sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
763e91ad522ad9d9ee9c2ae237981f31fdaf7afed2edfa1e03fcc261a3fc77dd | Text | 1,040 | 20 | Luo Lab fork with some customizations of [dixonlab/Taurus-MH](https://github.com/dixonlab/Taurus-MH).
* * *
# Taurus-MH
TAURUS-MH (Two-step Alignment with Unmapped Reads Using read Splitting for Methyl-HiC) is a mapping pipeline for methyl-3C/methyl-HiC data using a hybrid of ungapped and manual read splitting align... |
b135ec40e3f4840a9ec20d877f93be0278e3bc41dd619cb65339c315ed7f4b49 | Text | 1,042 | 26 | # A-causal-role-of-rDLPFC-in-random-exploration
Project name:
"A Causal Role of rDLPFC in random exploration"
Published in Scientific reports: " https://doi.org/10.1038/s41598-024-76025-5 "
felow chart of data-analysis:
step 1: pre-process the data for each participant (converting to CSV, removing redundant parts, c... |
93068d477bf472e7d3a886901aed5a3a30ccdeefec54b185689029132722dd60 | Text | 1,043 | 5 | # Abstract
Machine learning technology spans many areas and today plays a significant role in addressing a wide range of problems in critical domains, i.e., healthcare, autonomous driving, finance, manufacturing, cybersecurity, etc. Metamorphic Testing (MT) is considered a simple but very powerful approach in testing s... |
243e3ec52c80a7e5b579338964c018367c6c1abe18bb24cca3395eb63121f03f | Text | 1,044 | 24 | # Lasso-ML: Machine Learning Code for Stroke Study
## Overview
This repository contains machine learning code focused on a stroke study using Lasso regression techniques. It includes data preprocessing, model training, cross-validation, and statistical analysis.
## Contents
- `externalTest.ipynb`: Code for external t... |
18715b8302e4bb28b0d4541d2e52e10cfc14797368d5505be2c384a5667d56ea | Text | 1,048 | 12 | # watsons_u2
WATSONS_U2: Performs a permutation test based on Watson's U2 statistic for 2-sample testing of circular data.
The 2 functions provided perform a nonparametric permutation test based on Watson's U2 statistic for 2-sample testing of circular data (angles).
Watsons_U2 computes Watson's U2 statistic for 2 sa... |
1e3fc0ce45f77235af8bff65ec50601aee471d3a64c9d254718391ce5f12b9fe | Text | 1,054 | 36 | # Polarbear
Polarbear translates between different single-cell data modalities
install polarbear conda environment (in linux)
```
conda env create -f environment_polarbear.yml
conda activate polarbear
```
download data... |
302a8885b65c13aa2a952b3d55d6aa3fc6e61492672a81c22ff7cf8e08d6c607 | Text | 1,076 | 19 |
Codes used for validating the aSAGA model with Dreem Open Data.
Journal article available at https://onlinelibrary.wiley.com/doi/10.1111/jsr.14362
Preprint available at [, a Neural oscillations detection method
Codes for our simulation study and example hippocampal data are included.
# Information
The Matlab function of CHO is in the 'functions' folder.
Please run add_path.m file to run the following codes.
The simulation... |
3412ccd7022819c8c9db4fb5fb8e8185f060c1eda9805572774518d43377f8a3 | Text | 1,089 | 4 | ###### **Overview**
The code files in this directory are for the lower computer of the ESCIM hardware testing system, which needs to run on the ESCIM hardware platform. The ESCIM hardware system is designed for testing the 4K ReRAM array (128Row x 32Column). This system comprises three components: the upper computer pr... |
94853f595e5d0d4c9e8f5d84d329eb11e93e4159e06fd2b51326e8915e343a8a | Text | 1,094 | 14 | Distinct catecholaminergic pathways projecting to hippocampal CA1 transmit contrasting signals during navigation in familiar and novel environments
DOI: https://doi.org/10.7554/eLife.95213.4
Chad Heer, Mark Sheffield
The Department of Neurobiology, The University of Chicago, Chicago, United States
All code used in the... |
5d00dd46e2cde7389528421435aa45645acebcaf80304afadc00fcf421c8aa26 | Text | 1,098 | 23 | Dependencies
# Name Version
pytorch 1.12.1
tensorflow 1.14.0
anaconda-client 1.11.0
anaconda-navigator 1.9.2
tensorflow-base 1.14.0
tensorflow-estimator 1.14.... |
88f850e1ffae46bdc51ef61f1679abf8043e5fca5d9a04f98c506a8d18cd05b4 | Text | 1,105 | 12 | Each of the files:
- 1_electrophysiology_beforeKCl.txt
- 2_electrophysiology_duringKCl.txt
- 3_electrophysiology_afterKCl.txt
contains electrophysiological data acquired by the 32 channels of a microelectrode array. The spontaneous neural activity of neural spheroids was recorded with a commercial system (MEA-2100,... |
3c8c5e7008ddbfb30bd286d0450fcdc9931911fd3728a5f2abe01bc01b900fe9 | Text | 1,111 | 30 | # Tools for Auditory Pathway Neuroimage Analysis
This package provides tools for structural image analysis of the auditory
pathway using diffusion MRI. Built using the [Quantitative Imaging Toolkit
(QIT)](http://cabeen.io/qitwiki).
## Tutorial
In progress!
## Dependencies
The makes use of the following packages, w... |
2ccf91d0937dcafb0b05dcdc4cb87718ae4f6707a79a700993ac73b1d4e8dd92 | Text | 1,120 | 34 | ## ACBC Chip
This repository provides additional details pertaining to the ACBC chip used to capture, identify and phenotype bacteria from very dillute samples:
https://doi.org/10.1039/D4LC00325J
<div align="center">
<img src="./images/ecoli_gif.gif" alt="E. coli trapping" width="240" />
</div>
## Fluidics
For fl... |
38c76532a50d1c5673b4e49149108837152550f4dfc610110daade90ecd5feb3 | Text | 1,125 | 12 | ## Directory and File Descriptions
- **`Classification_validation/`**: This directory contains the code and results for classification tasks. It includes scripts for training classification models, evaluating their performance, and storing the output of the classification processes.
- **`discover-eeg-master/`**: Thi... |
51d45913a6b07535878f5d4b2b946ed43a2124f61095313338d0646fb188d07a | Text | 1,132 | 31 | # NAILS
Algorithm to identify color variations from fingernails using A.I.
We present an algorithm that allows to identify color variations from fingernails using Artificial Intelligence (A.I.). Healthy nails have a uniform color and are visually smooth. However, as one ages, nails may become more brittle and may have... |
23c419b870c0569e3d06eba2c66cbe9f6b40870742efa9ed6120486d8e6bc772 | Text | 1,143 | 26 | # osNMF: Unsupervised pattern discovery in spatial gene expression atlas reveals mouse brain regions beyond established ontology
Authors: Robert Cahill, Yu Wang, Alex Lee, Hongkui Zeng, Bin Yu, Bosiljka Tasic, Reza Abbasi-Asl
Manuscript link on BioRxiv: https://www.biorxiv.org/content/10.1101/2023.03.10.531984v1
## ... |
dbe5a07ec07cb3e57d9d2d33c24aaa32b5986deda098e19a3530172321a5b7f4 | Text | 1,144 | 12 | # [SOX2-driven enhancer landscape defines the transcriptional architecture of retinogenesis](https://doi.org/10.1242/dev.204986)
This repository is organized by the figures in the publication.
## Sequencing Data
The sequencing data have been deposited in the NCBI Gene Expression Omnibus
(GEO) database under accession... |
7e46eb1678a57a64e55953d9fee8ddd3617886b1fb05ae5a600fffa15553812d | Text | 1,145 | 33 | #  NIRFASTer
Open source software for multi-modal optical molecular imaging
## MATLAB Compatibility
May not work on MATLAB versions earlier than R2016b.
## CUDA Compatibility
- Compute Capability >= 3.0.
> A... |
f2318258f3d646e3f8fd961914b965ceeb5c7007b4fb8398cd6e7152bb073736 | Text | 1,146 | 14 | ACRs
====
This repository hosts the bioinformatic analysis worklow used in [Oppermann et al, **Robust Optogenetic Inhibition with Red-light-sensitive Anion-conducting Channelrhodopsins**, *eLife*](https://doi.org/10.7554/eLife.90100).
The [snakemake](https://snakemake.readthedocs.io/)-based code for the workflow is u... |
0473cd116be3d97cd69485b984bb0e0fc3b0218f26582cfb5e3d588aab64c3b1 | Text | 1,160 | 6 | [](https://zenodo.org/doi/10.5281/zenodo.12797409)
# Cell-Specific-Effects-of-Temporal-Interference-Stimulation-on-Cortical-Function-Code
The Code for the Computational Studies done in the paper "Cell-Specific-Effects-of-Temporal-Interference-Stimulation-on-Cortical-Functi... |
3baadff972305413704826e4124a00a5d268f543f479390dbc4bcff58fd37c03 | Text | 1,166 | 9 | # ADClassificationWithHetergenousData
This code is associated with the following paper titled
"Normalized Group Activations Based Feature Extraction Technique using Heterogeneous Data for Alzheimer’s Disease Classification"
The study proposes a novel deep learning approach for identifying Alzheimer's disease (AD) patt... |
7f39e45577c759a243e44fd48e81675673bd2fcd141f278e95567253a20a5e27 | Text | 1,174 | 7 | # Population genetic inference with Convolutional Neural Networks
This directory contains code for training and testing the neural networks described in this paper: _The Unreasonable Effectiveness of Convolutional Neural Networks in Population Genetic Inference_
by Lex Flagel, Yaniv Brandvain, and Daniel Schrider. htt... |
7f6f567c44e09e3765079889438c1ffc46af5193aea9226fef1fe7f0d1938aa1 | Text | 1,187 | 25 | # MARA
MARA ("Multiple Artifact Rejection Algorithm") is an open-source [EEGLAB](http://sccn.ucsd.edu/eeglab/) plug-in which automatizes the process of hand-labeling independent components for artifact
rejection.
The core of MARA is a supervised machine learning algorithm that learns from expert ratings of 12... |
e3a9b4ae9cc3ea09b296612b46b4ba413fcf6077fb450d38f9d783e149ed608f | Text | 1,205 | 29 | # animacy-perception
This is the code for the paper "A computational deep learning investigation of animacy perception in the human brain", currently in revision.
The original code was developed by Stefanie Duyck and can be found [here](https://github.com/SDuyck/animacy-perception).
## How to use:
### Get the data
A... |
6c35e3792bfa23783052be06638978e1e2d70bb8de6712bd33a92a99c53cc999 | Text | 1,211 | 18 | # Tillmon-et-al-microglia-scRNAseq-2024
#### Code to perform analysis for scRNA data described in:
### [**Complement and microglia activation mediates stress-induced synapse loss in layer 2/3 of the medial prefrontal cortex(*bioRvix*)**](https://doi.org/10.1101/2023.06.28.546889)
Haven Tillmon<sup>1</sup>, Breeann... |
e24f106019c104c42c82995843ffa45353f1c2b74bb9496ec96f12b46e38cc2d | Text | 1,213 | 21 | [](https://doi.org/10.5281/zenodo.13880099)
# Molecular simulations of the N-terminal domain of CPEB4
This repository contains Python code, [Jupyter](http://jupyter.org) Notebooks, and simulation data for reproducing the simulation results of the manuscr... |
70467869c26a17b8f2ddb3fabb2947df1250a544b6254c938528870dd657ec96 | Text | 1,216 | 31 | <p align="center">
<img src="https://github.com/caticoa3/malaria_hero/blob/master/images/malaria_hero.jpg?raw=true" alt="Malaria Hero"/ width="430">
</p>
Modified image from the [Center For Infectious Disease Research](https://www.cidresearch.org/blog/human-vs-pathogen-the-art-of-battling-infectious-disease)
## Mal... |
41d403f7e027e588236dc3b17e62af295dee1aea73e7f8feee0ab8ecf3ceb6a3 | Text | 1,217 | 35 | # PRiMeR
Code for the paper: [Genetics-driven Risk Predictions with Differentiable Mendelian Randomization](https://www.biorxiv.org/content/10.1101/2024.03.06.583727v1)
Accepted at RECOMB 2024 as a [Conference Paper](https://recomb.org/recomb2024/accepted_papers.html) (title: "Disease Risk Predictions with Differenti... |
57ec1028e15aa4613d31e5d65a841ec2f038963a315fd53c6928c89247411310 | Text | 1,220 | 50 | # Pyclamp
## Installation:
This code is intended for a GNU/Linux environment. It has not been tested
outside GNU/Linux. A version of Python version >= 3.11 is required and
the graphical user interfaces requires Qt6 to be installed within the
GNU/Linux along with associated dependencies (such the glib2 development
pa... |
124ced655f8e09781c4dd8c518b9328a6eb7ec508b94552c1ea642a5edf90ad5 | Text | 1,223 | 17 | This project has created a set of program files that can be used to extract step count data from multiple .tif files in a directory.
The user should first use the batch measure intensities imagej macro to extract the z projection profiles of all the spots in their files.
- The detection threshold should be previou... |
5bc8d271a07473c141a8234ad718ebad9c733161c013689e4e4fc67d2dd08a82 | Text | 1,239 | 25 | ReadMe for data and code repository for manuscript "Membrane potential states gate synaptic consolidation in human neocortex":
System requirements:
- Prefereably RStudio is available (We used RStudio 2022.07.2, Build 576 & R version 4.2.1)
- R Studio should be available for all common operating systems (we used Wi... |
3b7bd4442b7633c7356199537780286a68fcf51e00097a43fec7d0a3543e17a6 | Text | 1,241 | 8 | # Axonal-PathFinding
This repository contains the ABAQUS VUMAT subroutine code for modeling axonal growth and pathfinding during brain development. The folder "Abaqus_inp_sample" includes a sample geometrical input file. This code has been tested on Abaqus 2019. To run the Abaqus job, use the following command:
Abaqus... |
737292a2e56222b6512bc8df83ccafa94fea25b889de074323c15c445340408c | Text | 1,262 | 60 | # ETFT (Equiangular Tight Frame Transformer)
This project implements "ETFT: Equiangular Tight Frame Transformer for Imbalanced Semantic Segmentation".
---
## Table of Contents
- [Installation](#installation)
- [Training](#training)
- [Testing](#testing)
- [Results](#results)... |
c0e2fe96ba9341b939456fa3743f4cfa1bfcd2ab41c3dfc61a547113f8cc7bcb | Text | 1,263 | 20 | # Hierarchical quantitative analysis of Cerebrovasculature
An automatic deep-learning model-centric pipeline for hierarchical quantitative analysis of cerebrovascular structures is proposed to extract vascular (and also cortical) features hierarchically from 1) whole brain, 2) four common vascular regions including an... |
35e51e385077b4b4dabc29e2b8dece1b438c4c26d7c134d4af9ef2bc1ed03ba6 | Text | 1,266 | 42 |
<!-- README.md is generated from README.Rmd. Please edit that file -->
# Pupilla
<!-- badges: start -->
<!-- badges: end -->
An R package for the processing and analysis of eye-tracking and
pupillometry data.
## Installation
The package is currently available through
[GitHub](https://github.com/). The installati... |
f5679b6b53d1a5c94174c71de226e0109770f69696c9dedfa806b922a2cd55f9 | Text | 1,268 | 32 | # PV selectivity
Neural network models for Hong et al., [Calcium-permeable AMPA receptors govern PV neuron feature selectivity](https://www.nature.com/articles/s41586-024-08027-2), Nature, 2024-10.
## Setup
This software has been tested on Ubuntu 18... |
4d275cbef32cceb438dcf99488f6cdc8b9532e5dc5481cd2e3e19cecfd6ae736 | Text | 1,271 | 12 | This is the repository for the paper Dose distribution of proton therapy plans are robust against lowering the resolution of CTs in combination with increasing noise.
The folder data contains first the CT dicom image files for the different filters and pixelsizes used and second the gamma CT data from the FDG and Ga e... |
bdeaa704bb87a288bc30173cb7dc1da289ae80873e7086987e1f4a4d3a0f62b7 | Text | 1,271 | 31 | # Signatures of criticality in efficient coding networks
This repository gathers code for the paper:
[Signatures of criticality in efficient coding networks, S.Safavi, M Chalk, N. K. Logothetis, and A. Levina. PNAS 2024 (in press)](https://www.biorxiv.org/content/10.1101/2023.02.14.528465v1.abstract)
Matlab codes pr... |
73d0ea1316c60bc2c7ebcd493ceb58d10e19f6b86256b48d9b21b6d5ab1735ae | Text | 1,274 | 34 | # Retinal-Microglia-Segmentation
## Overview
This project provides a workflow for segmenting retinal microglia in Alzheimer's Disease (AD) datasets using a random forest classifier, trained with Ilastik. The code in this repository automates segmentation and quality control, enabling quantitative analysis of microgli... |
2de25a0703e943f36afa1ccd75e7b2be58c2ff70b274f4e3c89bbf33bb83df92 | Text | 1,276 | 27 | # Distributed representations of behaviorally relevant object dimensions in the human visual system
This repository contains the analysis code used for the paper "[Distributed representations of behaviorally relevant object dimensions in the human visual system](https://doi.org/10.1101/2023.08.23.553812)." by O. Conti... |
e47d84c508a09c74600677a057d3125726d2a5c3f9f6d73901fa0ebf2cacde49 | Text | 1,277 | 36 | ChunkFlow.jl 
==============
[](https://travis-ci.org/seung-lab/ChunkFlow.jl)
> Note that this package was deprecated in favor of <a href="https://github.com/seung-lab/chunkflow">python ch... |
7bb70d2cd13dddfdd1d63558144ffa179aa6b95dae0c242bcfc7f4b9b0ba2cb1 | Text | 1,278 | 36 | # koplenig-reply
[](https://doi.org/10.5281/zenodo.7752933)
This repository contains data and data analysis code for the following paper:
> Kauhanen, H., Einhaus, S. & Walkden, G. (2022) Language structure is influenced by the proportion of non-native sp... |
6527da6ca90cee51273effb73d17c4e15dd575f36928906ba95470c89c70fd20 | Text | 1,279 | 30 | # dCCov_rsfMRI
To reproduce the main figures of the study, follow these steps:
1. Python Version and Package Requirements:
Make sure you have Python 2.7 installed on your system.
Ensure you have the following packages installed: numpy, scipy, matplotlib, pickle, sklearn, and joblib.
2. Data:
The ... |
a02c3e96688bf3fe35b9fc9015f6d5b5d73532d9ad6d8821d3da64cdaa290580 | Text | 1,286 | 19 | # scScreens_ADARs
Investigating ADAR mediated A-to-I editing in fetal and fetal-like tissue such as organoids and teratoma
Code to reproduce the analysis seen in manuscript: Charting and probing the activity of ADARs in human development and cell-fate specification (Dailamy, Lyu et al.)
## Referenced Packages
1. scRN... |
a91bb18a56efa7035063e6db7ecfec8dd56a9b967cea128a7507f9b77d3a6ee2 | Text | 1,294 | 26 | # soundsig
Sound Signal Processing and BioSound.
# Content
The package has routines to perform signal analysis on time series and sond waveforms in particular. It includes:
Spectrogram
Modulation Power Spectrum
Coherence
Filtering
Power spectrum
Fundamental Estimation
The BioSound class is used to represent a b... |
3a1b8dc9425c2f284ab0b6ce2dcd4726f2e726c2fc7128460df609428329efe4 | Text | 1,295 | 9 | # nireject-publication
Artifact repository of NiReject publication
## Description
This repository contains artifacts generated from MLflow experiments (Q1, Q2, Q3, Q4) in zipped files, as well as the configuration files for the experiments.
## Licence
<p xmlns:cc="http://creativecommons.org/ns#" xmlns:dct="http://pu... |
92b5a5a54a62c82b9402010104e41069741f3c53980c82c8cb0d465e633f3798 | Text | 1,298 | 31 | # Neonatal apnea and hypopnea prediction in infants with Robin sequence with neural additive models for time series
<img src="overview_figure.png"
alt="Figure 1"
style="float: left; margin-right: 10px;" />
This repository contains the code for the paper ["Neonatal apnea and hypopnea prediction in infants w... |
f75f241b67c57339ca025a4e4da19b304669354880635960b4258c04b87df73b | Text | 1,298 | 33 |
[](https://doi.org/10.5281/zenodo.14165546)
# animacy-perception
This is the code for the paper "A computational deep learning investigation of animacy perception in the human brain", currently in revision.
The original code was developed by Stefanie Duyck and can be f... |
cdb439ff67536099964256e820774b7c45fd7e38b16324fb50844effe7ece76e | Text | 1,300 | 19 | # FB_model
All code and files used to reproduce the original results in Doorn et al. 2024: Breaking the Burst: Origins of Fragmented Network Bursts in Patient-derived Neurons Revealed
Preprint van be found here: https://www.biorxiv.org/content/10.1101/2024.02.28.582501v1
## Computational models
The realistic computa... |
443e5b7e3331667654e8890bee9554974ec971d69b8aa9fb08fcceb76e3affb1 | Text | 1,305 | 35 | # Myonset Package
Myonset is a python package to process and detect signal burst(s) onset and offset, especially developed for electromyographic (EMG) signal.
Myonset implements tools for signal preprocessing, automatic onset and offset detection, as well as vizualisation and correction of onset and offset latencies.... |
60ef647bb482f0cf8fadfb24270f4bd2343aeae61ab8fd6b275350fac513ef18 | Text | 1,310 | 10 | # FAST-IRES
An Electromagnetic Source Imaging Algorithm for Estimating Extended Brain Sources and Large-scale Networks
This readme document describes software codes and testing human data, which have been developed under support from the National Institutes of Health via grants NS096761, EB021027, MH114233, AT009263 a... |
22421935db719a692ac049737922b75f6f97345b0f4bb5be38a0f51d438d54e8 | Text | 1,322 | 27 | The following is the README for the “MEG - Prestimulus” dataset.
\===================
\## License details
Data usage is restricted to academic and non-commercial research upon appropriate attribution. All data provided are licensed under CC-BY-NC-SA.
Data collection was conducted by the researchers of IRCCS San Cam... |
5439c725b081f5ff7dce13ae8784d11d44b0ffd645060620c6ff566540cb085c | Text | 1,324 | 37 | # PRiMeR
Code for the paper: "Genetics-driven Risk Predictions leveraging the Mendelian Randomization framework" presented at [RECOMB 2024](https://recomb.org/recomb2024/accepted_papers.html) and published in [Genome Research](https://www.genome.org/cgi/doi/10.1101/gr.279252.124)
## Citation
If you find our code usef... |
a9337df6d6d3a336f3011cfc28b7d2bdc956a528c91a2ec8761622c571196132 | Text | 1,324 | 18 | # Real-time phase detection for closed-loop EEG-TMS
Matlab Codes for resting-state EEG recording and 3 methods of real-time EEG phase estimation for closed-loop EEG-TMS:
1) Autoregression-based prediction (AR),
2) FFT-based prediction (FFT), and
3) Educated Temporal Prediction (ETP).
Real-time EEG data acquisition is... |
ca6930d505c86a5d998cb8bc555b2644a9902cd3cd4eb5bb66337062c3a9009f | Text | 1,325 | 22 | ## BrainQCNet [version for CPU] : Detection of Artifacts on Brain T1-weighted Scans
<img src="https://github.com/garciaml/BrainQCNet/blob/master/T1_low_quality_2.jpg" width="3000px">
For more information about the specification of BIDS Apps see [here](https://docs.google.com/document/d/1E1Wi5ONvOVVnGhj21S1bmJJ4kyHFT7t... |
e867490b5de9a5d9a15005716e86ee5685931d8e725f6ba7d541ae3742b8ca48 | Text | 1,331 | 11 | # Characterization and closed-loop control of infrared thalamocortical stimulation produces spatially constrained single-unit responses
Source code for Coventry et al Characterization and closed-loop control of infrared thalamocortical stimulation produces spatially constrained single-unit responses. This repository in... |
88d70b7008713cb8f6e7e189a6539d7bc45446718a07b154e2a997f9f065f59e | Text | 1,337 | 41 | # Tridy
A pipeline for classifying binary dynamics on digraphs using closed neighbourhoods, proposed in:
[An application of neighbourhoods in digraphs to the classification of binary dynamics](https://arxiv.org/abs/2104.06519)
Pedro Conceição, Dejan Govc, Jānis Lazovskis, Ran Levi, Henri Riihimäki, and Jason P. Smit... |
b45f8414ca5c486695b0bbf3600d192dae8c0fe0e077d7a0037c0673d4567541 | Text | 1,342 | 26 | # Welcome to the Computational Brain Imaging Group (CBIG) repository!
We are from [Thomas Yeo's Computational Brain Imaging Group (CBIG)](https://sites.google.com/view/yeolab).
CBIG repository is a package that provides the following useful tools:
1. fMRI preprocessing pipeline
2. Brain parcellations and algorithms... |
3ffd5468b53220af95cc9515f430d0b4312587c794777bf181db869990c66644 | Text | 1,343 | 32 | Directory structure of the deposit:
code The python codes used in this study
eval_output The output of evaluation
GRCh37_coordinates The genome coordinate BED files of the on target, probe design and the chunks used to dissect the data
NN_summary The model summary for ea... |
669a8068e875dd37696d2adec565fcafaa16cf59fa6998cf8bd5cc9b292325ef | Text | 1,348 | 61 | # Sameer
Program to get mapping statistics, generate consensus and to get low frequency variats from a sam file.
## Installation
```
git clone https://github.com/vbsreenu/Sameer.git
cd Sameer
cc sameer_new.c -o SAMEER_NEW
chmod +x SameerReport
chmod +x *.R
```
** Set the path to the installation directory to access ... |
4f2c4b99f631f1cfe65a84f286ef44d67c6db2891e8ced894e238f12159ed171 | Text | 1,349 | 25 | # AdaMedGraph
Official code for AdaMedGraph and Personalized Progression Modelling and Prediction in Parkinson's Disease with a Novel Multi-Modal Graph Approach
## This project is divided into four main parts:
### Data Processing:
Description: This folder encompasses all the necessary code for processing the PPMI an... |
76d472d320907abfa383d03f652d09f2c589905b860a12c4d89792601ce8a154 | Text | 1,353 | 33 | # DCE-NET
Framework for estimating DCE-MRI physiological parameters.
## Getting Started:
To create the environment **dce** in anaconda, the following command can be used:
```bash
conda env create -f environment.yml
```
## Simulations:
Executing the framework on simulations can be done using **main.py**.
```
usage: m... |
f7a863fe432270939f61ab243b3020343261c2537886ff6baa530aecfbf6f84f | Text | 1,353 | 22 | ## BrainQCNet [version for GPU compatible with CUDA, CuDNN] : Detection of Artifacts on Brain T1-weighted Scans
<img src="https://github.com/garciaml/BrainQCNet/blob/master/T1_low_quality_2.jpg" width="3000px">
For more information about the specification of BIDS Apps see [here](https://docs.google.com/document/d/1E1W... |
edcd9ada20a6e97a54294584d174b5fc55eaafc093c3482b3fee881524388ca1 | Text | 1,355 | 50 | # Period Amplitude Analysis (PAA) EEGlab Plugin
Method for detecting slow waves using GUI in EEGlab for MATLAB
## Getting Started
These instructions will get you a copy of the project up and running on your local machine for development and testing purposes.
### Prerequisites
Mac, PC and Linux compatible.
Design... |
b8d8ea96baca827a44688d85163bdccc02b798735801a6e6685a549271d0d55f | Text | 1,379 | 58 | # Codex - Connectome Data Explorer for FlyWire
## Description
[Codex](https://codex.flywire.ai) is a web application for exploring and analyzing neurons and
annotations from t... |
99e319cbccc2e5013f8329467ea866b00dc1e512b75a7d0d7b6961317a6c8ef6 | Text | 1,381 | 21 | # Data description for the paper: What makes a language easy to deep-learn? Deep neural networks and humans similarly benefit from compositional structure
## Files
- `llm_mem_data.csv` holds the memorization test results from GPT-3.5 model text-davinci-003
- `llm_reg_data.csv` holds the generalization test results fr... |
68d8838a3ec03ecb12f205869a089b70100ed162fc0b9fb5ffdf31de6c56b854 | Text | 1,382 | 39 | # phenoscanner
phenoscanner allows users to query the PhenoScanner database of genotype-phenotype associations from inside R.
## Functions
* phenoscanner - this function allows users to query the PhenoScanner database from inside R
## Installation
1. install.packages("devtools")
2. library(devtools)
3. install_gith... |
75ac20d151c003716275fb9a44ae215c81a7290f77b96d3b6275167638785e60 | Text | 1,398 | 33 | Code associated with Yu GJ, Ranieri F, Di Lazzaro V, Sommer MA, Peterchev AV, Grill WM (2024)
"Circuits and mechanisms for TMS-induced corticospinal waves: Connecting sensitivity analysis to the network graph"
1. Install python dependencies (recommended to install into a virtual environment).
2. Full data generat... |
9ec0b472c648e283fff93a8cf512cd530229f11a893a5132434db40bd08bb685 | Text | 1,407 | 46 | .. -*- mode: rst -*-
|Build|_ |black|_
.. |Build| image:: https://github.com/vedb/pupil_recording_interface/workflows/build/badge.svg
.. _Build: https://github.com/vedb/pupil_recording_interface/actions
.. |black| image:: https://img.shields.io/badge/code%20style-black-000000.svg
.. _black: https://github.com/psf/bl... |
ada5dfd7c1a89266feccf8434480a93b753d034af1f15007b96881fd5c4b9bb2 | Text | 1,412 | 54 |
<!-- README.md is generated from README.Rmd. Please edit that file -->
# hot.dots
<!-- badges: start -->
[](https://zenodo.org/badge/latestdoi/252715866)
<!-- badges: end -->
This package provides the code used in Fabre et al 2020
(<https://doi.org/10.1038/s41559-020-1... |
624bb26d681c14d845719f874f75fbff89992c9d4097f4b6b5298fd0367888b4 | Text | 1,443 | 63 | # Brunner-Munzel-test-for-matlab
Brunner Munzel test for matlab (adapted to matlab from https://github.com/toshi-ara/brunnermunzel ).
Files:
approxbrunnermunzel.m
permutedbrunnermunzel.m
## Test data:
**x=[1,2,1,1,1,1,1,1,1,1,2,4,1,1]; y=[3,3,4,3,1,2,3,1,1,5,4];**
**result=approxbrunnermunzel(x,y,1); % 2-sided t... |
131d2839a49574c1226bcb7dbbc7e2f80bbc717b9116aee341838ec3ec2628a0 | Text | 1,446 | 48 | Larvae Behavior Analysis & Classifier Prediction
This project analyzes larvae behavior and classifies it using pre-trained models. It consists of two main scripts: one for behavior analysis and another for prediction based on pre-extracted features.
1. Larvae Behavior Analysis
Install the required Python packages:
... |
4b39a025cd28f4147c6e16fa1636e4ca049cd4ba03a5d3333473f1a985c10e1d | Text | 1,451 | 55 |
<!-- README.md is generated from README.Rmd. Please edit that file -->
# hot.dots
<!-- badges: start -->
<!-- badges: end -->
This paackage provides the code used in Fabre et al 2020 to calculate
per-landmark rate and variance
## Installation
You can install the development version of hot.dots from
[GitHub](http... |
8fcb8f249167bae88760a66b2aed172123ee9390336bcad45f6fa988e24512fa | Text | 1,461 | 39 | # DATTNet<br />
Coder for "DATTNet: a Dual-Attention Transformer-based hybrid network for medical image segmentation"<br />
## 0.Overview
## 1.Environment<br />
Please prepare an environment with Ubuntu 20.04, PyTorch 1.11.0+cu113 and CUDA ... |
64d15e5afb832c9d00ebe91be104807c9be010403a361458a82e25aef950c340 | Text | 1,468 | 30 | # Cobolt: Joint analysis of multimodal single-cell sequencing data
Cobolt is a Python package for
1. the analysis of the single-cell data from joint-modality platforms;
2. the integration of joint-modality single-cell datasets with single-omic data sets.
## Introduction
Cobolt is a metho... |
37422945429866e85e3baf9aeb29a1e907530280c19bcc73c1065584e734d21f | Text | 1,487 | 59 | %% GUAN et al. 2022. smFish analysis source code related to star Method smFish analysis
%% ImSAnE installation instructions
Download ZIP
Extract the ZIP
Set the file path wherever you want
E.g. C:\ImSAnE in windows or \User\Shared\ImSAnE
create a subfolder within ImSAnE, rename it as /external
copy the following... |
c7e10a1b9105d82f12c1187a3aa2057996382f6809fdbc14663d2b916d276209 | Text | 1,490 | 22 | # Analysis code for the article, [Cognitive control & the anterior cingulate cortex: necessity & coherence](URL)
1) [Graph lesion deficit mapping of fluency](gLDM_fluency.ipynb)
*Graph lesion-deficit mapping of phonemic fluency showing the behaviour-associated mean edge weights for stochasti... |
8d3c6a440151169243afb3e2512781ee062dd1492b9044b5a8df37de24a49f6f | Text | 1,494 | 24 | This repository contains the behavioral and MEG analyses associated with the paper:<br>
<strong>Anticipatory and evoked visual cortical dynamics of voluntary temporal attention</strong><br> by Rachel Denison\*, Karen Tian\*, David Heeger, and Marisa Carrasco<br><br> <a href="https://www.biorxiv.org/content/10.1101/202... |
0356f06ac797061ef05da5a4006414d75f695f548b56e77ee1ecb9571c1ff416 | Text | 1,495 | 50 | Unsupervised Learning for GW (autoencoder)
==========
# Package requirements
The Python packages below are required:
- [gpaw](https://wiki.fysik.dtu.dk/gpaw/) 21.1.1
- [ase](https://wiki.fysik.dtu.dk/ase/) 3.22
- [numpy](https://numpy.org/) 1.19.4
- [pandas](https://pandas.pydata.org/) 1.1.4
- h5py
## DFT-GW:
`cond... |
238d4688589f71966ed1ab221b50e05b597da1705adf4ec7179ff871ba81abb3 | Text | 1,497 | 36 | # Hi-C_ML_structure-dynamics
# Code Requirements
Ensure you have the following Python packages installed to run the code:
1. [numpy](https://numpy.org/)
2. [tensorflow](https://www.tensorflow.org/)
3. [scikit-learn](https://scikit-learn.org/stable/)
## Structure Folder
Inside the **structure** folder, you'll find ... |
a0bfdda2cd81ad4ad5f93e8da42452392c95fa1c4debfc43f35a78ccbb631190 | Text | 1,498 | 35 | METAMER CODE
This package includes code used to analyze images and
generate metamers using the model described in:
Freeman, J & Simoncelli, EP (2011) Metamers of the ventral stream.
Nature Neuroscience, 14 (9)
The model analyzes local, higher-order statistics that capture properties
of visual textures and are thoug... |
1f7f9adfdfa66d9467c894b854a4f059b63ba1d32ca35ebd65bfc65ff7b09cb3 | Text | 1,507 | 32 | # Mesocircuit Model
[](https://mesocircuit-model.readthedocs.io/en/latest/?badge=latest)
<p align="center">
<img src="docs/source/_static/images/network_model_sketch_upscaled.png" alt="Mesocircuit network model sketch" wi... |
c389c1b195e1a75c1924034a8f3a7f9fa91712b930c5b83dbaaa9bb2d03ec89e | Text | 1,510 | 28 | # Single-cell Regulatory-driven Clustering (scregclust)
<!-- badges: start -->
[](https://CRAN.R-project.org/package=scregclust)
<!-- badges: end -->
![A diagram illustrating the *scregclust* algorithm.](man/figures/overview_fig1A_bg.png "Illustration of... |
bd6adbd0b343fda5b3c8917b1c3b89e470f4a23769045fd51a1ff8e11519d528 | Text | 1,518 | 16 | # RFEAIC
A tool for feature selection based in Recursive Feature Elimination and Akaike Information Criterion
cite this with:
https://doi.org/10.3390/diagnostics14151623
MDPI and ACS Style
Morgan-Benita, J.A.; Celaya-Padilla, J.M.; Luna-García, H.; Galván-Tejada, C.E.; Cruz, M.; Galván-Tejada, J.I.; Gamboa-Rosales, H.... |
7dcd22c94f9ea00e012e4a490e4e8728d00d55dc7da2e4ab463d799c9976c9ac | Text | 1,548 | 38 | # RESL-SIRS postprocessing analysis
This code generates the figures and results presented in the publication:
Capiglioni M, Beisteiner R, Cardoso PL, et al. Stimulus-induced rotary saturation imaging of visually evoked response: A pilot study. NMR in Biomedicine. 2024;e5280. doi:10.1002/nbm.5280
## Visual-stimulation... |
f0396b09d2f3c8365bc2789a9e9ddccdba99c5e6a385c1860fb6a48a741291f0 | Text | 1,552 | 62 | # 🦀 crabsort
[]()
# Installation
## Using git
Clone these repos:
```
# bash
git clone https://github.com/sg-s/crabsort
git clone https://github.com/sg-s/puppeteer
git clone https://github.com/sg-s/srinivas.gs_mtools
```
and add th... |
0bac87c57a52b75c605434e7b4ce352a323a9bef77ee632818369aa2d6c20f46 | Text | 1,568 | 36 | # shapelearningtheory
Theoretical investigation on why neural networks fail to learn shape perception
This code implements data generatino, experiments and analyses for the paper
Jarvers & Neumann (in preparation).
Teaching deep networks to see shape: Lessons from a simplified visual world.
## Running the experiments... |
7e139afb2a0bfe0df6541a5a6e60be2d429a302ead115e953b7c874682c8322c | Text | 1,569 | 12 | # Bias Reduced Neural Networks for Parameter Estimation in Quantitative MRi
This repository aims to partially reproduce the results in the paper https://arxiv.org/abs/2312.11468. These neural networks have reduced bias compared to those trained with the typical mean-squared error loss, and a variance that is close to t... |
20397b000ca08cac8a5d95e374e18a4a49afc4a64426d67c7c0387ac4308ec65 | Text | 1,577 | 21 |
<p align="center">
<img width="250" alt="relax-jr-head" src="https://github.com/aronthill/RELAX-Jr/assets/31600263/b30f9969-c529-4df4-a389-fbff8f8fe03f)">
</p>
# RELAX-Jr
The Reduction of Electroencephalographic Artifacts for Juvenile Recordings (RELAX-Jr) is an open-source EEGLAB toolbox for automated preprocessing ... |
49c79b9240c84b9fb450be264e8bc76e568ce46438073a45ad1d52adfbe1ecd3 | Text | 1,584 | 8 | # BNC2
This is a code repository for the following BNC2 study:
[Preprint](https://www.biorxiv.org/content/10.1101/2024.01.25.577315v2.abstract)
Leptin is an adipose tissue hormone that maintains homeostatic control of adipose tissue mass by regulating the activity of specific neural populations controlling appetite a... |
a5282e603a8887fecf594cf9a075b75e99c1d141ce1dd658cc5545176053cda5 | Text | 1,596 | 32 | # A Kernelized Multi-level Localization Method for Flexible Shape Modeling with Few Training Data (MICCAI 2020 paper)
This repository contains Python code for the MICCAI 2020 paper
*A Kernelized Multi-level Localization Method for Flexible Shape Modeling with Few Training Data*
by Matthias Wilms, Jan Ehrhardt, Nils ... |
55521bbaedd569b4a4bb736e091b186515cd9cad5530bddbd3017c06c3146c96 | Text | 1,602 | 43 | # Reference implementation of Synaptic Predictive Processing (SPP) learning model.
## License information
Author: David Kappel
Copyright (C) 2024, by the author.
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
... |
e55327b528ff1ad165b43a4a65c8576be4f40ae9d5303ad96d1a45b4fb0dd38a | Text | 1,603 | 23 |
# Introduction:
I-spin Quattrocento is a Matlab app interfacing with a multichannel EMG recording system (i.e., EMG-Quattrocento, 400 channel EMG amplifier; OT Bioelettronica, Italy) to identify the firing activity of single motor units in real-time and translate it into several forms of visual feedback. Users can imp... |
9c68860fb74d6a910b2a45a263a3e5d68e718f7304fe1c00bbd74425646e7b90 | Text | 1,604 | 28 | Open Babel
----------
[](https://github.com/openbabel/openbabel/releases)
[](https://github.com/openbabel/openbabel/releases... |
c261beb72731017a2f36590392b8ab3578cc3c5584d975319fb532134ab7baa3 | Text | 1,629 | 37 | ###### **Overview**
This code repository is partly to support robot skill learning experiment in the submitted manuscript 'Deep Bayesian Active Learning Using In-memory Computing Hardware'.
The segment of code (https://github.com/caelan/LTAMP) associated with LTAMP incorporates and references the code from the subseq... |
ba0fb41c83b6d53dc1f61750ab787da651b48fc3d11739ccaf5b85016120ba9f | Text | 1,646 | 44 | # ACC-sn-Multiomes
Data Analysis Process of the Anterior Cingulate Cortex (ACC) in Humans and Macaque.
The project files include preprocessing of snRNA-seq and snATAC-seq data, differential accessibility peak analysis, peak functional analysis, and analysis of human genomic features (hsSNCs and HARs).
For citation o... |
3fc7acc0bbd39a3f25126189ae17b82f3f6b7ccfee7fd96be6cea803280101eb | Text | 1,652 | 37 |
# RAISING Repository
This repository contains the source code, simulation data, and documentation for the **RAISING**, a two-stage neural network(NN) framework that first performs hyperparameter tuning to devise the best NN architecture and then performs training on the entire data to estimate the feature importance.... |
4f5422e5b12d3511f7c5bbd1435d459778c2b7900d8cdc4b10897d0cae5aaa39 | Text | 1,658 | 24 | # POFP
The POFP.py contains python functions to generate photo-oriented fingerprints.
## Dependencies
- Numpy
- RDkit
## `GenSpecFP` Function
#### Description
The `GenSpecFP` function generates a specific fingerprint for a given molecule. The fingerprint is a bit vector based on substructure matching within the molec... |
8d82746a3edc78b68c9b3de2fc23088f0472d7be9fa0a75fdd32bc84b1ffcc49 | Text | 1,665 | 34 | Dataset Title: Variation in forest root image annotation by experts, novices and AI
Lead Author: Grace Handy
University of Birmingham
gih849@student.bham.ac.uk
Files
Image_dataset_1_results (CSV)
Image_dataset_2_results (CSV)
Image_dataset_2_change_results (CSV)
Attributes
Image_dataset_1_results
1. Age... |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.