sha256 stringlengths 64 64 | language stringclasses 27
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|---|---|---|---|---|
a796d14d2e2fb8525c99a8848a7137d59b4747ba275a3db846d533b2bb649663 | Text | 1,112 | 22 | # PRISM: Prior-Regularized Inference for Spatial Transcriptomic Cell Type Mapping
PRISM is a prior-regularized framework for **cell-level cell type mapping** in spatial transcriptomics (ST).
It transfers biological knowledge from annotated **single-cell RNA-seq (scRNA-seq)** references to **unlabeled ST** cells.
<im... |
a2a8e4146542dea88a90798cb77c158561ae2b7bd8165bce4571237b8aa9ff54 | Text | 1,128 | 26 | # An Integrative Systems Microbiology Algorithm for Reproducible Multi-Dataset Omics Analysis with Application to Long COVID
## Installation
The code runs with scikit-learn and a few necessary packages
```bash
pip install -r requirements.txt
```
## Datasets
- [GSE275334](https://www.ncbi.nlm.nih.gov/geo/query/acc.... |
9530ccbcf3ecbb2cd2c06eb8f32c2137c86800680f68fdb8eefc94e33f77a012 | Text | 1,169 | 38 | # rCPG–swCPG interaction model
Computational model of the synaptic interaction between the respiratory (R-CPG)
and swallowing (Sw-CPG) central pattern generators, together with the LaTeX
source of the accompanying paper.
## Layout
```
code/ Python model, Hydra configs, and figure-generation scripts
(see ... |
1677bc7b1c26f85cf9e3c3c7fe6c404bf4d63611816f4c39e0f477633b837ea1 | Text | 1,202 | 15 | # Gratton2020_NI_HFmotion
The included MATLAB scripts were used in the study: Gratton et al. (2020) Removal of high frequency contamination from motion estimates in single-band fMRI saves data without biasing functional connectivty. Neuroimage.
These scripts will allow users to make measurements of the frequency conte... |
7a8d392b900635f5d825d7679f6cbeed384b7c030e3382a39926adb9ed3d8e8c | Text | 1,205 | 32 | # PIP-seq: Figure Reproducibility Code
This repository contains the analysis code used to generate figures for the manuscript:
**“Spatially Guided In Vivo Single-Cell Functional Genomics of Postnatal Heart.”** :contentReference[oaicite:0]{index=0}
The code is organized by figure and includes scripts written in **R**... |
ec84991ee0c94aca16e4c06704f071e58b255858eec1b5e54a8a0c8ac4564b12 | Text | 1,211 | 29 | # AI-based Prediction of Cognitive Function
In this study, we used a deep learning approach to evaluate the predictive power of the functional connectome during various states (resting state, movie-watching, and n-back) on episodic memory and working memory performance.
M. Esmaeili, E.B. Bjørkeli, R. Pedersen, F. Fal... |
f08297d6158f7e85f30e32a97670ed65bfa152a5748d4bd1bb2bf3e1a89a3120 | Text | 1,219 | 19 | # Patent License Prediction Using Deep Survival Analysis
This repository contains the official implementation for the paper:
"Patent License Prediction Using Deep Survival Analysis: A Comparative Study"
## Overview
This study evaluates deep survival analysis frameworks for predicting patent licensing events. We syste... |
4314a1b1c48df406891ae2e83cd26489ee088bc7b1957b5ca99206bb043737a1 | Text | 1,220 | 15 | # A large-scale MEG and EEG dataset for object recognition in naturalistic scenes
This repository provides the codebase for the preprocessing, validation, and visualization associated with the [A large-scale MEG and EEG dataset for object recognition in naturalistic scenes](https://doi.org/10.1038/s41597-025-05174-7)
... |
954585e8795847b193cb2e660a16e74780e17e566046a4d3076d75198ca149e2 | Text | 1,242 | 27 | # Neuralplexer_Ligand_Scoring
This script generates a pipeline for finding the rank 1 ligand and the related protein structure generated by the NeuralPlexer generative model. It scores the ligand binding affinity using Schrodinger Maestro.
## Requirements
- **NeuralPlexer Generative Model**
- Install from their [G... |
6f143032a251758ecca4ecbe2489674f1d640394c9e3390f12bb19c1f7aa7ee6 | Text | 1,283 | 43 | ## Repository Summary
- **Git-tracked files**: 1208
**Top file clusters (by extension)**
- **Perl (.pl)**: 585 — automation, text parsing, bioinformatics and utility scripts.
- **Python (.py)**: 153 — analysis, automation, small tools, and ML experiments.
- **R (.r) + R Markdown (.rmd)**: 135 + 37 — statistical analy... |
846153363a9b29ebb62062a1ce2ee12440d9f16ff8409cb989be403280a623eb | Text | 1,335 | 15 | # Application of machine learning models to identify differences in neural electrophysiological properties across estrous cycle phases
## Background
Using whole-cell patch clamped cell recordings from female rat medium spiny neurons across four assessed estrous phases and three recording techniques (action potential b... |
bbc1bdc6757027a519dda93ea3090dc44ed3e0f1db3e78633210fab8285ea1b0 | Text | 1,346 | 33 | # Network-based stratification of allele-specific expression reveals patient subgroups in Huntington's disease
## Docker Images
Pre-built Docker images are available on Docker Hub:
| Environment | Tool | Pull Command |
|-------------|------|-------------|
| STAR | RNA-seq alignment | `docker pull ashviyer/hd-ase-st... |
1b61d4445297e5750ba7052b877663b4957cf31ef2c8b9343952747700723e78 | Text | 1,410 | 69 | # FCD_Asymmetry
MRI_based Morphological Asymmetries beyond the lesion locations in the human brain in focal cortical dysplasia
The BIDS-compatible rawdata are available on https://openneuro.org/datasets/ds004199/versions/1.0.6.
## References
TBA The preprint on bioarxiv
## Workflow
please see the 'images' fo... |
ff4c888fb4fd4a53d7abb3de2c90fff2a05572ba3bf099ef99b13372f9e536ac | Text | 1,444 | 45 | # `snakemake_paper_demo_workflow_data`
This is a Snakemake workflow for acquiring the raw data for the "Orchestrating neuroimaging data processing using the 'Snakemake' workflow manager" paper.
This raw data can then be used in the [demo workflow](https://github.com/unimelbmdap/snakemake_paper_demo_workflow).
In part... |
c4a25167dcd6194773fc35b925104a932ccecd0322eeaac6275f2b477b1f3989 | Text | 1,450 | 13 | # Variable selection with false discovery rate control in deep neural networks
The code in this repository implements the variable selection procedure (SurvNet) proposed in [https://arxiv.org/abs/1909.07561](https://arxiv.org/abs/1909.07561).
## Getting started
In order to run SurvNet, an operative version of Python... |
127d1719c78fc7c874e494ac3b702a4e06474327bae8f35acd21d6066ea85418 | Text | 1,485 | 47 | PUP
===
PET Unified Pipeline
PUP is a package for processing PET images. It is developed by Yi Su, PhD (ysu001@gmail.com)
The package includes the following subfolders of different components:
4dfp
----
A package developed by Dr. Abraham Z. Snyder (azsnyder@wustl.edu) at Washington University School of Medicine in ... |
b361d026dce173674212cea4ce1b77fec8bc1424742d498ef54985359312ab06 | Text | 1,517 | 35 | # riksneurotools
Some Matlab functions from Rik Henson. Use at your own risk!
GLM contains functions related to the General Linear Model (particularly for fMRI)
SPM contains functions specific to SPM (eg bypassing 2nd-level batch interface)
Conn contains functions for functional connectivity (particularly for fMRI)
... |
df5aba6381559abc55308a46419cbb03b7e01a342aef97dbc5abf3be60ef884a | Text | 1,548 | 25 | # IAAFT functions
This repository provides **Matlab** and **Python** functions implementing the IAAFT algorithm for generation of surrogate time series.
The **IAAFT** (**i**terative **a**mplitude **a**djusted **F**ourier **t**ransform) algorithm was first proposed by T. Schreiber and A. Schmitz in Phys. Rev. Lett. **... |
5d2751d9553bd2fcaef0b0a1b10c79b01a2de67a033e469024ebfbbfbcd9929d | Text | 1,549 | 64 | # LENS
This is the official repository for "LENS: a mammography-specific hybrid CNN-Transformer with lesion-aware evidence modeling"
## Installation
```bash
cd share/lens_hybridv5
python -m venv .venv
# Linux/macOS
source .venv/bin/activate
# Windows PowerShell
# .\.venv\Scripts\Activate.ps1
pip install -r requiremen... |
563ec24cc3eea2a266ccc2ac84be9bdef7bf1b85decb79b1857f3c6a9a72c2cc | Text | 1,557 | 62 | # NeuroFit Randomised Controlled Trial – Statistical Analysis Code
## Overview
This repository accompanies the manuscript:
**Farmand et al. 2026 - Effects of a three-month exercise programme on cognition, mood and neurogenesis: the NeuroFit randomised controlled trial**
It contains representative R Markdown scripts... |
a690a232b5030111aaa02a6d4847055487eaaa8a92fab0161e8a2926513b300d | Text | 1,599 | 11 | # ABCD-HCP BIDS fMRI Pipeline
[](https://zenodo.org/badge/latestdoi/171551109)
[, on a i7-12700H 2.30 GHz (32 GB RAM) laptop running Windows 64-bit. No errors were encountered (only some warnings sometimes related to the polyshape function of MATLAB, but these can safely be ignored).
The c... |
947d3ecadabe7776efd181ff1665f5d00a2175cf8b801bceff12f6a8538826d9 | Text | 1,702 | 43 | ====================
BrainSpace
====================
BrainSpace is a lightweight cross-platform toolbox primarily intended
for macroscale gradient mapping and analysis of
neuroimaging and connectome level data. The current version
of BrainSpace is available in Python and MATLAB, programming
languages widely used b... |
6228c99903de1738ef1bab55b63877f1838bb2d985d69a39fa122ff3bc4ba15b | Text | 1,714 | 36 | # Automate-Neural-relational-inference-NRI
Automate Neural Relational Inference (NRI) to accelerate the analysis of residues and ligand trajectories by learning complex residue-residue, residue-ligand, and ligand-ligand interactions.
## Requirements
- **NRI**
- Install from their [GitHub page](https://github.com/j... |
d1f01ab42c33cbd22dc095a3cba588bf84115b7fe4e50e17ea5350746f7e76ca | Text | 1,729 | 35 | # Defective-EV-Mediated-Transport-of-SHH-Alters-Neural-Fate-Specification-in-EPM1-epilepsy
# Analysis Pipeline: Single-Cell and Bulk RNA-seq
This repository contains two independent analysis pipelines:
1. **Single-Cell/Pseudo-bulk Pipeline:** Processing for the mvCO and vCO datasets.
2. **Bulk RNA-seq Pipeline:** Sep... |
870e61625ae83fd16774f07368eb47fa5f352f28c854ac6592c18fbc6d971d0c | Text | 1,756 | 24 | [](https://doi.org/10.5281/zenodo.17990782)
# Boeken Tau aggregate interactome
This repository contains the analysis code associated with the tau aggregate interactome proteomics and single-molecule characterisation project, led by Dorothea Böken. This manuscript has bee... |
7b7a830bdbe39a7bbb14c30a6d46dd3fa2eebd7a5e0aad9249b3e913199f9d98 | Text | 1,764 | 62 |
# Unified Representation Learning for Spatial Multi-omics
This repository includes scripts and Jupyter notebooks for SpaAlign, which are necessary to reproduce the benchmarking results presented in the paper. Each notebook contains the corresponding experimental data, and all results can be regenerated using the pro... |
87245cbf091321df519b93d4d9448b9fb0eb007f38302f91c786f7659ca19550 | Text | 1,815 | 45 | # TSvelo
This is the code page for the paper "TSvelo: Comprehensive RNA velocity inference by jointly modeling splicing, transcription and its regulation network".
TSvelo is a comprehensive RNA velocity framework that can jointly model splicing, transcription processes and its regulation network using highly interpr... |
f58a0394d03950b69caf04fde2969b76bdf82d5f0a3f704253128fdd5060eed4 | Text | 1,938 | 14 | # HCPex
An extended Human Connectome Project multimodal parcellation atlas of the human cortex and subcortical areas
HCPex is an extended version of the original atlas in which 66 subcortical areas (33 in each hemisphere) have been added, including the amygdala, thalamus, putamen, caudate nucleus, nucleus accumbens, g... |
d2f3b0972e907beaf65792e2f4ca963e1fa7f3164a12b2d57d0b2bca6e2cb81c | Text | 1,993 | 32 | # CortExplore
Analyse experiments on the cell cortex
1. How to start
1. Open CortexPaths.py in your favorite code editor.
2. Make sure to add Code_Python folder (containing CortexPaths.py) to the working directories of the code editor.
3. Run section "0. Imports" to print your computer name.
4. Complete section "... |
319182c684cfa83505abc4022e24ed9326f160cf90a784865cc30f87587028b6 | Text | 1,997 | 51 | # snakemake_paper_demo_workflow
This contains the Snakemake workflow for the paper "Orchestrating neuroimaging data processing using the 'Snakemake' workflow manager".
## Preparation
### `uv`
This is used to manage the Python environment and is installed via:
```bash
curl -LsSf https://astral.sh/uv/install.sh | s... |
5a839954074a683e5cf67f7643675311c5db5f84a90da6b361ed8a61ff25d42f | Text | 2,035 | 69 | # pyMocoKit
MRI reconstruction pipeline with retrospective motion correction and option to reverse a prospectively applied correction.
Supports raw data (Siemens `.dat` files) from MPRAGE and T2-SPACE sequences (an extension to diffusion EPI support is planned).
Includes: noise prewhitening, OS removal, iPAT/GRAPPA, ... |
82b273f72b5333b7fbe3b1e24201f6f70aebf7fae2f89b337f4cde5114c85176 | Text | 2,079 | 57 | # GPDLBP: a novel genomic prediction method that integrates genomic-prior deep learning locally connected networks and the best linear unbiased prediction (GBLUP) framework.
## Model summary
GPDLBP integrates two distinct marker variant types (SVs and SNPs) by synergistically combining DL networks with the GBLUP mo... |
c51cfb80d002476d0dc66bc78ee798e16333cf14817380b7c6aa80398d94fd91 | Text | 2,130 | 43 | 
# sgcount
[](./LICENSE.md)
[![codecov](https://codecov.io/github/noamteyssier/sgc... |
8913dc6c4a3ca503bc8e1485e4be40e3653988678281717f9cf7b02fdb7df224 | Text | 2,136 | 42 | # Spl-IsoFind Reproducibility
This is GitHub for reproducing analysis from
[Michielsen, L., Prjibelski, A.D., Foord, C., Hu, W., Jarroux, J., Hsu, J., Tomescu, A.I., Hajirasouliha, I. and Tilgner, H.U., 2025. Spatial isoform sequencing at sub-micrometer single-cell resolution reveals novel patterns of spatial isoform... |
97d66a5eb749e30c9b677950c1ae3ee9043f3c959eda7a5e15b121e256eb92a2 | Text | 2,246 | 72 |
<!-- README.md is generated from README.Rmd. Please edit that file -->
## scisorseqr - a comparative analysis of alternative splicing patterns
<img src="man/figures/scisorseqr.png" width="25%" style="float:left; padding:20px" />
scisorseqr is a linux based R-package for analyzing differential isoform
expression in ... |
bd84d3140720a40a8dbfc62e1f6319c15bbe5488fff8d12bc59e2423868dcae9 | Text | 2,256 | 47 | # Restricted q-space trajectory imaging (resQ) fitting code
This repository contains fitting code for resQ (for powder-averaged signal).
This code is written in Matlab and intended to be compatible with the md-dMRI framework (https://github.com/markus-nilsson/md-dmri), and relies on some of its functions to run.
##... |
426b19e5abe4c7d8bf8116b3f48331c81952863cc36a4e045802372d5d47cb95 | Text | 2,261 | 36 | # Brain Connectivity Toolbox (BCT)
The Brain Connectivity Toolbox (brain-connectivity-toolbox.net) is a MATLAB toolbox for complex-network analysis of structural and functional brain-connectivity data sets.
### Reference and citation
Complex network measures of brain connectivity: Uses and interpretations.
Rubinov M,... |
e62700464984e68d156c9b02cafcdc91c734c864927375711fcb0b2b46ced431 | Text | 2,282 | 36 | # A Data-Driven Closed-Loop Control Approach to Drive Neural State Transitions for Mechanistic Insight
This repository contains the code and analysis notebooks used for the study "A Data-Driven Closed-Loop Control Approach to Drive Neural State Transitions for Mechanistic Insight".
It includes model training utilities... |
db9540e07cb90bc1acb165264d02ad3575aae66ddb4c161d0680c78aeb5124cf | Text | 2,286 | 46 | # ElectroMap
ElectroMap - optical and electrophysiological mapping software.
5th Jan 2020 -
ONLY WORK WITH MATLAB 2019B CURRENTLY
Updated version of software including optical wave similarity and dFdt mapping can be found in new folder 'Source Code - OWS and dFdt update'. .exe version of updated software will be on... |
f66d332669b359cfc0b3b9f249d58e39982824036e66effc232543a909d68935 | Text | 2,336 | 80 | # P-unit model
Cell specific integrate-and-fire type models for a population of
P-unit electroreceptors of *Apteronotus leptorhynchus*.
## Model parameters
Model parameters are stored in csv files.
- `models.csv`: the best fitting models from both fitting attemps.
Use these models!
- `models_old.csv`: the origin... |
40f03d1083877dc7d933f7067e93f69aead75be3c613f07d3f2302cc62c39fd9 | Text | 2,363 | 72 | # Tommy's MRI-Volume-Masker-3000-TM
Use to draw volumetric masks for brain data. Requires python >= 3.7
```
################################################
Button mapping Tommy's MRI Volume Masker 3000 TM
################################################
set slice: enter
slice up: up
slice down: down
increase bright... |
58c58a7b81da399fa8a13378c7af6dfaa5e9f4c7ee6b2e160d44eae308fc216f | Text | 2,371 | 31 | <img src="https://raw.githubusercontent.com/BodenmillerGroup/steinbock/main/docs/img/steinbock-logo.png" align="right" alt="Logo" width="150" />
# steinbock
<a href="https://python.org"><img alt="Python" src="https://img.shields.io/pypi/pyversions/steinbock"></a>
<a href="https://github.com/BodenmillerGroup/steinbock... |
6ccfeb550b6cb642d196845920a8f1536fd1e2ed4bc26da8adc8b1577efa0071 | Text | 2,414 | 45 | # Spatial-Spectral Fusion Enables Drug Repositioning by Capturing Indirect and Long-Range Associations in Biological Networks
Drug repositioning is often hindered by therapeutic associations that are indirect (transitive chains) or long-range (multi-step drug–protein–disease mechanisms) rather than directly observable... |
cba96364d5d80de5ac210f63c49094187508ecd3bd7106f0d2707c3d9c468ce6 | Text | 2,440 | 83 | # benchmark_cross_species_integration
This project benchmarks 13 cross-species single-cell integration methods and provides a machine learning model for automatic optimal method recommendation.
script/
├─ core_method/ # 13 integration method scripts
├─ evaluation/ # ARI_LISI, ASW_NMI, scib
└─ model... |
d65cd52673a68c7eb76f194321d53a453a8c419ceb1a548abda4189e39536890 | Text | 2,458 | 42 | # NeuralEncodingManifolds
Here you will find code and data for the analysis of neural populations in response to an ensemble of stimuli. For more information, please refer to the papers:
> Dyballa, L., Field, G. D., Stryker, M. P., & Zucker, S. W. (2024). Functional organization and natural scene responses across mous... |
89d5e3defc7daa56a1c02886b57bbc58fdef8aac075bf3ae24c1c65650c4645d | Text | 2,471 | 74 | # Tommy's MRI-Volume-Masker-3000-TM
[](https://doi.org/10.5281/zenodo.7211758)
Use to draw volumetric masks for brain data. Requires python >= 3.7
```
################################################
Button mapping Tommy's MRI Volume Masker 3000 TM
####... |
8f7769c41361f5dfb300882af678156fe764b587678eb19e969ccdb8c063422e | Text | 2,471 | 51 | # Guides:
Quick PDF guides:
Thresholderer workflow: https://github.com/Jorvalgl/Thresholderer/blob/main/Thresholderer%20%20guide.pdf
ThresholdererFilters use: https://github.com/Jorvalgl/Thresholderer/blob/main/ThresholdererFilters%20guide.pdf
md extended guide: https://github.com/Jorvalgl/Thresholderer/blob/main/... |
a0104b04c43c2a0ce60c3f0fd3055da75388b028a2e973e12ec99af4abbec5fb | Text | 2,475 | 46 | # Sholl Analysis in R
R analysis code for analyzing fluroescence microscopy images to determine the complexity of cultured astrocytes.
Required programs:
1. ImageJ/FIJI https://imagej.net/software/fiji/ We have tested the Sholl analysis with ImageJ v1.53c and Java 1.8.0_172
2. R and R Studio: https://posit.co/downlo... |
d49854cbce56369fb76d4ca837ad57ae26f32eb9ad6f5180e26037ca89d85bcd | Text | 2,519 | 41 | # Alchemical free energy calculations with custom potentials in OpenFE
This is a fork of Open Free Energy's `openfe` package, which we have modified to calculate relative binding free energies (RBFEs) with our Garnet force field.
## Introduction
Garnet is a graph neural network that assigns force field parameters f... |
54df9b531f3507801a27973f8f2f904375716036d9869424ccacd033e8889cc3 | Text | 2,527 | 60 | <img src=".github/Detectron2-Logo-Horz.svg" width="300" >
Detectron2 is Facebook AI Research's next generation library
that provides state-of-the-art detection and segmentation algorithms.
It is the successor of
[Detectron](https://github.com/facebookresearch/Detectron/)
and [maskrcnn-benchmark](https://github.com/fac... |
cc7a193bbdd1a5c8b49572580a9d5cb62f9fe5d5edfa8d1483d6130fb4df83fd | Text | 2,549 | 68 | Tristan Pipeline
================
fMRI preprocessing and analysis pipeline for ultra-high-field data
Overview
--------
Tristan Pipeline is a modular Python workflow for preprocessing and analyzing ultra-high-field functional MRI (fMRI) data.
The dataset used for development and validation was acquired at 11.7 T using ... |
08c3703a3e3de519604fd30d1e0edcd3a3b12b57c0f987805151be13ee59eaf8 | Text | 2,553 | 107 | # BreathingRP2025
This repository contains the code for Jeay-Bizot et al. (in review) Matters Arising following Park et al. (2020) article.
### Repository Structure
````
.
├── binning\_corrected.m
├── binning\_original.m
├── generate\_simulateddata.m
├── make\_figure1.m
├── make\_figureS1.m ─ make\_figureS5.m
├── p... |
d940230b8f099a0c68ebd343fef7341c5cf6d37f1657693a3339d175ee6f0251 | Text | 2,561 | 52 | # Aperiodic Clinical Review
`AperiodicClinical` project repository: a systematic review of clinically related studies of aperiodic activity.
## Overview
Aperiodic neural activity has rapidly become a common feature of interest in clinical investigations. This rapid proliferation of studies of aperiodic activity acro... |
0c3978610c8df7e23343319930771b5bf2cd5366fd17e7b74feb95c9b600830a | Text | 2,570 | 57 | # micorr
## Description
This project provides a framework that can be used to test different pairwise similarity estimators on simulated waveforms.
The intended use of the code provided here, is to compare common mutual information, including Kraskow-Stögbauer-Grassberger (KSG), kernel density estimator (KDE) and ad... |
e0ce6963a185e33f0ceb2bc4828aa85af377833110347907093810e473ab80ea | Text | 2,579 | 59 | C++ code of multimodal Bayesian homeostatic recurrent neural network model (MBH-RNN)
1. Tested environment
-OS: Ubuntu (20.04)
-gcc/g++ version 11.2.0
2. Installation guide
This code requires only gcc/g++.
3. Demo and Instructions
The file structure is below.
“network.hpp”: Network hyperparameter s... |
84283b6568225d6bf4177385caff6f2aa3195eaaab9eea28459ffd4c58bb8661 | Text | 2,634 | 91 | # cshift
A tool to perform cluster enrichment/depletion analyses
## Background
This is a tool to perform cluster enrichment/depletions with known groups.
It was built with single-cell perturbation studies in mind to answer the question
of how each perturbation potentially shifts leide... |
f27d21fe526228a9c2e59162ce3ff678e6306e9402ccf9d7aba45e9bf7887783 | Text | 2,695 | 83 | # Fiber Photometry Analysis - Veleanu et al. (2025)
Code and examples for the fiber photometry analysis featured in Figure 3 of [Linking Brain Circuitry and Neural Plasticity in Antidepressant Response: The mPFC-Reuniens-Hippocampus Pathway](https://www.researchsquare.com/article/rs-6348176/v1)).
## Overview
This re... |
4470322803e77abed94cd2c4be2b11751241775af691f73dd64dc9dcb0418987 | Text | 2,725 | 93 | # cshift
[](https://doi.org/10.5281/zenodo.20736462)
A tool to perform cluster enrichment/depletion analyses
## Background
This is a tool to perform cluster enrichment/depletions with known groups.
It was built with single-cell perturbati... |
b150d723c4059103675820900907567d411691e9d87642bc14b9e9bf042d5335 | Text | 2,762 | 44 | # Author:CBJ
# FWI-MSNet: Forest Fire Risk Prediction Framework
## Project Overview
This dataset needs to be obtained from a Chinese website, and the retrieved data information is in Chinese.
Data Source：https://www.nesdc.org.cn/sdo/list?searchKey=%E4%BC%9A%E5%90%8C%E7%AB%99
Dataset：
1、会同站2005-2022年大气环境要素观测数据集：
... |
20fd798710106f12e343f383709ad855e2acc88c24ce9392deb6f9aa7f440c44 | Text | 2,786 | 46 | # NIRSTORM
Current features include:
- classical within-subject analysis comprising motion correction, MBLL, and window-averaging.
- statistical analysis usi... |
41ce1ec6f065271f1fdbf4482ed2d12c269ba30315fa37a4754999e4a414140e | Text | 2,840 | 62 | <a name="README"><img src="https://raw.githubusercontent.com/jasmine/jasmine/main/images/jasmine-horizontal.svg" width="400px" alt="Jasmine"></a>
# A JavaScript Testing Framework
Jasmine is a Behavior Driven Development testing framework for JavaScript. It does not rely on browsers, DOM, or any JavaScript framework. ... |
3f809bb4933d1a7aec3b0d0de6381c2b0f258748e5e073eab6a494593dfe394b | Text | 2,843 | 60 | This repository contains the code required to reproduce the results presented in:
> Capiglioni, M., D. Tabarelli, S. Tambalo, F. Turco, R. Wiest, and J. Jovicich. 2026. “Exploring the Sensitivity Limits of Neuronal Current Imaging With MRI and MEG in the Human Brain.” *Human Brain Mapping* 47, no. 11: e70624.
> https:... |
43dedfe99986216d66bf9bf6c15b2c4719f3152877ce85e92074f8ad3fda2608 | Text | 2,933 | 74 | # ICMS Plasticity - Figure Reproduction Code
Code for reproducing the figures in:
**"Learning induces activation-mechanism-dependent neural plasticity in an intracortical microstimulation task"**
Robin Kim, Roy Lycke, Pavlo Zolotavin, Jon Montes, Chong Xie, Lan Luan.
Science Advances (2026), accepted.
- **Source cod... |
c1020aedfd79dc213f2ce0cf4c129a3458e6b8b988928f40c78cf60c26aafc4f | Text | 2,973 | 35 | ## Analysis pipeline and example data for ExM, EM and STED
Here, the analysis pipeline of for all dendrites reconstructed using ExM, EM and STED are provided as well as example reconstructions for each microscopy method.
Analysis of diameters extracted from imaging files is performed in python analysis code is provided... |
2da12ef76f5391555c036b76fadda99b51c32b94de5b6a4a3bb3200498d32233 | Text | 2,983 | 62 | # NeuralDataAnalysis_MATLAB
This repository collects MATLAB functions developed for published papers and for future research work, with the goal of maintaining a single, organized, and reusable codebase.
## Purpose
The main purpose of this repository is to provide a unique place where MATLAB functions can be stored,... |
12bf7218e967a1d86946873489f67081b925b98c98a5c01490eea396c8755cfe | Text | 3,045 | 115 | # cbgt-intermittent-postural-control
# CBGT Intermittent Postural Control
Official Python code associated with the manuscript:
**Tsugaya, Nakamura, and Nomura**
*Neural mechanism of postural sway-related beta-band oscillations:
a cortico-basal ganglia-thalamic network model of intermittent control*
This reposito... |
02fcc9104a8887c3f67e1be47d17a7253476628dbacde3fccec67a76deef285f | Text | 3,092 | 54 | # Natural Stories Corpus
🚨 **Update 2025-05-12** 🚨 We have discovered that the SPR data in the original release was misaligned by one position. The current repo corrects the misalignment. The other data is unaffected. If you have been using the dataset, we recommend re-running your analyses on the realigned data.
*... |
9909a146d0afb49d06d64f5ddebf2d157461e1b39a9e717a2b2aa60579510367 | Text | 3,092 | 40 | # pKa-Dataset
A dataset of $pK_a$ values created for the publication "Can graph neural networks understand chemical
elements ?"
## Construction
The dataset contain 2374 compounds with associated aqueous $pK_a$ values gathered from literature and online sources, with $pK_a$ range of $1-13$. In this dataset all bases ha... |
90787b1d46db429baab1422716c72fcbb0fa31ba0e6fdd8aea63e6ac1d37aff0 | Text | 3,112 | 89 | # corticalreading
# Heritable and Experience-Dependent Cortical Traits of Reading Ability
**Author:** Mikael Roll
**Institution:** Lund University
**Date:** 2025-10-27
**Repository:** [corticalreading](https://github.com/USERNAME/corticalreading)
---
## Overview
This repository contains code and analysis scripts fo... |
f6232fe4ab789f0bec954a0a4591c64d031b213d46bfbb24f3ffe72b6810432a | Text | 3,134 | 94 | # Neural Variability Analysis — MATLAB Code
Code accompanying the publication:
> **On variability in local field potentials**
> Mohsen Parto-Dezfouli, Elizabeth L. Johnson, Eleni Psarou, Conrado Arturo Bosman, B. Suresh Krishna, Pascal Fries
> *biorxiv*, doi: 10.1101/2025.03.27.645661
---
## Overview
This... |
e29bd801880bf5f19af36dc27377c56620702f8da38b31d6ca2ec32c4ef3905f | Text | 3,144 | 53 |
# Spin Test
This toolbox includes scripts to perform a "spin test" of anatomical correspondence between
cortical surface maps in either FreeSurfer or CIVET.
These methods are described in "On testing for spatial correspondence between maps of
human brain structure and function," Alexander-Bloch et al., NeuroImage, ... |
d9d71c7cee948426622925e2eaa3105600a9f190b1a7e626fa7b80d8f5e288ef | Text | 3,148 | 36 | # Code repository for the publication
### Feature specific neuronal oscillations in cortical layers
The manuscript can be accessed via [eLife](https://doi.org/10.7554/eLife.108408.1)
## Analysis pipeline
Scripts in this repository have been partly used for developing and partly for producing the final results.
The [... |
45b520f5cabbdd079f3c2b3e861177980e52cf1913b526beec3083e92edb7d11 | Text | 3,190 | 68 | # MAME: Multidimensional Adaptive Metamer Exploration with Human Perceptual Feedback
This repository provides the analysis programs for the experimental results reported in the following paper, together with the programs used to run the experiments.
Kamao, M., Ono, H., Yamashita, A., Amano, K., & Sawayama, M. (2025).... |
94596f902158e02ec22011667cfe55fa0ae224e54c8ed6b5602f53731d84c199 | Text | 3,218 | 154 | # Clinical Risk Scores and Alzheimer’s Disease Endophenotypes
This repository contains the full data processing and analysis pipeline used in:
**“Associations of dementia polyexposure scores to Alzheimer’s disease endophenotypes in a diverse population”**
The project evaluates how clinical risk scores (CRS)—mCAIDE, ... |
ecb7804afa39ae94a967769e6660099c12bdd907e935df4606147144d66315a9 | Text | 3,246 | 128 | # Insular iEEG Analysis for Chronic Neuropathic Pain
This repository contains MATLAB code for preprocessing, spectral analysis, connectivity analysis, and mixed-effects modeling of intracranial EEG (iEEG) data from patients with chronic neuropathic pain.
This repository contains the exact code used to generate all re... |
7c54c246fe9862a0a335b80e636abae4193081ae54ca39844c87b6751b35e980 | Text | 3,318 | 51 | # MAsP, R Shiny-based web application
[](https://zenodo.org/badge/latestdoi/499283690)
Micro-scaffold Assisted Spatial Proteomics (MASP) is a novel method for spatial proteomic studies. MASP precisely procures spatial information by precise tissue spatial compartmentaliza... |
52e1e875c5d5e915349ccd1f16908ebbbe96ea809d0f5e40768dcffcad6db62e | Text | 3,405 | 107 | # {shapviz} <a href='https://github.com/ModelOriented/shapviz'><img src='man/figures/logo.png' align="right" height="139" /></a>
<!-- badges: start -->
[](https://github.com/ModelOriented/shapviz/actions/workflows/R-C... |
97919b402def3ee11ea2bb642057f8b3b8d825a3c75eaf695910b5c38307a8cb | Text | 3,490 | 37 | # DMG_ONC201
## Single-nucleus profiling of postmortem diffuse midline gliomas identifies mitochondrial biogenesis as a resistance mechanism to imipridone therapy
## 📌 1. Overview of the study design
## 📌 2. Sample su... |
eea1a55529535dcb02283c3b913b8df25fa799f1218b2e05efe53b109a2f3524 | Text | 3,526 | 69 | [](https://doi.org/10.5281/zenodo.17434560)
# Activation of transposable elements is linked to a region- and cell-type-specific interferon response in Parkinson’s disease
This repository contains code, processed data, and environment files supporting the publication:
*Ac... |
8d682f4bae29308d44c0ec6d104f700e59fad5622ce3290d48fc200d6452e196 | Text | 3,608 | 71 | # DNAInterpolator
## Environment
To install all required packages for interpolation and training, download the environment.yml and requirements.txt files and run the following:
```bash
conda env create -f environment.yml
```
## Overview of files
### data
Contains tiny_data with the input data necessary to produce t... |
602bffc08d3790adbd3fc08db1ddfaa818712c264d8e815f78f1881936911ebc | Text | 3,656 | 93 | # BrainModules
BrainModules is an interactive browser-based viewer for exploring anatomical
seed-correlation maps in the mouse brain. Move the pointer over the cortical
map to select a seed position; the viewer displays regions with similar
corticocortical or thalamocortical input patterns.
## Use BrainModules online... |
1150943243fa902b523919b8a5c57c78f423da8e99d393d91a6038851b70b7aa | Text | 3,663 | 78 | ================================================================================
README - Frequency Domain Optical Tomography Dataset
================================================================================
Title: Frequency Domain Optical Tomography Dataset
Author: Jonna Kangasniemi, University of Eastern Fin... |
ee6f839ef3885a75edc86328f4dfd7865932f8c2ac411f951aa16f1b2e9ec2e6 | Text | 3,703 | 107 | # CRISPR Screen
[](./LICENSE.md)
[](https://codecov.io/gh/... |
a80a8a28e0bca01313226c22d8b41e61f96fe6e33680c6527a2bdab6500a2833 | Text | 3,789 | 93 | # Multi Task AMP Discriminator based on Multi Scale Feature Fusion and AMP Generator Guided by MIC
### This framework includes 2 parts:
**AMP-Hunter** (a multi-task discriminator that fuses convolutional neural networks with graph neural networks) in AMP classification and MIC predictiontask.
**AMP-Forge** (a gener... |
d3a82fa5cdc2f6b729fe5f2000cf592c55eaae7e9399baecaa78de0a246491f8 | Text | 3,790 | 112 | # CRISPR Screen
[](./LICENSE.md)
[](https://codecov.io/gh/... |
031296e93232547400ca7379d1226a9940bad957deba743b43e91f01a41ea4eb | Text | 3,799 | 88 | # eeg-ecg-music-review-agent
Turns a published scoping review into two things an AI assistant can use
directly: a reading package, and a small tool server over its charted
evidence.
> Leimroth, S. R., Barry, R. J., De Blasio, F. M., & Byron, T. P. (2026).
> Exploring EEG and ECG in music listening: A scoping review.
... |
501187b7229040f7d65b3033f6c23b816870edbe772facee958f8299de22b912 | Text | 3,902 | 100 | # RAVEN
### IMPORTANT NOTE: RAVEN was trained on different modality images denoised with FONDUE (FONDUE_LT from https://github.com/waadgo/FONDUE). It is recommended to denoise them first with FONDUE, as performance was not measured on other denoising methods (nor on non-denoised images)
Install the recorded Python de... |
5a7a23ab1d65cd09c0bda19a247be17e92999dd56bb4247c3684d63e9535b8fc | Text | 3,907 | 49 | # An End To End Computational Framework for Record-seq Transcriptional Recording Data
This repository provides the computational framework and benchmarking scripts required to reproduce the results presented in: **"An End-To-End Computational Framework for 'Record-seq' Transcriptional Recording Data"** (*Bioinformatic... |
44f8073d4f6470a8c8d7b47c6aa7da1292033ba207b921f95a96689467bd7e9f | Text | 3,919 | 139 | # Spyne
[](https://handle.test.datacite.org/10.5072/zenodo.519053)
## Description
**Spyne** is a Python package designed for advanced analysis and visualization of neuronal morphologies and dendritic spines calcium imaging data. :brain:🔬
`spyne` parses, processe... |
24789be81e92d4d2b23ad6e0dbb417fccb31c02a3f5d550d51778121470250d7 | Text | 3,970 | 90 |
# Description
This repository contains the original code of the paper *A unified model of short- and long-term plasticity: Effects on network connectivity and information capacity*. The workflow can be divided into three phases:
1. Model fitting
2. Network analysis
3. Information capacity simulations
# Installation
P... |
65522b44ed2cba53e464d7c5a81b70a621e2f6f5455712b5ac04bf852d971328 | Text | 3,996 | 59 | # Accurate brain-age models for routine clinical MRI examinations
This repository contains scripts to enable readers to run the trained models presented in [Accurate brain-age models for routine clinical MRI examinations](https://www.sciencedirect.com/science/article/pii/S1053811922000015?via%3Dihub#fig0003), (Wood et... |
c1d25fbd5f215a7de3023e0866ec1644e6c40fad77bf4140bfee6e9f888577c4 | Text | 4,077 | 52 | # GMX NNPot Tools
This repository contains a collection of example wrappers around popular Neural Network potentials for use with the [NNPot interface in GROMACS](https://manual.gromacs.org/2025.0/reference-manual/special/nnpot.html). We also provide an example notebook to export the models, as well as an example use ... |
206920832ad01396fd9e7f86668c31518ba6d75d9e76209eed06fbd6447f6edf | Text | 4,093 | 104 | 
# **SPIDER: Spatially Integrated Denoising via Embedding Regularization with Single-Cell Supervision**
<p align="center">
<img src="resources/Model.png" width="700">
</p>
**Figure:** *Overview of SPIDER framework.* SPIDER integrates spatial transc... |
2e65a0d7eef663398b7e6070a2e4b6f7dfcccd5ef967da8cbc6573c005ecc8e2 | Text | 4,103 | 78 | # nnU-Net
nnU-Net is a semantic segmentation framework that automatically adapts its pipeline to a dataset. It analyzes the training data, creates a dataset fingerprint, configures suitable U-Net variants, and provides an end-to-end workflow from preprocessing to training, model selection, and inference.
It is primar... |
26f4151965453c67fa53aa9822d7b5f2bb97b59d01c7ca5ec86a491b82ac9aa2 | Text | 4,191 | 99 | # VascuMap
Label-free phenotyping of human microvessel networks using deep learning segmentation and graph-based analysis.
## Installation
Create and activate conda environment
```bash
conda create -n vascumap python=3.8
conda activate vascumap
```
Install PyTorch (adjust cuda version as needed)
```bash
conda install p... |
55b24d635221e817bff60c64fcd638a237038cc4268aa326dfb7608d29e08b99 | Text | 4,352 | 103 | [](https://github.com/ctlab/fgsea/actions/workflows/R-CMD-check.yaml)
# fgsea
`fgsea` is an R-package for fast preranked gene set enrichment analysis (GSEA). This package allows to quickly and accurately calculate arbitrarily ... |
2e0620acb51fe5db791992c9703d2905cefe99acc12a3b25ab1001cf880708bc | Text | 4,618 | 90 | .. image:: https://github.com/netneurolab/neuromaps/raw/main/docs/_static/neuromaps_logo.png
|
.. image:: https://zenodo.org/badge/375755159.svg
:target: https://zenodo.org/badge/latestdoi/375755159
:alt: Zenodo record
.. image:: https://img.shields.io/pypi/v/neuromaps
:target: https://pypi.python.org/pypi/... |
df3e1c621162d3f0763cb3001cfc5f879e435ad7f84877b21b2c1b81ba1c1763 | Text | 4,665 | 93 |
# MAP4SL - Multiband Artefact Probe for Slice Leakage
beta version
MAP4SL is a Matlab tool which is designed to identify the effect of an artefact in MRI data on other areas depending on the slice leakage in MR multiband EPI functional images.
This tool calculates the possible artefact positions of a given seed re... |
f6d819e3b85d642ff66a2260c6e3047622f4ac247a462af37c167a79fe2a48f3 | Text | 4,882 | 55 | # Spherical rotation (permutation) of a parcellated cortical map
Code (in Matlab and R) to perform a spherical rotation (permutation) of a parcellated cortical map.
Includes coordinates on the Freesurfer sphere of 360 regions from the Glasser et al. *Nature* 2016 HCP parcellation.
For details, see the Váša et al. ... |
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