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6854ce213209cc53dc8a6d82d104c98f8535189edd41d189a0435721a3e51e2b | Text | 3,734 | 74 | # Polar Fourier Transform (PFT) for 2D Radial MRI Reconstruction
This repository contains the reference code and documentation for:
> **"Polar Fourier Transform in Practice: Its Efficiency and Characteristics in Reconstructing Radially Acquired MRI Images"**
> Accepted in *MAGMA* (Magnetic Resonance Materials in Ph... |
9117f4d03a84b49a29accc2decb0282caad9ba7bc52244763ac1b7076d124799 | Text | 3,734 | 72 | # Chow-Wing-Bom et al., 2025, _eLife_
This repository contains the codes used to produce the figures in **Chow-Wing-Bom et al. (2025) Mapping Visual Contrast Sensitivity and Vision Loss Across the Visual Field with Model-Based fMRI. _eLife_.**
Dataset can be downloaded here: https://doi.org/10.5281/zenodo.19051439
... |
6ca2210de279334f523cb70487dbeb0e5c453409c433b741223afa9e98432929 | Text | 3,801 | 117 | # AdjustEccTool - Benson Map Eccentricity Adjustment Tool (Docker)
This repository provides a Docker-based tool for correcting the eccentricity distribution derived from the **Benson atlas** (via *neuropythy*). The method implements the procedure described in:
**Chow‑Wing‑Bom et al. (2025). _Mapping Visual Contrast S... |
9d4f219c684227944fd37f57317d5b9b894ae6ab39491d7a8263efef70dfbfef | Text | 3,814 | 72 | # ExMechEva - Experimental mechanics evaluation
Evaluation of data determined by means of experimental mechanics.
Automation and standardization, considering special requirements of project and test specimen.
## Installation
`ExMechEva` is developed under Python 3.7.10 and is available in the [Python Package Index (P... |
bb72221b931fda72cad76a5f286c0b25269c9ff602a19f1b51a0edabcd53cd0d | Text | 3,886 | 110 | |Logo|
Toolbox for laminar inference with MEG, powered by `FreeSurfer <https://surfer.nmr.mgh.harvard.edu/fswiki>`_ and `SPM <https://github.com/spm/>`_
|PyPI version| |Unit tests| |Coverage| |Linting| |Python| |License| |Repo size| |PyPI downloads|
Operating system
================
* Windows: Tested on WSL (using U... |
49d6ccc79cc4eeeb297afe122c0a9771de687af5a93d4260a22d01d45f4356d9 | Text | 3,934 | 59 | # Hybrid protein-ligand binding residue prediction with protein language models: Does the structure matter?
This is the code repository for our paper "Hybrid protein-ligand binding residue prediction with protein language models: Does the structure matter?" by Hamza Gamouh, Marian Novotny, and David Hoksza.
## Envir... |
4a156c97958c0ad0164e2497bb1088d07d518871054e8e7bb4bd1046a82f1c31 | Text | 4,008 | 137 | # Analysis of Bulk RNAseq from HP1FEC Adult Hippocampi
Snakefile for alignment & count using TETranscripts:
```
#! bin/env/python
WT_YOUNG = "WT_young_S10422 WT_young_S10424 WT_young_S10425 WT_young_S10602"
WT_OLD = "WT_old_S10604 WT_old_S10631 WT_old_S10632"
BKO_YOUNG = "BKO_young_S10625 BKO_young_S10626 BKO_youn... |
7dbfe062d17a609a7bad2690f61292ccb82f3457e11278a7a702575bff6bc47c | Text | 4,030 | 89 | # DualNetM
An Adaptive Attention-Driven Dual Network Framework for Constructing gene regulatary networks and Inferring functional markers
DualNetM is a computational tool for Inferring Functional Markers from single-cell RNA-seq data.
It takes a prior gene interaction network,expression profiles and prior markers from... |
a0b454cd31d29b0f0558cdbe49c5f3e12d898d516bc86f437efcf3bb0fd2ef10 | Text | 4,141 | 59 | # WormTracker3000
The ultimate Bryant/Hallem Lab worm tracking software system.
A combination of the Thermotaxis and Chemotaxis trackers, with additional code for custom linear behavioral assays.
In order to function properly, this software requires a specifically formatted excel spreadsheet containing tracking data.... |
989f28ce595adec2395ac375771ba965ecf30d778426ebb9e545f5491ed5374e | Text | 4,296 | 54 | # Combined statistical-biophysical modeling links ion channel genes to physiology of cortical neuron types
*Yves Bernaerts, Michael Deistler, Pedro J. Gonçalves, Jonas Beck, Marcel Stimberg, Federico Scala, Andreas S. Tolias, Jakob Macke, Dmitry Kobak & Philipp Berens. (2025)*
Th... |
37124a168f69f2e784da9dce881c3a16067031f2ad209c4bf7d9f31fc26896cb | Text | 4,301 | 75 | # High-level visual representations in the human brain are aligned with large language models
**Authors: Adrien Doerig, Tim C Kietzmann, Emily Allen, Yihan Wu, Thomas Naselaris, Kendrick Kay, & Ian Charest**
Accepted in Nature Machine Intelligence
🔗 You can find our preprint [here](https://arxiv.org/abs/2209.11737) �... |
a5599337c355e7f7e11257052bd539b6178d9ae1d19db54c5bf2dc85de014c1a | Text | 4,337 | 136 |
---
# TCM-Navigator: Command-Line Toolkit for Molecular Generation and Evaluation
`TCM-Navigator` is a two-component command-line toolkit designed to streamline **molecular generation** and **property evaluation**, particularly for traditional Chinese medicine (TCM)-related ligands and target-specific drug discover... |
c61a9ae642fc20a782918dc6d88fc8570519307e5d7831b4cbaa9fcde5ea4cea | Text | 4,398 | 53 | # Brainwave Authentication Dataset and Experiment Material
This repository contains the brainwave data and additional material used in following publications:
Patricia Arias-Cabarcos, Thilo Habrich, Karen Becker, Christian Becker, and Thorsten Strufe (2021), _“Inexpensive Brainwave Authentication:
New Techniques and ... |
fa128ffc24733cd2afd0d0744eb3b89a7a69cf9add00f5d3ded11f6d801240c9 | Text | 4,435 | 114 | # Rhythm-SNN
Codes for ***Efficient and robust temporal processing with neural oscillations modulated spiking neural networks***
Yinsong Yan<sup>†</sup>, Qu Yang<sup>†</sup>, [Yujie Wu](https://yjwu17.github.io/), Hanwen Liu, Malu Zhang, [Haizhou Li](https://www.colips.org/~eleliha/), [Kay Chen Tan](https://www.p... |
e44adb37e748c4995db28423b8ad73b4408e8360f0090ab5c23681170fc2c5b0 | Text | 4,441 | 79 | # High-level visual representations in the human brain are aligned with large language models
**Authors: Adrien Doerig, Tim C Kietzmann, Emily Allen, Yihan Wu, Thomas Naselaris, Kendrick Kay, & Ian Charest**
Nature Machine Intelligence
🔗 [Link](https://www.nature.com/articles/s42256-025-01072-0) 🔗
### Abstract
*The... |
3fc01bffae4b6d60d071f4eb2d5ad9f9e3baf458eb647c6dab3f498fce8226ab | Text | 4,450 | 63 | # consHLA
A Next Generation Sequencing Consensus-based HLA Typing Workflow <br><br>
 <br><br>
The sub-workflow (blue box) <br>
A: Bowtie2 Alignment to IMGT HLA reference (generates .sam) <br>
B: Mapped reads extraction ... |
1b0aa77fa5b496d24875616c93c3fc76051c981b852d729e3ac873dd766a0cce | Text | 4,480 | 70 | # Lysophosphatidic Acid selectively modulates excitatory Transmission in hippocampal Neurons
Neuronal model to investigate the neuromodulatory effects of LPA.
## Model description
For modelling LPA effects on the level of the synapse we adapted the single-pool, four-state model developed by [Sara 2005](https://www... |
ece718c90ed19626d6016f894304f1bf5506b66f458535f91f1ea3b28c4cd84f | Text | 4,498 | 85 | # COVID-19 Modelling Code for Thuringia
This repository contains the code and data files used to reproduce the modelling results for the manuscript submitted to PLOS ONE. It includes the final reproducibility files: eight Julia notebooks, five CSV data files, and the Julia project environment.
## Tracked Files
The r... |
8e00b2a646e798a67ce749ed85794d4a66710d6e2771aa5790e7b72b1a1117ba | Text | 4,514 | 124 | # ENINet
## Introduction
**ENINet** (Equivariant N-body Interaction Networks) is a deep learning architecture designed to improve molecular property predictions by integrating equivariant many-body interactions. Unlike traditional message passing networks, which may lose directional information due to opposing bond v... |
e38f5e5eb8a2fa275167d8e02b5ed8d0364ed35befc18d06b6dc65414beaa6ba | Text | 4,640 | 95 | # S-GMAS: Genome-wide mediation analysis with Brain Subcortical Shape Mediators
## Abstract
> Mediation analysis is widely utilized in neuroscience to investigate the role of brain image phenotypes in the neurological pathways from genetic exposures to clinical outcomes. However, it is still difficult to conduct m... |
a5b498ba57c08f8559621981ccdde30901ea29541d744f59a41c0633164997ac | Text | 4,711 | 71 | # PanSci
A Panoramic View of Cell Population Dynamics in Mammalian Aging
## Overview
Welcome to the PanSci project repository. This project presents a comprehensive single-cell transcriptome atlas profiling over 20 million cells from >600 mouse tissue samples, providing insights into cellular population dynamics acros... |
161328cb0a699358e54e969fb0797249ee63d24b4be099142ed2efe8dfb52f97 | Text | 4,742 | 77 | # SumRank
These are the relevant scripts for the SumRank software and additional scripts for the following manuscript:
**Citation:**
<br/>
Nakatsuka, N.; Adler, D.; Jiang, L.; Hartman, A.; Cheng, E.; Klann, E.; Satija, R. “A Reproducibility Focused Meta-Analysis Method for Single-Cell Transcriptomic Case-Control Stu... |
1a934e4fc573fe093d83459f73fb90c905c665b956848463bb3a132175182c26 | Text | 4,744 | 91 | # COVID-19 Modelling Code for Thuringia
[](https://doi.org/10.5281/zenodo.20069396)
This repository contains the code and data files used to reproduce the modelling results for the manuscript submitted to PLOS ONE. It includes the final reproduc... |
aab1a9d147f7c1a280e4843578f721643420123d62138cf212d7d2fd8e6ac45e | Text | 4,754 | 62 | # VBT_INS_Stimulation
VBT for Stimulation in epilepsy
Codes for the published paper:
Wang, H. E., Dollomaja, B., Triebkorn, P., Duma, G. M., Williamson, A., Makhalova, J., Lemarechal, J.-D., Bartolomei, F., & Jirsa, V. (2025). Virtual brain twins for stimulation in epilepsy. Nature Computational Science. https://doi.o... |
d392d302054b5d0cf43fcf245bf280f940448597773937a1c7779845bc227ea7 | Text | 4,813 | 77 | # SumRank
These are the relevant scripts for the SumRank software and additional scripts for the following manuscript:
**Citation:**
<br/>
Nakatsuka, N.; Adler, D.; Jiang, L.; Hartman, A.; Cheng, E.; Klann, E.; Satija, R. “Improving reproducibility of differentially expressed genes in single-cell transcriptomic stud... |
c9a666ab2cfc931f07a9aaee11447b40221e76f379e9258f68477131bf715dc8 | Text | 4,833 | 113 | # Application of Protein Structure Encodings and Sequence Embeddings for Transporter Substrate Prediction
## Installation
### Requirements
- Linux (tested on Ubuntu 24.04 LTS in WSL2)
- [miniforge](https://github.com/conda-forge/miniforge)
- To recreate feature datasets (optional):
- Up to 200GB disk storage (P... |
c50da383910a61f041c8e5d9c21f9c18ed9dbd57c0baab48ca0bf88ef9edfa06 | Text | 4,848 | 111 | # RpiBeh
RpiBeh is an open-source, cost-effective, and versatile software system designed for real-time neuroethological research in rodents. It integrates behavior tracking and closed-loop control in a modular and customizable framework suitable for various experimental setups.
## Features
* **Affordable and Cust... |
1b525bafba9398a7430f8beef4b4af07197b186fdbb52d4980ef3819b9778aa0 | Text | 4,855 | 52 | # SVS_STEAM-sLASER_3T-7T
## This is the code for paper named "Reliability and Reproducibility of Metabolites Quantification Measured in the Human Brain at 3 T and 7 T".
### Zeinab Eftekhari and Thomas Shaw 2024
This repository contains a set of R and bash scripts designed to process, transform, and analyze metabolite... |
95490d564a8dc39e615681040977638ac0d537940055e1dbcbaed948595682b8 | Text | 4,871 | 96 | # Code for "Temporal coding carries more stable cortical visual representations than firing rate over time"
This repository contains MATLAB code for reproducing key analyses and figures from the manuscript titled:
**"Temporal coding carries more stable cortical visual representations than firing rate over time"**
... |
6ba97017410d61561666e1dee8cb16fc643f90696ef0a2e68d49a96a0ad75d74 | Text | 5,125 | 145 | |Logo|
Toolbox for laminar inference with MEG, powered by `FreeSurfer <https://surfer.nmr.mgh.harvard.edu/fswiki>`_ and `SPM <https://github.com/spm/>`_
|PyPI version| |Unit tests| |Coverage| |Linting| |Python| |License| |Repo size| |PyPI downloads|
Operating system
================
* Windows: Tested on WSL (using U... |
e4f2d114a43083700e22b213411d2263c50c363eaf15bb491f3002fc3da65ae9 | Text | 5,169 | 72 | # Gene Category Enrichment Analysis including Custom Null Ensembles
[](https://zenodo.org/badge/latestdoi/79196471)
This is a Matlab toolbox for performing gene-category enrichment analysis relative to two different types of null models:
1. ___Random-gene nulls___, in whic... |
f8697022cf2bb31c811b8f7c96e7655a0615665baeb117b57836f2a24097bb5d | Text | 5,229 | 73 | This code and data allow to reproduce the computational modeling part of the manuscript:
# Sub-type Specific Connectivity between CA3 Pyramidal Neurons May Underlie Their Sequential Activation during Sharp Waves
**Authors:** Rosanna P. Sammons*, Stefano Masserini*, Laura Moreno-Velasquez, Verjinia D. Metodieva, Gaspa... |
8f6d28164ee34ece84233361471c3d8575d570920e1a76ad3eef1beadab8f107 | Text | 5,286 | 117 | [](https://github.com/sankaranlab/SCAVENGE)
[](https://github.com/sankaranlab/SCAVENGE/actions)
[.
# Introduction
This repository implements a transformer-based model for predicting amyloid-β (Aβ) and tau (𝜏) PET positivity in Alzheimer’... |
18e6ff1c845bc1978068b773b2b3df56776300b353fa940cd85690a113b2da49 | Text | 5,322 | 78 | # TDGM major-revision reproducibility package (version 5.0)
Version 5.0 accompanies the technical resubmission of manuscript **PONE-D-26-30678R1**. It supersedes version 4.0 for reproducing the files supplied with the resubmitted manuscript.
Relative to version 4.0, this version renames the synthetic firm attribute `... |
bf227822d1204aa84b04c0d3a720c40b9ca228e30fdde5b54e608b47e37a8bab | Text | 5,328 | 70 | # Psilocybin Pharmacological Fingerprinting
<!-- ALL-CONTRIBUTORS-BADGE:START - Do not remove or modify this section -->
[](#contributors-)
<!-- ALL-CONTRIBUTORS-BADGE:END -->
Sample code to replicate analyses and figures ... |
07796a7aa89976368ea144bb1cf67e5c89f15de44093ad1c6643a77fa61758e1 | Text | 5,354 | 79 | # fragMap.py #
Juan F. Santana, Ph.D. (<juan-santana@uiowa.edu>), University of Iowa, Iowa City, I.A.
This improved fragMap program is simplified, more powerful, and runs faster than the original fragMap program (https://github.com/P-TEFb/fragMap/blob/main/original_fragMap_programs.md) and v1 (https://github.com/JuanF... |
179a899eaac95e4286cf729c890bb26ecb332c437528f0a3d54366ec65167e34 | Text | 5,354 | 147 |
# 📊 Analysis Reproduction: Srinivasan, Koyanagi et al., 2025
This repository provides the datasets and custom code used to perform the key quantitative analyses from **Srinivasan, Koyanagi et al., 2025**, including mixed-effects modeling, population vector similarity analyses, and regression with covariates.
---
#... |
eb3e1c9749f29d94a7a42721e871f67f48d90245f179cec301705d3d6079e171 | Text | 5,430 | 104 | 
# junifer - JUelich NeuroImaging FEature extractoR
<!-- <a></a> -->
Due to the sophisticated nature of complex diseases, finding interpretable associations between multi-omics data can be challenging using st... |
ebc1012e4fd2243e7ae8e9758efbeb4a450292ab8dae44e9055df44eb5ada1c8 | Text | 5,664 | 127 | # HiDT
HiDT is a method for identifying **differential topologically associating domains (TADs)** between **two Hi-C samples**.
It is particularly recommended for **sparse chromatin contact maps**, especially:
- **low-sequencing-depth Hi-C data**
- **pseudo-bulk contact maps**
For user reference:
- **Benchmarking**
... |
00bbc44a2216e3a67569417cb548d0d99338bb404e010d6ca16f7e2fb934ab77 | Text | 5,686 | 97 | This repository contains the scripts used for the following study:
## Combinatorial expression of neurexin genes regulates glomerular targeting by olfactory sensory neurons
### Sung Jin Park<sup>1</sup>, I-Hao Wang<sup>1</sup>, Namgyu Lee<sup>2</sup>, Hao-Ching Jiang<sup>1</sup>, Takeshi Uemura<sup>3,4</sup>, Kensuke... |
c4eace84c44b85c1684d57aba6167366a095a081f18a27e1661239f30b27cd51 | Text | 5,758 | 106 | # GPCNDTA
GPCNDTA: prediction of drug-target binding affinity through cross-attention networks augmented with graph features and pharmacophores
1 System requirements:
Hardware requirements:
train.py requires a computer with enough RAM to support the in-memory operations.
Operating system：windows 10/Linux
Code... |
6dc0826b99fc451102075507271321e8b75da3843417fb01491e022d60ea01f8 | Text | 5,870 | 142 | # PSF toolkit
<!-- badges: start -->
[](https://github.com/hakobyansiras/psf/actions)
<!-- badges: end -->
The **PSF Toolkit** is an R package developed for **topology-aware (TA) pathway analysis** of various types of omics data. The ... |
fb411e53870a0a9eaa9eb842ddc292059bc1672e2ea3a6f694a46ac75725a94a | Text | 6,016 | 140 | # **HNSC-classifier: an accuracy tool for head and neck cancer detection in digitized whole-slide histology using deep learning**
an accuracy tools for head and neck cancer detection and stage inferred in digitized whole-slide histology using deep learning
# The HNSC-classifier scheme and Deep learning framework:
.
It mainly enables the following avenues of analysis:
1) Exploratory analysis u... |
531dce8a8cae86cd20d9c88b10c55d49739207de43c1590a1574af29b0aa973a | Text | 6,217 | 207 | # microcolony-domain-adaptation-frai
This repository is for the article **"Enhancing AI microscopy for foodborne bacterial classification using adversarial domain adaptation to address optical and biological variability"**, published in Frontiers in Artificial Intelligence.
- Preprint: [doi: 10.48550/arXiv.2411.19514... |
82daf95bb3006f523db67a9f0da8f28c86fe452f51186111d23c55800b978938 | Text | 6,254 | 57 | # <div align=center> [WORD: A large scale dataset, benchmark and clinical applicable study for abdominal organ segmentation from CT image](https://arxiv.org/pdf/2111.02403.pdf)</div>
<!-- * [**New**] **We further annotate several open available and unseen datasets (20 cases from MSD Liver, 20 cases from MSD Pancras, an... |
53911302ab9d36c8f2537ab042b9963b86c79160c97b40f59ef4ee19a42dfe67 | Text | 6,325 | 144 | ```
___ ____ __ __
/ __)( _ \( \/ )
\__ \ )___/ ) ( Statistical Parametric Mapping
(___/(__) (_/\/\_) SPM - https://www.fil.ion.ucl.ac.uk/spm/
```
[](https://www.mathworks.com)
[
In this study, we investigated how preprocessing choices shape late life structural connectomics in cognitively healty subjects.<br>
We held tractography and parcellation constant while varying two upstream factors: the reference template and the tissue segmentation s... |
e90cb7c7d6c978baf57a04be8d72640cb1fb73def3e9b109bff7075bae4d5501 | Text | 6,474 | 160 | # Predicting Long-Term Opioid Use from PDMP Data
This project trains and evaluates multiple machine learning models to identify patients at risk of developing new long-term opioid use using real-world prescription data.
The repository provides an R-based, reproducible modeling pipeline built on features derived from P... |
7b4214f6e72b5c05b4af2114df499d626a119dfbc4c1b7e551975fcf20ef81e5 | Text | 6,503 | 150 | <div align="center">
<a href="https://infomeasure.org/">
<img src="https://infomeasure.org/assets/wordmark.svg" alt="infomeasure logo" width="616">
</a>
</div>
<div align="center">
<a href="">[](https://infomeasure.readthedocs.io/)</a>
<a hr... |
89cd318e43c2294d016016a3339fbbbcd82cb32cc32623a16bcd80cc4a584e5a | Text | 6,581 | 150 | [](https://arxiv.org/abs/2211.09648)
<div align="center">
<img src="https://github.com/Event-AHU/HARDVS/blob/main/figures/HARDVS_logo.png" width="350px">
**HARDVS: Revisiting Human Activity Recognition with Dynamic Vision Sensors**
------
<p align="ce... |
f4d676133dbd8412403e15cf752c87914670e95683a539d6d4d4c1845b462263 | Text | 6,811 | 206 | # SCopeLoomR v0.13.0
An R package (compatible with SCope) to create generic .loom files and extend them with other data e.g.: SCENIC regulons, Seurat clusters and markers, ... The package can also be used to read data from .loom files.
## Requirements
- HDF5 >= 1.10.1
For **Linux** and **MacOS** machines, version 1.1... |
01e73a087c26d3d8f043a16f5ff4991aed634dfaa59239dffdfc8ec72f714974 | Text | 6,861 | 67 | # dedup
dedup selectively removes redundant reads from paired-end libraries generated with random base molecular indices.
## About:
Random base molecular indices (also called unique molecular identifiers or UMIs) are molecular tags that can be introduced adjacent to your fragments of interest during sequencing libra... |
c6e2d4dbd9705ba9b5bf0726b1272f035186e048cdfb510bb3193161fdd844a6 | Text | 6,861 | 99 | <img src="https://github.com/welch-lab/liger/raw/newObj/inst/extdata/logo.png" width="120" style="display: inline;">
<a href="https://github.com/welch-lab/liger/actions/workflows/r.yml"><img src="https://github.com/welch-lab/liger/actions/workflows/r.yml/badge.svg?branch=master" alt="R" style="display: inline;"></a>
<... |
6fd969499cf7b3f718553d78e6fcb3b7892d4fd7872c1ac510922af84d113515 | Text | 7,120 | 174 |
LIPSIA 3.1.1: fMRI analysis tools
======================================
Lipsia is a collection of tools for the analysis of functional magnetic resonance imaging (fMRI) data.
Its primary focus lies in implementing novel algorithms, including laminar-specific fMRI analysis (cylarim),
statistical inference (LISA), and... |
de0e05b510b178e66a836d86701c4dab3d7e167291afa49b128719580a5ab457 | Text | 7,134 | 162 | <div align="center">
<h1>The Potential of Cognitive-Inspired Neural Network Modeling Framework for Computer Vision</h1>
<div>
<a>Guorun Li</a>;
<a>Lei Liu</a>;
<a>Xiaoyu Li</a>;
<a>Yuefeng Du*</a>;
</div>
<h3><strong>Accepted by [Advanced Science](https://advanced.onlinelibrary.wiley.com/doi/10.1002... |
b3c7c1d625f58372920dd1474fe7355f8ace83511a7ff21de5733718dc230250 | Text | 7,262 | 151 | # A New Graph Node Classification Benchmark: Learning Structure from Histology Cell Graphs
## Overview
Accompanying repository for **[A New Graph Node Classification Benchmark:
Learning Structure from Histology Cell Graphs](https://arxiv.org/abs/2211.06292)**
(New Frontiers in Graph Learning, NeurIPS 2022).
This re... |
cc229e1be145c317ec65e3262b544403c1e1cffa65bf0bd57cc3fa80a666e167 | Text | 7,356 | 125 | # HPL-prediction-of-response-to-ICI-in-Melanoma
Use of the Histomorphological Phenotype Learning self-supervised tools to study the response to ICI in Melanoma. This repository is related to the manuscriot titled: "Artificial Intelligence Algorithm Predicts Response to Immune Checkpoint Inhibitors." It is provided as ... |
38ac9d779b06fd73948283c7aa76792d73c9013ccca478516f9d49491c1bb7e7 | Text | 7,364 | 102 | # MR Reconstruction Pipeline
This is a reconstruction pipeline to reconstruct raw MRI data acquired with a Siemens MR scanner using gradient recalled echo (GRE) sequences. It is built to process raw data which is larger than memory, however, data can be processed entirely in memory and/or parallelized across as many ph... |
945662e463c5704fa6a2484783876810e255378f5fa9f6f33309aff20d68af0e | Text | 7,376 | 191 | # Neuronal Subnetwork Clustering and Statistical Analysis
[](https://doi.org/10.5281/zenodo.15856748)
## Protocol to detect neuronal subnetworks via clustering and analyze nested data using statis... |
6ba9a8a165c1f52f13e05d91d821bffe7a0d0a20f6bfc10248ef01f089682373 | Text | 7,434 | 121 | # Platelets-GBM
Platelet RNA profiling for glioblastoma: GSEA, TDEA, and Elastic Net analysis.
This repository contains code and data accompanying the manuscript:
> **Deepening the Understanding of Platelet RNA as Biomarker for Glioblastoma through GSEA, TDEA and Elastic Net Regularization Analysis**
>
> Anna Giczew... |
696b1ad2e31943af69164fc3dc7a203fd1a64826f6f5be7983a41b5312adcd5a | Text | 7,678 | 157 | # Visual Prompt Tuning
https://arxiv.org/abs/2203.12119
------
This repository contains the official PyTorch implementation for Visual Prompt Tuning.
## Environment settings
See `env_setup.sh`
## Structure of the this repo (key files are mark... |
a26706ede9e60669b27ddcf91031ccc48b4c1553c66d059a85afd2cb734f0bea | Text | 7,698 | 205 |
# 🧠 Doubly Stochastic Renewal Process
A Set of Tools for Simulating and Analyzing Spiking Irregularity.
## 📘 References
The source code for the following publication:
Aghamohammadi, C., Chandrasekaran, C., & Engel, T. A. (2024). A doubly stochastic renewal framework for partitioning
spiking variability. bioRxiv.... |
d14b4b8f94a1290b0097f474b87f4b924a1234759138aafd21e1835e3226b3df | Text | 7,709 | 60 | # Multiscale mathematical model-informed reinforcement learning (M4RL) framework supporting codes and usage instructions
## Article short title ##
M4RL for dynamic optimization of cancer treatment
## Abstract ##
Dynamic tumor-microenvironment interactions greatly affect growth and drug resistance, highlighting the ... |
243d98b0b8d79af2d0fd53e9b294301b4fd11e5bcc16c7b80f15ec47c430db9a | Text | 7,948 | 100 | ## This repository contains scripts necessary to reproduce figures presented in the PAL-AI paper.
Please download the source and processed data files from [Zenodo](https://doi.org/10.5281/zenodo.15461000) and place them in the `Data` folder.
In each folder, source the `helper.R` and run the `main.R` script to perfor... |
1ef4aac6b33ceff0fc6bd5c12ada205be55b2a484b76028573319b1f08bc6402 | Text | 7,998 | 270 | [](https://doi.org/10.1038/s41598-025-09114-8)
[](https://doi.org/10.1038/s41598-025-09114-8)
# BioLogicalNeuron Layer
A sophisticated biological neural network la... |
81e8df493d27df6fbbb706a045927222819e11870965e026a63cf9405a03720e | Text | 8,044 | 124 | <div align="center">
<img src="https://github.com/NeuroDiag/PyNoetic-official/assets/62457915/4c6aa260-66b5-4859-8c2e-5294ebf28fcc" width=60% />
**A Modular Python Framework for No-Code Development of EEG Brain-Computer Interfaces**
</div>
-----------------
<a href="https://www.python.org/"><img alt="Python" s... |
ed3faac18a684471ae0a336d2b156dd96ef561ab9e7fcfae967c31a2bbc49629 | Text | 8,645 | 95 | <p align="center">
<a href="https://github.com/delucaal/MRIToolkit">
<img src="img/MRIToolkitLogo.png" height="150"/>
</a>
</p>
# [MRIToolkit](https://github.com/delucaal/MRIToolkit) [Last update: 03-02-2026 v1.7]
## What is it?
MRIToolkit is a set of [command line tools](https://github.com/delucaal/MRIToolki... |
7cf7a7cb28078503325806307c16b74b197c1fb16f1f5356f3003f8f75717972 | Text | 8,679 | 183 | # Learning protein fitness models from evolutionary and assay-labelled data
This repo is a collection of code and scripts for evaluating methods that combine evolutionary and assay-labelled data for protein fitness prediction.
For more details, please see our pre-print [Combining evolutionary and assay-labelled data ... |
6f56bb54645d284403d6810e61b1b0fe5f1aaad09a46388937f9877ba2481266 | Text | 8,709 | 231 | # **RCM Analysis Paper**
This repository contains the code for the paper: Automated Detection of Benign and Malignant Skin Lesions from Reflectance Confocal Microscopy Images Using Deep Learning
## **Overview**
This project implements deep learning models for analyzing Reflectance Confocal Microscopy (RCM) images, s... |
fd52baa73278128ddf225d981493e95e9bc63e27a9eaa6a2d7a0602e719d325c | Text | 9,059 | 113 | [](https://github.com/mancusolab/sushie)
[](https://opensource.org/licenses/MIT)
[![Project generated with PyScaffold](https://img.shields.io/badge/-PyScaffold-005CA0?logo=pyscaffo... |
adc6148d6980fb1598cff6e0cc79ef11a44b1f2f6a9f4c96df2797bd5ed45c6b | Text | 9,681 | 62 | # UCLA 2P Miniscope
UCLA miniature multiphoton microscope resources and design files.
The UCLA miniscope project is an open-source inititive to design open-source miniature microscopes for neuroscience. Here, we present a multiphoton miniature microscope developed at UCLA which is able to record from fine structures ... |
35da26fea8d4ba549ebccd88c384ff1bd2469d77bfb89c835516f0660ad428f2 | Text | 10,108 | 235 | # TCRdock
Python tools for TCR:peptide-MHC modeling and analysis
Described in the manuscript: "Structure-based prediction of T cell
receptor:peptide-MHC interactions" by Philip Bradley. bioRXiv link:
***[NEW 2024-03-06]*** The AlphaFold code was updated to alphafold v2.3.2
from alphafold repo commit f715f016d875e2f... |
a865aced4d53815fdde3edd879f473ac75790d2a40d0e6fdb4ca19d8e31b9905 | Text | 10,672 | 191 | # Getting Started With the Pipeline
This repository contains the pipeline codes for the long-term multiple-brain-region imaging of neuronal and neurochemical dynamics in *Drosophila* brain by the two-photon synthetic aperture microscopy (2pSAM). This pipeline includes Δ*F/F* extraction and data analysis, organized by ... |
b9ca82d3d6a1e17ea175dee53e8d6218c7144f0c9a3ea14b785c0ef288932538 | Text | 11,203 | 246 | # OpDetect: A convolutional and recurrent neural network classifier for precise and sensitive operon detection from RNA-seq data
## Abstract
An operon refers to a group of neighbouring genes belonging to one or more overlapping
transcription units that are transcribed in the same direction and have at least one ge... |
5a23aabab1aafd9eead774373bd597d4181be8cf37eafee8ee07df8f0115853e | Text | 11,454 | 198 | # spec2nii
[](https://doi.org/10.5281/zenodo.5907960)
A program for multi-format conversion of in vivo MRS to the [NIfTI-MRS format](h... |
3e194d0e6cdb2911a72d82a9ecf2296afe191092df4fd332a4cd2e31943299f2 | Text | 11,761 | 200 | # SamSrf X - Read Me
This major release includes a standalone application for integrating into
NeuroDesk & eventually browser-based analysis platforms. It includes the
most recent updates which involved a better & faster algorithm for fitting
population receptive fields, support for microtime resolution (i.e. smoot... |
3d2312d275f139c6d67e19a50edefe16a6197b1e6228ca64ea707aa8371d2baf | Text | 11,788 | 232 | # The Open Kidney Ultrasound Data Set
<!-- PROJECT SHIELDS -->
<!--
*** I'm using markdown "reference style" links for readability.
*** Reference links are enclosed in brackets [ ] instead of parentheses ( ).
*** See the bottom of this document for the declaration of the reference variables
*** for contributors-url, fo... |
a7b21fec75343736e439433138603c41a6080e3d8686a9df234120b4f682aebe | Text | 11,988 | 253 | # physio-bold-aging
Source code for "Physiological Component of the BOLD Signal: Influence of Age and Heart Rate Variability Biofeedback Training"
## Overview
This repository contains the analysis code for investigating the relationship between physiological signals and the BOLD fMRI response across different age gr... |
931c47ee7d494ebe493783dac8c904b0a314e6c08650f58533f7c28bd9631362 | Text | 12,201 | 272 | <h1 align="left">AP-10K: A Benchmark for Animal Pose Estimation in the Wild <a href="https://arxiv.org/abs/2108.12617"><img src="https://img.shields.io/badge/arXiv-Paper-<COLOR>.svg" ></a>
</a> </h1>
<p align="center">
<a href="#introduction">Introduction</a> |
<a href="#Updates">Updates</a> |
<a href="#Overvi... |
6d16b33c48a41e248afc872b5f019732dc35d1fc7598a3b39913c6613b94743b | Text | 12,392 | 271 | # T-cell_and_glial_pathology_in_PD
Code and data for:
**“The spatial landscape of glial pathology and adaptive immune response in Parkinson's Disease”**
---
## Overview
This repository contains code, processed data, and analysis pipelines for spatial cross-correlation analysis of cellular interactions in Parkins... |
dd02d0738be1b2a6f3c1a3fe4af1890fbe2f878bf74222315165859c15d2604c | Text | 12,536 | 259 | # NeuroCAPs: Neuroimaging Co-Activation Patterns
[](https://pypi.python.org/pypi/neurocaps/)
[](https://pypi.python.org/pypi/neurocaps/)
[ as originally
described in [*DeepInsight: A methodology to transform a non-image data to an
image for convolution neural network architecture*][di] [\[1\]](#1). This is not guarantee... |
7affa5cd6130287365507cd7551e93d80668978e03b9bd928faab55fad4024fe | Text | 13,737 | 410 | # Expression Graph Network Framework (EGNF)
## ⚠️ Note on Graph Construction and Data Leakage
The graph (tree) generation process differs between **feature selection** and **prediction** tasks:
- **Feature selection stage**
Graphs need incorporate `group_label` (e.g., outcome or class labels) to identify informa... |
ed82498cd9659bacb4bdfbb6fcb92ef1f5aa5c94b2e7c3d022eae585eea0e074 | Text | 15,053 | 345 | # Enhanced Detection of Age-Related and Cognitive Declines Using Automated Hippocampal-To-Ventricle Ratio in Alzheimer's Patients
This repository contains the analysis code, derived measurements and
manuscript sources for the study above, published in *Human Brain Mapping*
(2025). We trained and evaluated three automa... |
f7acf38cb613160542d9ac2dc5ef509a98af46c2f94241ac958a7dd4a83f205d | Text | 15,103 | 284 | # SynthSeg
In this repository, we present SynthSeg, the first deep learning tool for segmentation of brain scans of
any contrast and resolution. SynthSeg works out-of-the-box without any retraining, and is robust to:
- any contrast
- any resolution up to 10mm slice spacing
- a wide array of populations: from young an... |
300232873a41be0e90693bda3b764e6d21cc57110d1625f7415c04a0746787f4 | Text | 15,340 | 506 | [](https://doi.org/10.1038/s41598-025-09114-8)
[](https://doi.org/10.1038/s41598-025-09114-8)
# BioLogicalNeuron Layer
A sophisticated biological neural network la... |
9c77a44b3681d0b3287158ab98458561c2d416bdee7897554580edf62f046d44 | Text | 15,754 | 233 | # iQuanta
## Description
### iQuanta is a Python module designed to establish an innovative framework for quantifying the information content within neural data by leveraging machine learning techniques.
One of the primary methods neurons employ to communicate is through the generation of action potentials, also kno... |
753c7c9af3f68a33449906ceb73c0ede685d298fbc12b30d616a303f87fe29b0 | Text | 15,931 | 245 | # LRGB: Long Range Graph Benchmark
[](https://arxiv.org/abs/2206.08164)
<img src="https://i.imgur.com/2LKoGbu.png" align="right" width="275"/>
We present the **Long Range Graph Benchmark (LRGB)** with 5 graph learning datasets that arguably require
lo... |
483fce92676a2fdff535515449a27358f6df80ae83af72940d2f300232bc1b2b | Text | 16,593 | 406 | <div align="center">
# COBRAI toolbox
<!---
<a href="https://pytorch.org/get-started/locally/"><img alt="PyTorch" src="https://img.shields.io/badge/PyTorch-ee4c2c?logo=pytorch&logoColor=white"></a>
<a href="https://hydra.cc/"><img alt="Config: Hydra" src="https://img.shields.io/badge/Config-Hydra-89b8cd"></a>
[
---
Copyright © 2016-2023 Medical Image Analysis Laboratory, University Hospital Center and University of Lausanne (UNIL-CHUV), Switzerland
This softwar... |
447cd9d8bfdd2c5903248084893475bd238392a662397e06fb48895a13c43501 | Text | 19,432 | 342 | # OnSIDES
**Just looking for the data?**
Click on the "Releases" tab on the right.
## Table of Contents
- [Introduction](#introduction)
- [Downloading the Data](#downloading-the-data)
- [Loading into a database](#loading-the-data-into-the-database)
- [Database design and organization](#database-design-and-organizati... |
f70a44e0b95929f89547a9220322b80a446e8941b46f369e1d46ea8648bb1147 | Text | 21,184 | 313 | # heterogeneous_synaptic_homeostasis
### Introduction
This GitHub repository contains scripts for implementing heterogeneous synaptic homeostasis, a novel synaptic mechanism designed to elucidate shifts in the propagation pattern of information across the cortex during the sleep-wake cycle. Detailed information on thi... |
2d64858ba0630d6da908168b861351985b74c4a3885d7ce302e681a61c8eeab9 | Text | 23,436 | 622 | # :star2: MAPIT-seq Pipeline
:bust_in_silhouette: Author: **Gang Xie**, PhD candidate
:school: Affiliation: PKU-THU-NIBS Joint Graduate Program, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
:e-mail: Email: **gangx1e@pku.edu.cn**
:date: Date: July 25th, 2025
:white_check_mark: V... |
eefd804b167f1645d666980b8fef734c83f39848b4c108a57b049ddadefb78a5 | Text | 24,144 | 578 | .. image:: https://travis-ci.org/popgenmethods/smcpp.svg?branch=master
:target: https://travis-ci.org/popgenmethods/smcpp
SMC++ is a program for estimating the size history of populations from
whole genome sequence data.
.. contents:: :depth: 2
Quick start guide
=================
1. Follow the `installatio... |
cc219c5c7a7f23211b36cebc6952a28df8ae221f4756ab81251cc30cb7d01a48 | Text | 25,874 | 388 | <p align="center"><img src="misc/porechop_logo_knife.png" alt="Porechop" width="600"></p>
Porechop is a tool for finding and removing adapters from [Oxford Nanopore](https://nanoporetech.com/) reads. Adapters on the ends of reads are trimmed off, and when a read has an adapter in its middle, it is treated as chimeric ... |
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