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a1d18daa58c674437951616ca18e894a94fd3538fba19966cad5bfef4125076b | Text | 4,912 | 66 | [](https://hippunfold.readthedocs.io/en/latest/?badge=latest)
<img align="rig... |
a5d1a936a827571eef234620592dbb2aa9f5650e78b436265931ddc94e7c84d6 | Text | 4,946 | 157 | # ROIpy
## Description
**ROIpy** is a python package for ROI (Region of Interest) semi-automatic generation and placement for functional imaging of neuronal dendrites of individual neurons. It provides a tool for defining, managing and visualizing dendritic ROIs. In addition, provides a benchmark for analyzing morpho... |
457a0ee08d2b64892bfb7a7b4d839381b80779b99b93a9759f09210180e19b1c | Text | 4,948 | 110 | DATASET: HIF-1α and HIF-2α Are Upregulated in the Hippocampus but Not
in the Medial Prefrontal Cortex in Experimental PTSD
================================================================================
AUTHORS
================================================================================
Denys Porkhalo (1), ... |
3db2d946482d46e377831e90edb3ef5496febaa621edc08c25ce58d99a015c5c | Text | 4,963 | 143 | HYDRA
Section of Biomedical Image Analysis
Department of Radiology
University of Pennsylvania
Richard Building
3700 Hamilton Walk, 7th Floor
Philadelphia, PA 19104
Web: https://www.med.upenn.edu/sbia/
Email: sbia-software at uphs.upenn.edu
Copyright (c) 2018 University of Pennsylvania. All rights... |
f8b1f051651b4b09314505cbe2fb36b08d7fb7610c6a5c6e92c9f0d8097004c1 | Text | 5,037 | 159 | # ROIpy
[](https://doi.org/10.5281/zenodo.21334248)
## Description
**ROIpy** is a python package for ROI (Region of Interest) semi-automatic generation and placement for functional imaging of neuronal dendrites of individual neurons. It provides a tool for defining, mana... |
5f892c8872a854c9029ac77fce0c6523512d10a9e1b064122112bc2a5c7c5475 | Text | 5,062 | 109 | # Snakebids
[](https://github.com/khanlab/snakebids/actions/workflows/test.yml?query=branch%3Amain)
[](https://codecov.io/gh/khanlab/snakebi... |
9117f9d255d6b6e810d224a600d381192bccccd3f0cd417fed9559d49ca8fffd | Text | 5,065 | 83 | # Pangolin
Pangolin is a deep-learning based method for predicting splice site strengths (for details, see [Zeng and Li, Genome Biology 2022](https://doi.org/10.1186/s13059-022-02664-4)). It is available as a command-line tool that can be run on a VCF or CSV file containing variants of interest; Pangolin will predict ... |
9796b0d9b81dfe27a214021811289d8e5587a572d7ba0c3b7f3f453a83f5bceb | Text | 5,122 | 68 | # Numerical optimization of gradient waveforms (NOW) for tensor-valued dMRI
A MATLAB package for optimization of gradient waveforms that yield b-tensors of arbitrary shape that can be tailored to pulse sequence timing and hardware restrictions.
The optimizer supports the following:
* Arbitrary b-tensor shape
* Varia... |
c047127cebef46379bdf65c765e3b5a515b520466033011f0ba2a87207b87ae9 | Text | 5,223 | 137 | # Dynamic Functional Connectivity Toolbox (`dFC_toolbox_app`)
This repository includes portions of the following freely available software:
- Brain Connectivity Toolbox available at https://www.nitrc.org/projects/bct/
- Tools for NIfTI and ANALYZE image available at https://www.mathworks.com/matlabcentral/fileexch... |
552bda787b4b79ec60b3671f04c67659c6242a1119a5c148436c86f43e239ea7 | Text | 5,284 | 98 | # allen_conn_maker — shareable bundle
This folder contains a two-stage pipeline that builds a single-cell synaptic connectivity matrix for the mouse brain by combining:
- per-neuron MERFISH coordinates from the Zhuang Allen Brain Cell Atlas (ABCA), and
- the Allen Institute mesoscale voxel connectivity model (Knox et... |
6ce87c2dab378518bd081d99d038be3460de732cd67f3ea0bf54a135ba066d85 | Text | 5,352 | 120 |
# "Stabilized hierarchical deep neural networks with multiple knockoffs (Stabilized HiDe-MK)"
## Overview
Deep neural networks (DNN) have been used successfully in many scientific problems for their high prediction accuracy, but their application to genetic studies remains challenging due to their poor interpretabil... |
a861ccefa033ab477947e115ece467c52a8931213275edfd27823c308cf7ac25 | Text | 5,434 | 153 | # adpbulk
# Summary
Performs pseudobulking of an `AnnData` object based on columns available in the `.obs` dataframe. This was originally intended to be used to pseudo-bulk single-cell RNA-seq data to higher order combinations of the data as to use existing RNA-seq differential expression tools such as `edgeR` and `DE... |
dacf861714b8c4547bf4dd83a41d898ade80d7b5247c366fcd492baaffa7394f | Text | 5,525 | 155 | # adpbulk
[](https://doi.org/10.5281/zenodo.20736457)
# Summary
Performs pseudobulking of an `AnnData` object based on columns available in the `.obs` dataframe. This was originally intended to be used to pseudo-bulk single-cell RNA-seq data to higher order combinations o... |
a287ca9c9c199c898ba2fa3b7a4b5d00cef82b10dd9630c59c77e9b8fca6f4a6 | Text | 5,533 | 82 | # DeepLINK: Deep Learning INference using Knockoffs
DeepLINK is a variable selection algorithm that guarantees the false discovery rate (FDR) control in high-dimensional settings. It consists of two major parts: an autoencoder network for the knockoff variable construction and a multilayer perceptron network for featu... |
ba542916d9bb584807649c1c8f3974e7098c8d245fdac8d36d4d1011cd734da2 | Text | 5,537 | 124 | # CELER: A 365-Participant Corpus of Eye Movements in L1 and L2 English Reading
Eye movement recordings of 69 native English speakers and 296 English learners reading Wall Street Journal (WSJ) newswire sentences. Each participant reads 156 sentences: 78 sentences shared across participants and 78 unique to each partic... |
a0982c590937157412d00a884667544b7589bc6dff667cea7a511efc3bbd2eee | Text | 5,561 | 116 |
# EB-Segmentation-Mask2Former
Code to train and evaluate the Mask2Former architecture for Epidermolysis Bullosa (EB) wound image segmentation, developed for the paper **'AI-based segmentation of wound types caused by Epidermolysis Bullosa'**.
*Note: A link to the paper will be provided here following its a... |
ba97b14dde36322c24f729c3b64734076d6779bf47b9ee6aa066fa3695f6024b | Text | 5,593 | 117 | # Hierarchical Spiking Neural Network
This project models the primate ventral visual system (PVVS) as a hierarchical spiking neural network (HSNN) trained via spike-timing-dependent plasticity (STDP). This is to study the emergence of feature selectivity of shapes and to evaluate a hypothesis for feature binding - hie... |
f53daa5fdd1ee6ca5ec4c3b75eafe83b9c858a5698cc02e8cf9441fcb6a4cf7e | Text | 5,698 | 122 | # Update Jan 16, 2026
### A more recent implementation of LD score regression in python 3 can be found at https://github.com/CBIIT/ldsc. See also the accompanying [web browser](https://ldlink.nih.gov/ldscore) and [preprint](https://doi.org/10.64898/2025.12.19.695639).
# LDSC (LD SCore) `v1.0.1`
`ldsc` is a command l... |
8c8100e208b15a89ee8b93cb87b6d575a73a266a2924906a8307cc84fe650784 | Text | 5,712 | 146 | ————————————
GENERAL INFORMATION
————————————
This readme file was generated on [2026-05-26] by [Emily Meeus]
This repository contains the R scripts and source data tables used to generate the expression, morphology, and developmental phenotype analyses reported in the paper “ATP13A4 gates extracellular polyamine l... |
e9884266d5ff2075876b4cb91ad334a06e049cadb88fdbb49720da33fb9fa2da | Text | 5,720 | 97 | <img src="yanat.png" alt="drawing" width="400"/>
At the moment, this bad boy containts a few network communication metrics and models at its `core` and a game-theoretical network generation framework at `generative_game_theoric`. I'll just add more stuff as I go.
## Installation
Guess what, `pip install yanat` is all... |
7a351ac16738da2ef0ccd22c731b18d6c94d78a161db58124eef73f69576756b | Text | 5,769 | 175 | # *Stoic*
Fast and accurate protein stoichiometry prediction.
[](https://github.com/PickyBinders/stoic/blob/master/LICENSE.txt)
[](https://www.biorxiv.org/content/10.64898/2026.03.13.71... |
1d7f910968a7fc8c2707b9236a67923b7068de2a604647c60c013eadd4bd993b | Text | 5,833 | 132 | # SlotDeconv
<p align="center">
<img src="framework.png" alt="SlotDeconv workflow overview" width="900">
</p>
SlotDeconv is a reference-based spatial transcriptomics deconvolution method for estimating spot-level cell-type proportions from spot-based spatial transcriptomics data. It learns discriminative cell-type... |
7f145b15811926cf78d67d1a4fb169f7384812b74e6f61fefecfc0a0b7d8f83b | Text | 5,957 | 195 | # **DiffusionOT**
**DiffusionOT** is a dynamic **Regularized Unbalanced Optimal Transport (RUOT)** model that reconstructs cellular trajectories and landscape from time-series scRNA-seq snapshots as well as a **Stochasti... |
3a3a5d37264180878784fed928dc645aa1d335e389985e73b53db474b4cd070c | Text | 6,095 | 183 | # **DiffusionOT**
**DiffusionOT** is a dynamic **Regularized Unbalanced Optimal Transport (RUOT)** model that reconstructs cellular trajectories and landscape from time-series scRNA-seq snapshots. Additionally, a **Stochastic ... |
df7326673650d6f3c502311634de6ab20b94867b8941698d54c22151f7784917 | Text | 6,182 | 110 | # mcw_Preclinical_MRIsequences
Public-facing repository for various MRI pulse sequences developed by M Budde at the Medical College of Wisconsin.
This repository is replacement for the previous [OSF sharing site](https://osf.io/ngu4a/)
:bangbang: **To access sequences (private repositories), follow these [instruction... |
1edbaf669cf27dd23651022d85d352edc368412d7003a14b8dd3a9d023a3cb24 | Text | 6,289 | 140 | # Brain STRIDE: Longitudinal Harmonization and Atrophy Analysis
R Markdown pipeline for harmonizing longitudinal brain volumetric measures across
imaging protocols and analyzing individual atrophy trajectories in relation to
lifestyle factors.
## Overview
This repository contains three analysis scripts that are inte... |
e99e1501c44612f49fb3d5df36b65d00b11a943f8efc7a00b7df0b41e4284442 | Text | 6,294 | 53 | ### :tada: Update (Aug 2021):
Interested to see how well your model copes with challenging stylized images? Check out the comprehensive toolbox at [bethgelab:model-vs-human](https://github.com/bethgelab/model-vs-human), which supports stylized data (complete with human comparison data) and comes with code to evaluate a... |
d590ee7781b9c180d7aa0c4e29737723bc7ea8ed8fb2ee7936ce52f3c9eab7de | Text | 6,310 | 134 | # A data-driven evaluation of optimization techniques in cell culture media
Code and input data for the *Bioinformatics* paper **"A data-driven evaluation of
optimization techniques in cell culture media."** It benchmarks Bayesian
optimization, design-of-experiments, and baseline search strategies on six
published cel... |
58eecd3ec8cf8489563a99c0f04ecc5ec237637460e0bcf4203b34bf0cb3d79e | Text | 6,409 | 164 | # HIF and PACAP gene expression in SPS-induced rat PTSD model
Statistical analysis of HIF-1α, HIF-2α, HIF-3α, PACAP and PAI-1 gene expression in hippocampus and medial prefrontal cortex of rats with an SPS-induced PTSD model. Includes normality testing, two-group comparison (t-test / Mann-Whitney U), and publication-r... |
478bbcbcfef0f19365da174b5ef82481109bdf437ba7e2d26b818d21c53e7306 | Text | 6,470 | 173 | # MiniMORPH: A Morphometry Pipeline for Low-Field MRI in Infants
## Overview
This script is designed to run the ANTs pipeline for segmenting infant brain images on Flywheel. The pipeline consists of the following steps:
1. Register segmentation priors (tissue and CSF) and segmentation masks (ventricles, subcortical G... |
2ae911bd488b212e030492ebcbdbbc70ba4cb7d2538535765c691f248bc194ce | Text | 6,506 | 141 | # iEHM
Image analysis code used in the iEHM (innervated Engineered Human
Myocardium) publication, "Innervated human cardiac muscle model reveals
sympathetic drivers of KCNH2-associated arrhythmias" (accepted, *Nature
Communications*). The pipeline segments vasculature and axons
(neurofilament) in confocal microscopy s... |
67599558bcc70ea7061cf7573a26e1f77e6a05a2b457d73ea58fae131a80a246 | Text | 6,519 | 178 | # nfml
Machine learning for the computational discovery of **ferroelectric nematic
(N<sub>F</sub>)** liquid crystals.
The package does two things. It **predicts N<sub>F</sub> properties** — whether a
molecule exhibits the N<sub>F</sub> phase (classification) and at what
temperature it transitions (regression) — using... |
177795145138902f960e8ea4fa9c8bc1807511855256dae9b8493d701ed10434 | Text | 6,566 | 144 | # Garnet force field
[](https://github.com/greener-group/garnet/actions/workflows/CI.yml)
[](https://github.com/greener-group/garnet/blob/main/LICENSE.md)
If you use... |
827f4304258fd84aa83e202a39a80fc73c333eb66b5e546ee9e1e8fb4bc465ff | Text | 6,701 | 108 | # Glia_3740732_Data
Repository of series of data sets used in the publications of the paper "Dorso-Ventral and Night-Day Regulation of Extracellular K+ Dynamics in Mouse Hippocampal Astrocytes" in Glia
# Electrophysiological and Structural Dynamics of Astrocytic Currents across Circadian Rhythms (ZT) and Brain Regions... |
73af3bedfc34fed1b03b584e9a5721cf7b5baa0e50020c5ee10fc630152dc230 | Text | 6,778 | 108 | # Glia_3740732_Data
Repository of series of data sets used in the publications of the paper "Dorso-Ventral and Night-Day Regulation of Extracellular K+ Dynamics in Mouse Hippocampal Astrocytes" in Glia
# Electrophysiological and Structural Dynamics of Astrocytic Currents across Circadian Rhythms (ZT) and Brain Regions... |
da9d333594cae6065b8ea67ecff8b8a0a8836be6405915996f74fb9a8dc92ae8 | Text | 6,839 | 93 | # Fgfr1_analysis
To be written
sessionInfo()
R version 4.3.3 (2024-02-29 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19045)
Matrix products: default
locale:
[1] LC_COLLATE=English_Sweden.utf8 LC_CTYPE=English_Sweden.utf8 LC_MONETARY=English_Sweden.utf8
[4] LC... |
dbf11762504513fd57167ce3c12c04c72f9baf567496b88d05837c564b689722 | Text | 7,148 | 140 | # Vox2Cortex and related methods
*Note*: This repository has been refactored entirely, you can find the old Vox2Cortex repo [here](https://github.com/ai-med/Vox2Cortex/releases/tag/v0.1.0).
*Note*: For an implementation of V2C-Long, see [this](https://github.com/ai-med/V2C-Long) repo.
This repository implements sev... |
902392247ae7b6ce859a3b331071a2360bbed773a381ea2ddcc89794632ff76d | Text | 7,260 | 157 | # Frost & Microstructure Classification
[](https://doi.org/10.17605/OSF.IO/TYDSM)
[](https://github.com/SofiaKouki/frost_action_classification#CC0-1.0-1-o... |
629d9e571828c113518ebebe31551e29cc7652353bb64c26059352a67feb1e97 | Text | 7,400 | 66 | <picture>
<source media="(prefers-color-scheme: dark)" srcset="docs/source/_static/images/logo/chemprop_logo_dark_mode.svg">
<img alt="Chemprop Logo" src="docs/source/_static/images/logo/chemprop_logo.svg">
</picture>
# Chemprop
[](https://b... |
d5316af44ab77f36efcc1f7b6466598fd4d726ef4757e55e54ba2f21431bee75 | Text | 7,436 | 193 | # File descriptions
### AlphaMissense_hg19.tsv.gz, AlphaMissense_hg38.tsv.gz
Predictions for all possible single nucleotide missense variants (71M) from 19k human protein-coding genes (canonical transcripts) for both hg19 and hg38 coordinates. These files are sorted by genomic coordinates.
### AlphaM... |
72203c8f27dc0c97e629bf5beec67799854bdcb4380023b598ff61ca04e60aab | Text | 7,470 | 135 | # neuronephys — mouse cortex simulation engine (minimal share package)
GPU-accelerated large-scale simulation of the mouse isocortex: ~300K Hodgkin–Huxley
neurons with realistic Allen Brain Atlas (Zhuang MERFISH) connectivity. CUDA C++ with
Thrust, targeting NVIDIA GPUs.
This folder is a **minimal, self-contained cop... |
c7e733f33c2b2dce6735e620179e8f95fc82f42bd367bc8b7d9489938f6e2172 | Text | 7,523 | 202 | # Postpartum Brain Age Prediction
**Conceptual implementation of the postpartum brain age prediction model**
This repository provides a PyTorch implementation of the deep neural network used to predict brain age from structural MRI in postpartum and nulliparous control women. The model:
- Uses three CAT12-derived ti... |
10e6054aab9ad8fdd86bc605f2b72d01503cd8d1ada4fd9aa39b031b9efc81e2 | Text | 7,528 | 142 | <p align="center"><em>Mesa 4 is in active development! Checkout our latest <a href="https://github.com/mesa/mesa/releases">pre-releases</a> and <a href="https://github.com/mesa/mesa/issues/3132">issue tracker</a>.
<br>For GSoC, checkout our <a href="https://github.com/projectmesa/mesa/wiki/Google-Summer-of-Code-2026">G... |
80bd67831926ef6fb20ccd199787cd7b67b124a2b391e9b984642ee60d91fe4a | Text | 7,657 | 52 | Shield: [![CC BY-NC-SA 4.0][cc-by-nc-sa-shield]][cc-by-nc-sa]
This work is licensed under a
[Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License][cc-by-nc-sa].
[![CC BY-NC-SA 4.0][cc-by-nc-sa-image]][cc-by-nc-sa]
[cc-by-nc-sa]: http://creativecommons.org/licenses/by-nc-sa/4.0/
[cc-by-nc-s... |
345f4b00e26107c5a217cb6fedef264e4993cda047b67040d622aed7efcab5de | Text | 7,698 | 350 | # Early Detection of SARS-CoV-2 Variant Dominance and Hospitalization Impact
This repository contains the analysis pipeline used in the study:
**“From Sequences to Strategies: Early Detection of New SARS-CoV-2 Variants via Genetic Distance to Reduce Hospitalizations.”**
The project integrates genomic surveillance, m... |
ca5a86e105bfdd6f277b484a71591267a41f362c401abb1cea4152a8f1b57ae0 | Text | 7,754 | 123 | [](https://github.com/navis-org/navis/actions/workflows/build-docs.yml) [](https://github.com/navis-org/navis/actions/workflows/test-package.yml)... |
d09e98f442ee039564880b86b2dab723cd8e86626d6f7d398f44d8880451c3f3 | Text | 7,862 | 155 | RingFinder
==========
Automated image analysis for finding the fraction of structure presenting a given pattern. Originally developed to identify the 190 nm periodicity in the actin/spectrin cytoskeleton of neurons.
Installation
~~~~~~~~~~~~
Ubuntu
^^^^^^
Run in terminal:
::
$ sudo apt-get install python... |
ba8f9cd01b3630936c5525f29bec2ce7377f3358e4104dbbb32af3e3fba46c49 | Text | 7,874 | 134 | # WORC: Workflow for Optimal Radiomics Classification (v3.7.1)
<a href="https://bigr.nl/"><img src="https://bigr.nl/img/bigr.jpg" alt="Your Image Alt Text" width="200"/></a>
## Information
| Unit test | Documentation | PyPi |Citing WORC |
|-... |
192d9a630a0d929019e4dc369bebd897b8f38aeb4049b661c4ba2f4763fb9d12 | Text | 7,908 | 201 | # SpatialModal
## Overview
SpatialModal is a multimodal graph learning framework for spatial transcriptomics analysis. It integrates gene expression, spatial coordinates, and optional histological image features to learn spatially aware latent representations for... |
39cb28cd9ebb023d922427ebf5805c102eee450f72ffbf20c46599f2f8bc6f7c | Text | 7,987 | 166 |
<img width="100%" height="300px" alt="NoClaMe_GitHub" src="https://github.com/KylleV/noclame/blob/main/NoClaMe_GitHub.svg" />
# Node Classification Metrics, (NoClaMe)
A small script containing four different metrics for binary node/vertex classification: top-k and three new metrics **NRD**, **ANPI** and **RRCS**.
... |
2932d9a528fc4c5ca928cf8f87088d2a2bb8a1b679122ed02bcbf782588869dc | Text | 8,040 | 144 | WORC: Workflow for Optimal Radiomics Classification (v3.7.1)
============================================================
Information
-----------
+-------------------+------------------+------------------+-------------+
| Unit test | Documentation | PyPi | Citing WORC |
+===================+===... |
d4705ee4678e07f77dbb85342ed14ca8b7b2ad317b23afb97c722870532f529a | Text | 8,108 | 178 | # Visual Prompt Engineering for Multimodal and Irregularly Sampled Medical Data
Malte Tölle, Mohamad Scharaf, Samantha Fischer, Christoph Reich, Silav Zeid, Christoph Dieterich, Benjamin Meder, Norbert Frey, Philipp Wild, Sandy Engelhardt
Paper link: https://arxiv.org/abs/2501.18237
## Abstract
A multitude of exami... |
9930615e5307c6cc027102e8f479ebe7ba48132ef7641ffd482a52134aeb82d2 | Text | 8,146 | 193 | # Alzheimer's Disease Biomarker Visualization Tools
<!-- badges: start -->
<!-- badges: end -->
<p align="center">
<img src="raindrop_animation_demo.gif" alt="Longitudinal biomarker trajectories" width="450">
</p>
> Interactive Shiny applications for visualizing longitudinal Alzheimer's disease biomarker trajector... |
39be8950b2745908c700e7c5c247071520d15eebabacbf4823b9a6b9b6be605d | Text | 8,156 | 187 | # Biostatistics WD - Postural Asymmetry and SF Analysis
A comprehensive R-based biostatistics project for analyzing postural asymmetry (PA) measurements in rats, with a focus on withdrawal (WD) studies using Bayesian statistical frameworks.
## Project Overview
This project provides tools and analyses for studying po... |
03db4c0b1fd91b01a7ba7d135cc655204972053b8dff48e17757622c24b3c40a | Text | 8,408 | 93 | # PyBrainAge
## PyBrainAge development
Here we introduce PyBrainAge (beta version) which is a Brain-age model designed to estimate age (brain-age) based on structural T1-weighted MRI brain scans. Below, you will find additional information about the model and instructions on running it with your preprocessed T1-weight... |
e8ed60134fb9cf9ece9c87bba9c4a296f18907372a0e9e21f62206e0702b2cfd | Text | 8,448 | 170 | [](https://www.python.org/downloads/)
[](https://www.gnu.org/licenses/old-licenses/gpl-2.0)
[](https://... |
849482de545771e3a41cd0a3dc52e1bbd447d1e1d6687a6e790c96dc47520eba | Text | 8,500 | 143 | ## Repository information
This repository contains the code and data resources used to reproduce the behavioral, EEG, computational modeling, and figure-generation analyses reported in the manuscript “Impaired midfrontal-motor theta phase synchronization characterizes maladaptive motivational behavior in obsessive-com... |
976e339e35ccb21961d0096a6b1610881ae36fe673078ab30105ced304b413e4 | Text | 8,612 | 181 | [](https://pypi.org/project/scMethyAnno)
# **MethyAnno: An Interpretable Automated Annotation Method Leveraging Multi-scale Information and Metric Learning Framework for scDNAm Data**
## Introduction
**MethyAnno** is an interpretable... |
8f20353d3200285e2cdb54475d4ab2875432cb82f3b9def6351c0e769452d2c4 | Text | 8,664 | 157 | 
[](https://github.com/JuliaMolSim/Molly.jl/actions)
[**.
Includes dataset generation, training, prediction with attention export, and visualization & analysis tools.
---
## Features
- **EGNN model** with attention and edge features (`egnn.py`... |
5b982f8be69e67815ca87aa869f58011a521f0253235174aa13f5782b7eb8650 | Text | 8,903 | 128 | # PISA 2022 Science Association and Model-Attribution Analysis
This repository contains the analysis code supporting the revised manuscript, *Recurrent and system-specific model-attribution patterns in PISA 2022 science performance across nine education systems*.
## Scope
The repository provides the workflow for bui... |
6db25e56fb100bdea58762948c2a04402b1a23aaed083844603efd336d5ec56c | Text | 9,371 | 252 | <img width="100%" alt="STABL" src="./front_page.png">
# Discovery of sparse, reliable omic biomarkers with Stabl
[](https://doi.org/10.1038/s41587-023-02033-x)
[ for:
> Romer, A. S., et al. 2026. Prioritizing removals of a highly cryptic invasive species using machine lea... |
f21589f5a30cb0d2670f55a727ee53326d6b049b60b102060e1945a9f129dc6e | Text | 9,750 | 189 | # CW-Net Reproducibility Capsule — Autonomous Driving
This repository contains all code, data, and materials to reproduce the results from the CW-Net paper on concept-based explanations for autonomous driving.
*Figur... |
8d2d6aeff1d2e4001018b57424a12554d958dcf45335ab09bc5246312a91995a | Text | 9,838 | 152 | # Decomposing condition-related signals, effect modifiers, and batch effect of complex forms in scRNA-seq studies with neural discrete representation learning
by: Xiao Xiao (xiao.xiao.xx244@yale.edu)
---
## Abstract
Advances in single-cell sequ... |
395dd380215ca928940c39bbf4808283cf9e06baa85b0fd075abd081a4a18903 | Text | 9,909 | 153 | # brainageR
Software for generating a brain-predicted age value from a raw T1-weighted MRI scan. This uses a Gaussian Processes regression, implemented in R, using the kernlab package.
The software takes raw T1-weighted MRI scans, then uses **SPM12** for segmentation and normalisation. A slightly customised version **... |
8788f5562779478188758e6b671aa22095d95b6c44154332446790045a79c9e2 | Text | 9,978 | 235 | 
# MICAFlow: Accessible, fast, and pythonic MRI processing pipeline
<div align="left">
[](https://github.com/MICA-MNI/micaflow)
[![PyPI v... |
7d4c741dd55f4667997f10c70b7356d45a4703e514f2cfa33efebec858519421 | Text | 10,273 | 187 |
## Perceptual Similarity Metric and Dataset [[Project Page]](http://richzhang.github.io/PerceptualSimilarity/)
**The Unreasonable Effectiveness of Deep Features as a Perceptual Metric**
[Richard Zhang](https://richzhang.github.io/), [Phillip Isola](http://web.mit.edu/phillipi/), [Alexei A. Efros](http://www.eecs.be... |
8c0972cab4c4d32230cdca7242d141b88b97bda3a0b3e1271c6f4261702ab948 | Text | 10,318 | 190 | # RINAMI: Residue-attributed Interpretable Neural network for predicting Absolute folding free energy by Merging structure and sequence Information
## Tested environment:
```
- NVIDIA Driver: 530.41.03
- CUDA: 12.1
- GPU: NVIDIA GeForce RTX 3080 (10GB)
```
#... |
adce9ef65be00334b2cb992ead71a7150b984865784364b8526d8317217d1ac0 | Text | 10,818 | 318 | # mmVelo Tutorials
This directory contains tutorials for **mmVelo**, a deep generative model designed to estimate cell state-dependent dynamics across multiple modalities. By utilizing splicing kinetics and multimodal representation learning, mmVelo infers cell state dynamics on joint representations and estimates tem... |
79dbb69ae161cc0087fe63741ffdaf6c5eb247a452f7dd06076f2a38cc33376d | Text | 11,012 | 123 | > [!Warning]
> **Project deprecated**
>
> LSL-actiCHamp is no longer maintained and has been deprecated.
> Please find the new BrainVision LSL Connector for actiCHamp and corresponding documentation directly on the [Brain Products website](https://www.brainproducts.com/downloads/more-software/#lsl) as free downloads.
... |
c941f18b44957fe1fbb713af3c3ce51884da7c6227cdb34bf21bbbdf851c36b1 | Text | 11,293 | 171 | # IJ BAR
[](https://zenodo.org/badge/latestdoi/8709403)
[](https://github.com/tferr/Scripts/releases)
[](https://zenodo.org/badge/latestdoi/362894234)
The `react-fmri` softwa... |
e2588e2d6d8975758ecef8f6e4c6926bbbf3ebe1281f0366d6c4072d8ede289c | Text | 11,752 | 299 | # MorphoScope
A Python-based GUI application for quantifying structural plasticity in neuronal projections, implementing the methodology from Petsakou et al., 2015 (*Cell*).
## Overview
This tool provides automated 3D quantification of neuronal structural plasticity from confocal microscopy images. It calculates:
- ... |
d0cc90d952cb0bcc543e8016574bff243d44d6e4363a19aeb95dd5e4f46e5ae5 | Text | 11,911 | 223 | # Proseq2.0
Preprocesses and Aligns Run-On Sequencing (PRO/GRO/ChRO-seq) data from Single-Read or Paired-End Illumina Sequencing. It is a new version of ProseqMapper (https://github.com/Danko-Lab/utils/tree/master/proseq).
Currently we provide two commands: proseq mapper and bigWig merge.
## Overview
Our proseq2.0 pi... |
8c30bfcbf596349c281e138265bb03611973084a98e239fdece2d7501e2ce708 | Text | 12,367 | 142 | # Compressed Stochastic Orthonormal Projective NMF (cs-opNMF)
## Introduction
Accompanying code for [Taming Dimensionality in Big Neuroimaging Data: Efficient Orthonormal Projective NMF via Stochastic Learning and Data Compression](https://doi.org/10.1162/IMAG.a.1355).
## Prerequisites
This code was tested on Linux... |
1b7eb9156f8dfaa2dfae7dacea97fc7390ead716481f0f396d546d78cdeba56a | Text | 13,027 | 306 | # MorphoScope
[](https://doi.org/10.5281/zenodo.17901990)
[](https://opensource.org/licenses/MIT)
A Python-based GUI application for quantifying structural plasticity in neuronal project... |
84fd72db5c60c6ca1b1ad4c55cb342fdbf9f911b8e0c4f7e4bfa374d707bcc5e | Text | 13,253 | 310 | # SigNET: Spatial Signaling Network Analysis
## Overview
**SigNET** (Signaling-to-transcription regulatory NETwork) is a computational framework for reconstructing ligand-receptor-transcription factor regulatory cascades from spatially resolved transcriptomics data. SigNET identifies co-expression patterns between th... |
1bfbb828905fcc58d9ed79741aae3ec40e2fc976f1496db156a950cb7e0d66bb | Text | 13,880 | 321 | # LAMAReg: Label Augmented Modality Agnostic Registration
<div align="left">
[](https://github.com/MICA-MNI/LAMAReg)
[](https://pypi.org/project/LAMAReg/)
[ [](https://bids.neuroimaging.io/news.html) [](https://gi... |
a3476273556ca4e7e532c8c059cadffb0ca77817dc5521b2a1398dbba32b020f | Text | 14,200 | 288 |
<!-- README.md is generated from README.Rmd. Please edit that file -->
# spacexr (Spatial-eXpression-R): Robust Cell Type Decomposition (RCTD) and Cell type-Specific Inference of Differential Expression (C-SIDE)
<!-- badges: start -->
<!-- badges: end -->
**Note**: The *spacexr* package is now available on
[Biocon... |
419ac0c5c9e01945bc43fdcb25cd97e4895efa3ab62b71b02d0cd3d1bc25a795 | Text | 15,220 | 389 | # abCRISPR: MLP-based design of abasic gRNAs for specific genome editing using high-quality mismatch library data
## Overview
abCRISPR is a deep neural network (DNN) framework for the rational design of abasic (ØXØ) gRNA sequences with minimized off-target activity. It leverages informative few-shot training on paire... |
26287714ffd2d3755625f973a8e108a593be9ced2c275a7f782a56ebd9cac596 | Text | 15,932 | 251 | # dcHiC: Differential Compartment Analysis of Hi-C Datasets
[](https://opensource.org/licenses/MIT)
[](https://zenodo.org/badge/latestdoi/274827002)
dcHiC is a tool for differential compartment analysis o... |
f5a9a3327806f13fa76088047751d8ae88fc21647c324a2bda242eb13c185e4d | Text | 16,134 | 393 | # Geode Dataset: Preprocessed Data and Analysis Guide
## Overview
This repository contains a preprocessed dataset (`preprocessed_data.RData`) and comprehensive analysis code (`data_analysis_final.R`) for a study examining cognitive performance differences between typically developing (TD) and autism spectrum disorder... |
cefa4c2a376247af72057747109c7cb3aa346c61c7f381643db3566e08d30f18 | Text | 16,272 | 202 | # Leading Eigenvector Dynamics Analysis Toolbox - Matlab
This toolbox enables the neuroscience community to apply the Leading Eigenvector Dynamics Analysis (LEiDA) method to functional MRI data with the goal of understanding brain dynamics. Below you can find a set of instructions that will guide the application of th... |
add66690bd6e6bc8085d6b26639a1c048cd231b7706a3d2223bf54188d9c1087 | Text | 18,669 | 175 | # MEG-SCANS: Code for Technical Validation
This repository contains the code used for the technical validation and generation of plots for the MEG-SCANS (Stories, Chirps, And Noisy Sentences) dataset publication.
## Dataset and Publication
The MEG-SCANS (Stories, Chirps, And Noisy Sentences) dataset provides raw mag... |
40cb5584f6024ab073ec85d7904465672fd438962be82a1415fa5427f25515c6 | Text | 18,737 | 176 | # MEG-SCANS: Code for Technical Validation
This repository contains the code used for the technical validation and generation of plots for the MEG-SCANS (Stories, Chirps, And Noisy Sentences) dataset publication.
## Dataset and Publication
The MEG-SCANS (Stories, Chirps, And Noisy Sentences) dataset provides raw mag... |
ee09fa769087c388c7b4954e853be08a3b97ff325b4a6c3aa36796d421c544e9 | Text | 18,756 | 452 | # Geode Dataset: Preprocessed Data and Analysis Guide
## Overview
This repository contains a preprocessed dataset (`preprocessed_data.RData`) and comprehensive analysis code (`data_analysis_final.R`) for a study examining cognitive performance differences between typically developing (TD) and autism spectrum disorder... |
51ece04bd199211fec441a33e39ceabc5e68f63d7d50aed82fb66490a55d8531 | Text | 18,758 | 320 | [](https://anaconda.org/bioconda/accusnv)
# <img src="readme_files/logo.png" width = "100" height = "100" > High-accuracy SNV calling for bacterial isolates using AccuSNV
### Version: V1.1.2 (Last update on 2026... |
4cf8398f7d56f4ff0389b5d341ed9949ae741088bd3f17eea98da6feceababec | Text | 19,238 | 442 | # SMILES2Docking
**[English](#english) | [Português](#português)**
---
## English
Desktop application and Python workflow for preparing ligands from `CSV`, `XLS`, and `XLSX` spreadsheets. The pipeline performs structural curation, multi-site protonation at configurable pH, 3D generation with `RDKit ETKDGv3`, force-... |
1e8797569bf2ba776d420c1f487868ffd9e7a203ef4dc4de0a7c9a53da30368c | Text | 19,252 | 574 | # Single-cell RNA-sequencing analyses of neonatal mouse microglia
This repository contains the analysis code supporting a study of early
postnatal microglial states in mice under physiological conditions and following
neonatal lipopolysaccharide challenge. The workflow includes primary
single-cell RNA-sequencing proce... |
14b5b84eddbfc06ea0398eb12c448bc2a230502d4e2b812fab7590ea57ea1294 | Text | 19,458 | 170 | # alps.sh
This is a ```bash``` script that automatically computes the diffusion along perivascular spaces (ALPS) metric from diffusion-weighted images (```dwi```).
The ALPS index has been described by [Taoka et al. (Japanese Journal of Radiology, 2017)](https://link.springer.com/article/10.1007/s11604-017-0617-z) ... |
682ff39b9fee02d391dcd4a71c86c6a81374c5d91a898c524591046d10ebc7eb | Text | 23,438 | 805 | # Supplementary Material: Coupled Cardiac System
## Overview
We present a software package designed for a coupled cardiac system that integrates real-time 2D cardiac simulations—implemented using the WebGL-based Abubu.js library—with living cardiac monolayers via a fully optical interface. This documentation provides... |
5c8ea392dc231a6dfe044bd85a637f89b458d9afdabdf74ac2b3dbb96c9b54f8 | Text | 24,382 | 430 | # Neuromuscular Junction (NMJ) Analysis Pipeline
This pipeline was used in *Self-organization of vascularized muscle from bovine embryonic stem cells*.
AI tools (Cursor and Antigravity) assisted with code and documentation. The authors reviewed, tested, and modified the generated code and manually verified results by ... |
6b11f79a3f28773868c133de0cf1391a54895b0563abf8ffc4687f8b31aae7c7 | Text | 25,125 | 535 | # CASCADE v0.8.0
**Criticality Avalanche Spike Cross-platform Analysis Detection Engine**
CASCADE is a modular Python pipeline for analysing multi-electrode array (MEA) recordings from multiple manufacturers. It reads manufacturer-specific spike files, converts them into a common internal format, and runs a standardi... |
6ff34ec33f7e5f15a027a551fa747716442c43f370eddfa9bc132c7bde530f83 | Text | 25,292 | 539 | # CASCADE v0.8.0
**Criticality Avalanche Spike Cross-platform Analysis Detection Engine**
<div align="center">
<img width="250" height="250" alt="CASCADE_Logo" src="https://github.com/user-attachments/assets/7a029bf6-93b7-4185-8859-888672b4bb65" />
</div>
CASCADE is a modular Python pipeline for analysing multi-elec... |
8436ad32834b3c55730c5a2753fa91d24e7ef4aae1623dc5c32a3153b395fdf1 | Text | 25,415 | 403 | # Scheib_2026
Code and data repository for the Scheib et al., 2026 manuscript in eLife from
the Kerlin Lab at the University of Minnesota, Twin Cities.
The repository contains the per-animal behavioral and two-photon calcium-imaging data used in the
study, the pre-computed trace alignments and example-ROI exports the... |
48810a205857a3c8abb11516536513171f2ea821e7f6297cb6b0b936a33c01fa | Text | 25,935 | 446 | # ECLIPSE — Dark Proteome Exploration of ESKAPE Pathogens
**ECLIPSE** (ESKAPE Connectome Linkage and Inference for Proteome Sequence Exploration) is a modular computational pipeline for the systematic identification and prioritisation of functionally ("dark") protein families in ESKAPE panproteomes.
ECLIPSE maps ESKA... |
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