EEG-Epilepsy-Datasets
This is the dataset we used in our research ***An Automated Detection of Epileptic EEG Using CNN Classifier Based on Feature Fusion with High Accuracy***. It include two datasets: Bonn EEG dataset and New Delhi EEG dataset.
If you want to request more information about our research, please ema... |
86ca422e2edfe67ddf2adbb244955fe4ecc636ef22d2638c00d1bf40bf9ccc9f | Text | 350 | 2 | # Concept-based explanations for the gastrointestinal tract
Code for explaining a deep neural network for predicting abnormalities in the gastrointestinal tract using GradCAM and the following two concept-based explainable artificial intelligence (XAI) methods: Testing with concept activation vectors (TCAV) and concept... |
9ba74a51ac471344d13f216574bdeddcc333f2f81c51cb2f3192f0a2b3072cd0 | Text | 363 | 8 | # ercc1-mouse-rob
Ercc1 KO mice raised in hypoxia and normoxia
## Description
This repository contains the pipeline code used to process the RNA-seq and mtDNA amplicon sequencing data from Rogers, et al. 2023.
## Dependencies
The pipelines expect to run on a cluster running the Univa Grid Engine (UGER). For package d... |
aca004254a7716032f7e2a683c6dd249397d0bd61eb207e956d46bf49b8ad033 | Text | 372 | 7 | # modular_network
Data and analysis code for paper 'Multi-regional module-based signal transmission in mouse visual cortex'.
Please cite
[X Jia, J Siegle, S Durand, G Heller, T Ramirez, C Koch, S Olsen. (2020) Multi-area functional modules mediate feedforward and recurrent processing in visual cortical hierarchy. b... |
542633598204f502fe0514a03ec99eac39bbe5af9ac628a8e38fb573b361b4a4 | Text | 412 | 4 | # LiangLab
Code for: Experience-Dependent Maternal Defense Behavior Mediated by Corticofugal Projections to the Medial Preoptic Area
This is a copy of the code used in "Experience-Dependent Maternal Defense Behavior Mediated by Corticofugal Projections to the Medial Preoptic Area" for animal behavior output predictio... |
90f206978d335a4e916ad33774e64cf1e52da354619ca027b1064413d8eaed2b | Text | 418 | 8 | # Higher-order synergistic interactions and information gain
Script associated with the preprint
**Higher-order and distributed synergistic functional interactions encode information gain in goal-directed learning**
_Etienne Combrisson, Ruggero Basanisi, Matteo Neri, Guillaume Auzias, Giovanni Petri, Daniele Marinazz... |
9853beb114bc3606614c847dfc2ac020f6c4008ac3bca43145021955353ec552 | Text | 424 | 17 | # motortransfer
Archived pipeline for Rezaei et al., 2025 (PLOS Biology).
This repository contains all code and data to reproduce the analyses and figures for Rezaei et al., 2025 (PLOS Biology).
## Project setup
Clone the repository and set up the Python environment:
```
git clone https://github.com/alirzar/gen-ma... |
90309d34b35a3ed706adb3e7139849486ee003cc4838990a664ae7ed3c9d0d71 | Text | 427 | 9 | Hong-ping Wei, Ka Chung Lam, and Hokto Kazama*
*corresponding author
hokto.kazama@riken.jp
RIKEN Center for Brain Science
Please note that the code was designed to run on our computing environment and therefore is not runnable out of the box on arbirary environments.
However, any additional information require... |
9d15fbb47f6345d7bcb6a848743d870b85e5f6975ac38c5943c1a1ec0224e347 | Text | 436 | 17 | # motortransfer
Archived pipeline for Rezaei et al., 2025 (PLOS Biology).
This repository contains all code and data to reproduce the analyses and figures for Rezaei et al., 2025 (PLOS Biology).
## Project setup
Clone the repository and set up the Python environment:
```
git clone https://github.com/alirzar/motort... |
5b71cb88578de28a52029c8dd0a16427f206b11a614683b1a2f5f8cb5309ea16 | Text | 462 | 6 | # Anomaly_Detection
Visual Anomaly Detection
2025 - Bilal, M.; Hanif, M.S. Fast Anomaly Detection for Vision-Based Industrial Inspection Using Cascades of Null Subspace PCA Detectors. Sensors 2025, 25, 4853. https://doi.org/10.3390/s25154853
2026 - Bilal, M. Lean GLASS: Efficient Edge-Deployable Visual Anomaly Dete... |
019d964d6db2ad4e5458a218e53f64e5b9a7356df777d6e12dc824e7aa1bbde3 | Text | 470 | 10 | # Higher-order synergistic interactions and information gain
Script associated with the paper
**Higher-order and distributed synergistic functional interactions encode information gain in goal-directed learning**
Etienne Combrisson, Ruggero Basanisi, Matteo Neri, Guillaume Auzias, Giovanni Petri, Daniele Marinazzo, S... |
f6f7645f40183706c0d487598f6d98e5785cc9b711235f6400dedba8556f67f4 | Text | 500 | 8 | # Longitudinal changes in striatocortical connectivity in first-episode psychosis associated with the emergence of treatment resistance
This repository contains all the code used for the analyses in:
Tepper, A., Vásquez, J., Díaz Dellarossa, C., Ramirez-Mahaluf, J. P., Aguirre, J., Barbagelata, D., ... & Crossley, N... |
aeb54be6cf5af55e6cba045b169c59de5f28b106c254b6f15947072fe5bb2525 | Text | 533 | 8 | # Code to do colocalization analysis of DRD1 and TDT channels
Two main scripts can be used:
1. `drd1Colocalization.m` which will do colocalization analysis on a set of DAPI, DRD1 and TDT images.
2. `drd1ColocalizationRandomShift.m` which will do the same as above, except it will do so over a set number of random trial... |
a37f97c80ecd91c84e00aa3b08542965007c52048e426a3a38c89bf63421440f | Text | 535 | 4 | # grail_switch
This is the code used for preprocessing and analyzing EEG and motion-capturing data for a project investigating the effect of cue modality (data glasses vs. in-ear headphones) on target processing during varying walking difficulties.
The analysis files are ordered consecutively starting with the capital... |
33cef8afd0797c686dacf503bfeca9d0351946c986bfcc65b8646490d2dd80ed | Text | 541 | 9 | # Social_familarity
MATLAB code for Park et al. (in review), identifying the generalization of neural representation of NAcSh-projecting IL neuron during social interaction.
MATLAB R2022b or later version was used to operate the code.
To visualize neural representations, Pycharm community editon 2023. 3.1 version ... |
760445e2b531efdac9ebb9cb2bc555041b823c03d709ba25913814f3c08b229f | Text | 551 | 4 | # scDYMO
This repository supplements the manuscript titled “Analyzing dynamics of metabolism in kidney repair at single-cell resolution”, which presents a method for dynamic analysis of metabolism on tissues at single-cell resolution using MALDI mass spectrometry imaging (MALDI-MSI). The manuscript is currently under r... |
74c94f3af4669253853bda0c1bb923325286c8d81c3176aa08904965f768e50f | Text | 570 | 9 | # Pakula_et_al_24
Repository assosiated with Pakula et al., 2024 'An increase in reactive oxygen species underlies neonatal cerebellum repair'.
## Description of files
NEPs_scRNAseq_processing.R - R code for processing mapped reads to generate a Seurat object with normalised, integrated, clustered and labelled cells
... |
f7e641708a7c6eea76b1b757c63053fb53383b053ee942b509a77a6749cfde74 | Text | 573 | 8 | # funNCion
The program funNCion predicts functional effects of pathogenic variants in voltage-gated sodium and calcium channels encoded by the SCN and CACNA1 gene families.
This repository includes the code and files to perform the machine learning based predictions.
Find out more on the bioRxiv version of our manusc... |
b93e8969f4eaf9d6931c8711f484c926a4337e55029a99ab004a6c73c4570410 | Text | 584 | 9 | # OGRE-pipeline
This is the OGRE (One-Step General Registration and Extraction) pipeline, which is intended to be general-purpose for fMRI data (especially task fMRI) preprocessing. OGRE integrates FSL and FreeSurfer tools for registration, brain extraction, and preprocessing, for subsequent FSL FEAT statistical analy... |
c3e8e4bb778625110fb4fbd42d67853930e9fa42416b39462e4cf9643597abff | Text | 586 | 10 | # Anima-Public
Open source software for medical image processing from the Empenn team
 
Main page for description and documentation: [... |
acb6770f09c77eccd895d2cccb09fc1d6421fdf2c619416384cfc04584b5a3e7 | Text | 604 | 10 | # Annotate m6A modification sites from m6anet
Annotates transcriptomic modification sites with: transcript biotypes, genomic positions and distances to both the upstream and downstream exon boundary using a GTF file.
Please see test_data_m6anet_mod_sites.csv for how the input should be formatted. The output from mult... |
74d79c3eb8be63092d2150ddd94ec343438890fd162af5c1d837e3cc40853f9a | Text | 610 | 4 | The source data (nex) file is large and maintained by the University of Rochester. Ask Marc (https://www.urmc.rochester.edu/labs/schieber.aspx) for the source data accessibility. The repository will not share the data. Each folder's name indicates its function.
- When you get the source data, you can first use `1-nex... |
43d0b5e53b9a12fdff670733e92fc5b538b3fe63945b57ebc576f32f4b0a2bba | Text | 663 | 4 | # 18445759-6e08-41f0-89c5-5953285c5aa2
This repository contains suplementary EEG data and pictures for the article **_"Modulation of alpha and theta waves by social stimuli in virtual educational environments"_** published in **Scientific Reports (ISSN: 2045-2322, Aug. 2025, DOI: [10.1038/s41598-025-13027-x](https://do... |
d8d3843e52d79741b549ac7c4e5bef3b0684a8975f84571ed2fc833294aad821 | Text | 707 | 11 | # Compare m6A modification rates between shared sites in different transcript isoforms encoded by the same gene
Applies a two-proportions z-test on the annotated output from m6anet to test for differences in the modification rates within multiple transcript isoforms that encode the same genomic position.
Requires the... |
40940e42e6ee8c4dba1510d1fabe95fb50b61de5143024d0deb63a9ba8e3f1ba | Text | 723 | 27 | # PGBTR
PGBTR：A powerful and general method for inferring bacterial transcriptional regulatory networks
### PGBTR ###
>Requirement
- Pytorch 1.9.1
- Cuda 11.1 (You can choose the appropriate version of your own GPU)
- scikit-learn 0.24.2
- joblib 1.3.2
- numpy 1.24.4
- pandas 1.4.0
- tqdm 4.66.1
>Usage
#Step1. Co... |
e031062016768f243db4ee75e991689aa38e1d8c3d21dcba6685361f026715b0 | Text | 737 | 19 | # Vessel Distance Mapping (VDM)
## Requirements
Please install (with pip/venv):
- scikit-image (0.17.2; 0.18.1 problems on win10)
- scikit-learn (for clustering/classification)
- pandas (for organizing data in the analysis)
- nibabel (nii-file i/o)
- h5py (h5-file i/o)
- Pillow (image i/o)
The remaining requirements... |
4d3fb6197920df089c9235af28011b34923aeafaa7c195a9c40ba7db265de47a | Text | 742 | 24 | # motortransfer - figures
Data and code for Rezaei et al., 2025 (PLOS Biology).
Dependencies: numpy, pandas, matplotlib, seaborn, scipy, openpyxl, nibabel, brainspace, surfplot, cmasher, natsort.
## Environment setup:
```
git clone https://github.com/alirzar/motortransfer-figs
cd motortransfer-figs/
conda env crea... |
cb6daf7674346e1f6e27133639122e7fc8e7451eaf0a60ae90e3092f9f0c5ab7 | Text | 745 | 18 | # PM2.5 Gap-Filling Methods
## Repository Structure
- `01_data_preprocessing.ipynb` - Data cleaning and preparation
- `02_correlation_analysis.ipynb` - Feature correlation analysis
- `03_gap_filling_evaluation.ipynb` - 46 methods evaluation
- `04_dynamic_models.ipynb` - Adaptive length models
- `05_gap_analysis.ipyn... |
895e113f4f4559c10010917b87b71619a5e14b530dbb88f38f40ede347d0a81f | Text | 769 | 25 | # Face Anonymization with OpenCV and MTCNN
This repository contains different algorithms and methods to anonymize faces in images by blurring or pixelating them using OpenCV and MTCNN in Python. This is particularly useful in situations where privacy and data anonymization is required.
## Installation
First, clone t... |
51dbc3ca908dee6d2b977c9a706ff628e383768b960ce12035e26288e3659865 | Text | 774 | 7 | # MusicianshipEEG
Analysis code for Whiteford et al. (in press, Nature Communications).
Data can be downloaded from the Harvard Dataverse (https://doi.org/10.7910/DVN/SKOWNK) and should be saved in a folder named "Data".
# References
Whiteford, K. L., Baltzell, L. S., Chiu, M., Cooper, J. K., Faucher, S., Goh, P. Y.... |
9a298ff2a9f5752505d6d2fa793cf1be996ee37abdb16ee32ee9d2e69a3d21c3 | Text | 781 | 6 | # 2025_marutani_pd_mouse
Code repository for RNA-seq and proteomics analyses from:
Marutani et al. Hypoxia ameliorates neurodegeneration and movement disorder in a mouse model of Parkinson’s disease. Nature Neuroscience. 2025.
This repository contains code to reproduce analyses and figure panels for the bulk RNA-seq ... |
3b0554ed682b39481cb420c658b9e6ebd5b79526b4ac6fe07ccf18ba50d4cdb5 | Text | 815 | 28 | OCD Modeling
============
Computational model of frontostriatal dynamics in OCD.
This work builds upon our baseline analysis published in Brain [Naze et al. (2022)](https://academic.oup.com/brain/advance-article-abstract/doi/10.1093/brain/awac425/6830574) and the clinical trial analysis published in Nature Mental Hea... |
18b273f96f221f8e5247edf77e288ada02d7869599d18b0c5f55163789319c0e | Text | 857 | 22 | # System requirements
This code has been implemented in Matlab 2024b, using EEGLAB (2021.0) and Fieldtrip (2023-12-20).
# Instructions
To run the scripts, open Matlab and add the additional_functions folder to the path
Use behavior.m to reproduce the behavioral results (Fig. 1). To generate _trlinfo.mat files for... |
657a546ba181d17024e76bbd116ddd3081087584416ee7c0db497cbfd66f5530 | Text | 884 | 16 | # Verbal Coordination and Neural Dynamics
Schwab-Mohamed et al. eLife 2024 "Bridging verbal coordination and neural dynamics" (https://doi.org/10.7554/eLife.99547.3)
This GitHub provides the codes to reproduce the results and figures of the manuscript with Python, Matlab and R. The conditions of our ethics approval d... |
aa63ce7c27ab5f5a2fc0ed7e0db073713358720c5bc4b4b99c3c4a0c5b8a32cb | Text | 885 | 16 | # Park_et_al_2024
This repository contains the code and sample data used in the manuscript titled "Astrocytic modulation of population encoding in mouse visual cortex via GABA transporter 3 revealed by multiplexed CRISPR/Cas9 gene editing", published in *eLife* (https://doi.org/10.7554/eLife.107298.2).
## Repository c... |
15468bb4c9c42b9e61a816904db22443008cbcd2012e22378c8aa77eddaeeeda | Text | 891 | 19 |
This repository contains code and data reported in this article:
Piray P, and Daw ND. Reconciling flexibility and efficiency: medial entorhinal cortex represents a compositional cognitive map, Nature Communications (2025).
GitHub: https://github.com/payampiray/compositional-predictive-map
The model is implemente... |
dfa20616bbf9952024a9c1c65500b279751b5f867148589eab160956139b1d04 | Text | 899 | 23 | # InfoTheory.jl
A Julia package for non-parametric estimation of information theoretic quantities such as entropy and mutual information.
# Usage example
To calculate the entropy of a 1-dimensional, continous, random variable from which we have 4 samples:
using InfoTheory
samples = [1.3 3.7 5.1 2.4]
dif... |
c0f4e1ba3660b4be086f365e7f77650b1ab60fbfb3c1af52f321b74652d75a7c | Text | 904 | 35 | # DM2021
**************
Program description:
to open and analyze spike/EEG/bahavioral database files (all Matlab structures) generated from electrophysiological experiments and to identity multi-cell firing sequence and replay events.
**************
Getting started
--------------
Prerequisites
Matlab (R2019a o... |
c26228dfec71cbda4dd24f5bab1d501b56d7ebb4f953b27f29b6e2d94e35c7a6 | Text | 944 | 17 | # MEGLyon Experiment Runner
Runs experiment created using MEGLyon
atm still under construction.
Run on Windows:
- open Anaconda3 shell (Terminal; NOT Powershell)
- type `cd <drag and drop meglyon-experiment-runner-folder here>` and hit ENTER
- type `python <drag and drop new_subject.py here> <subject ID>` and hit EN... |
065b61161994ec5df786e08d2af51ecc425087773402de236aa2a4346763d5cc | Text | 951 | 50 |
AwA Pose Dataset:
============
Download Images
------------
Download images from https://cvml.ist.ac.at/AwA2/
Download Annotations
------------
```bash
git clone https://github.com/prinik/AwA-Pose.git
```
Read pickle annotation file
------------
```bash
import pickle
with open('antelope_1234.pickle', 'rb') as f:
... |
48b79a05d765e9b89f92b4ffc313c530ff67b60d37cbb80bee96793846471e18 | Text | 968 | 20 | # PLR_RGC_analysis
This repository contains all the code used for analyzing the data and generating the plots present in the manuscript with title:
"Pupil-induced retinal binocularity potentiates low-contrast vision".
Each folder contains the code used for a specific experiment or type of analysis described in the ... |
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