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b6fe15ca8d78c04f907e65bbcc53d910c84456ab045a6252ae67810123696793 | Text | 3,247 | 63 | # FractalDB Pretrained ViT
This repo is the official implementation of ["Can Vision Transformers Learn without Natural Images?"](https://arxiv.org/abs/2103.13023) and contains a Pre-training and Fine-tuning in Python/PyTorch. The repo is based on the [FractalDB-Pretrained-ResNet-PyTorch](https://github.com/hirokatsukat... |
6a83697c7559238229b322ba6b02425d64210a7d83ebc6264739d71dfdc13668 | Text | 3,252 | 99 | # `dimensions`
Estimating the instrinsic dimensionality of image datasets
Code for: *The Intrinsic Dimensionaity of Images and Its Impact On Learning* - Phillip Pope, Chen Zhu, Ahmed Abdelkader, Micah Goldblum, Tom Goldstein (ICLR 2021, spotlight)
* https://openreview.net/forum?id=XJk19XzGq2J
 official implementation of popular CNN models, and trained those on CIFAR-10 dataset.
- I changed *number of class, filter size, stride, and padding* in the the original code so that it works... |
077d46842bb8f6d5359be13fa6c23edae39a3a8649535dcabe41cfac33573432 | Text | 3,258 | 100 | # AD_Predictive_Signatures
This repository contains scripts and data to recreate figures from our publication **Predictive Gene Expression Signatures for Alzheimer's Disease Using Post-Mortem Brain Tissue**.
---
## 1. Location of Required Scripts and Data to Reproduce **Figure 3A** (Upset Plot)
```
Data/
├── gene_... |
91410410357e7cf6d453c39c66a91dd10934496e2fa0b1d370126659498d1eea | Text | 3,266 | 32 | # variant-analysis
Tools to examine and analyze population genomic data
Related work is: https://doi.org/10.1016/j.bpj.2022.12.012
Protocol: Generation of a Figure Comparing Genomic Variant Types to Fractional Solvent Accessible Surface Area (SASA)
*Objective:* This protocol aims to generate a figure that compares ... |
4eab4a2fa0de757ff5231d4269d286babdb36714d05d47f44030f1b7376b6ffd | Text | 3,284 | 77 | MSKCC-CONFOCAL dataset
=================
DOI: https://doi.org/10.5281/zenodo.6460303
Overview
---------
The dataset consists of 3 confocal microscopy time series of C. elegans embryos, fully tracked with StarryNite followed by manual curation:
- 3 raw time-series and the corresponding tracks/lineage trees
- tempora... |
092ecfae6dad11c6fe362f54a12cd27c3572fc1a97728b4f8faf8d8b0dea0511 | Text | 3,296 | 104 | # Inference of differential splicing factor (SF) activity with SF-exon networks and VIPER
This repository contains the SF-exon networks obtained from experiments to estimate differential splicing factor activity from exon inclusion matrices (with [VastDB](https://vastdb.crg.eu/wiki/Downloads) exon identifiers, for the... |
e1201409dff513a1df80604aeb8ade1972c2e57f72676ab6c3e1f42ea973a2c0 | Text | 3,300 | 85 | # PyMARE: Python Meta-Analysis & Regression Engine
A Python library for mixed-effects meta-regression (including meta-analysis).
[](https://pypi.python.org/pypi/pymare/)
[](https://pypi... |
e49b4a9f9124ff193e10f5f3628b9ab95ecf8081516ebfba8caa0dec2f8f27f5 | Text | 3,307 | 113 | # Federated Graph Attention Network with Quantum Embeddings
This repository contains code for **federated graph neural networks with
quantum encodings** (QuanGAT) applied to **DNA mutation prediction and
protein--protein interaction datasets**.\
It combines **federated learning**, **graph attention networks (GATs)**,
... |
a3624dbb611c0b306bed589b0f2fd42d92fc90105bba3f272727623d74e76e9c | Text | 3,318 | 71 | # diffexpr #
[](https://github.com/wckdouglas/diffexpr/actions) [](https://codecov.io/gh/wckdouglas/diffexpr)
A python package using `rpy2` to port [DESeq2](https://bi... |
f9da0aff498e58eac8180e58adf22055fe228992436d06ef261820d68094c029 | Text | 3,320 | 82 | <div align="center">
<table>
<tr>
<td><img src="logo.jpg" width="150"></td>
<td><h1>FFTMed: <br>A PyTorch Implementation</h1></td>
</tr>
</table>
</div>
<p align="center">
<a href="">
<img src="https://img.shields.io/badge/bioRxiv-2024.09.28.615584-b31b1b.svg?style=flat" />
<a href="ht... |
7c06b97ec6f34a6cdc581257fbc9098e608054a15ac9f6aa5365fb08b9196888 | Text | 3,334 | 43 | # gusto_microbiome_brain_internalizingsx
Analysis scripts used for the manuscript "Childhood gut microbiome is linked to internalizing symptoms at school age via the functional connectome", accepted at Nature Communications.
Preprint can be found at: https://osf.io/preprints/psyarxiv/u9dw5
Supplemental materials for... |
f58add0806a4a2cd9e523b02bf51b5296e2c3f8101042ed441699dd85f8423c4 | Text | 3,339 | 75 | # ECIC-DBS-Tinnitus
This repository contains MATLAB scripts and data analysis tools used in the study **"Modulation of Auditory Cortex Activity in Salicylate-Induced Tinnitus Rats via Deep Brain Stimulation of the Inferior Colliculus"**. It includes code for spike detection, firing rate analysis, and inter-spike inter... |
e612dcd08bab4f4def60086ec53b55c4615fafe22e100c5220e3351bd07b7dea | Text | 3,340 | 58 | # Repository Content
This repository contains ViRMEn, the Virtual Reality MATLAB Engine. Various versions are archived as zip files in the `Software` folder. The VR design is documented in the `VR design` folder.
# Version History
2011-04-11
- First version of ViRMEn (not available on Webspace)
2013-02-27
- First v... |
acbfaca80fc0c98858df509f8cb209c19b76c3ea160ac44b048139a3e3692ea7 | Text | 3,353 | 57 | [](https://github.com/eippertlab/cardiac-artefact-removal/releases/tag/v1.1)
[](https://zenodo.org/doi/10.5281/zenodo.13693032)
[: trains image hashing models that output compact binary hashcodes and uses a... |
f7882d698ae5ec97f93edc076c64457804a3e3854ac09fec24a8576876e4cf39 | Text | 3,359 | 106 | # HEMF
This repository provides the supplementary code and data to the paper entitled "***HEMF: An Adaptive Hierarchical Enhanced Multi-attention Feature Fusion Framework for Cross-scale Medical Image Classification***".
 [![DOI](https://zenodo.org/bad... |
6febc0386e045c36ddf5737aeafdec33bad51adeacb9ff072b65762a2ea2b989 | Text | 3,362 | 93 | # WANG_NipahMProtein_2025
## Project Description
This repository contains code and data for the research project "Nipah virus matrix protein utilizes cortical actin to stabilize the virus assembly sites and promote budding".
## Repository Structure
- `k_stage_from_rawdata.py`: Main data processing script for analyzin... |
a1df79f51b94217fc437b7915da12f8227eab568533e38b64f4dce61f0c43c99 | Text | 3,371 | 35 | # Auditory Restoration
This repository contains analysis code to accompany Le et. al, "The zebra finch auditory cortex reconstructs occluded syllables in conspecific song" (preprint).
This README file describes the key steps in running the analysis, including links to data files hosted on public repositories. See the... |
a95ceae61afbf39a743538af84d0a2124c6ec939f2f9e850e7996ebd1a7a6fd1 | Text | 3,378 | 44 | ## A Stacked Generalization of 3D Orthogonal Deep Learning Convolutional Neural Networks for Improved Detection of White Matter Hyperintensities in 3D FLAIR Images
### Introduction
Accurate and reliable detection of white matter hyperintensities (WMH) and its volume quantification can provide valuable clinical informa... |
fa70894dae69a10dbfaafb966943082676058d49ffcb7c75c993c30693184a04 | Text | 3,405 | 66 | # stDiff: A Diffusion Model for Imputing Spatial Transcriptomics through Single-Cell Transcriptomics
A novel method named stDiff investigates the potential of employing diffusion models for single-cell omics generation.
## Framework
## Arguments
### stDiff
if gene num < 512, batchsize ... |
f58b005d43e9c48876e60813f4d9a0aa91815a38251a1aa9e72ceb23be5b7cea | Text | 3,407 | 49 | # Menstrual Cycle Brain Dynamics
[](https://doi.org/10.1038/s41593-025-02066-2)
[](https://www.nature.com/neuro)
[ framework.
Features
FASTA File Input: Reads protein sequences from FASTA files ... |
4cbdc4a047297350a0775451bbafd7d267d7f5286bb1a3e128af3d425bf4e083 | Text | 3,419 | 29 | # Salience Network Segregation and Symptom Profiles in Psychosis Risk Subgroups among Youth and Early Adults
This repository contains the code for the analyses presented in the paper, "Salience Network Segregation and Symptom Profiles in Psychosis Risk Subgroups among Youth and Early Adults". This code does not contain... |
a5062b978236d550464882cb71f23fd8c9d27b55822e1c001c2ee00291d66957 | Text | 3,424 | 46 | # snrnaseq-step1-preprocessing
Code used to perform dataset building and preprocessing on single-nucleus RNA sequencing data, starting from [CellBender](https://github.com/broadinstitute/CellBender/tree/master)-filtered sequencing data and [demuxlet](https://github.com/statgen/popscle) output.
This is the first code ... |
ac1af6b0c2193d67059c1bf2b72aa6778b10b08e524ccbaa94f02adc64cfd588 | Text | 3,439 | 73 | # GoFlow: Efficient Transition State Geometry Prediction with Flow Matching and E(3)-Equivariant Neural Networks
GoFlow is an open-source model for predicting transition state geometries of single-step organic reactions.
This repository contains the official implementation, including all scripts to fully reproduce the... |
99fc0bc7376bd70876f4f1252dfde88962cd44048dcf9a2046be62ebfd37bc73 | Text | 3,442 | 78 | NIH-LS dataset
=================
DOI: https://doi.org/10.5281/zenodo.6460375
Overview
---------
The dataset consists of 3 diSPIM microscopy time series of C. elegans embryos, fully tracked:
- 3 raw time-series and the corresponding tracks/lineage trees
- temporal resolution: 1min
- temporal extent: 350-400 frames,... |
1056923f64568d20ab956e8ffdece3bfd2d8b510af909481011bf283a6fb0598 | Text | 3,448 | 88 | # README
## Dataset Description
This dataset contains neural recordings from the ventral premotor cortex (VPC), dorsal premotor cortex (DPC), and secondary somatosensory cortex (S2) during the **foreperiod** of a tactile detection task and a time interval comparison task. The data are provided for open analysis and f... |
2bc70cc85867fa449327d54b3e8fa8b3e198d699171b6c9276724990a6208f33 | Text | 3,466 | 63 | # SCVR
Scripts for **Spinal Cord Vascular Reactivity** (SCVR) delay mapping. The main functions are contained in `groupdelay.py`. Example run files are provided for group delay and individual subject delay (with multiple runs).
---
[](https://tw... |
17ebb065abd96cb1273c7d58df30c4fbc80b63b5733399a807e1eb95f4294db9 | Text | 3,486 | 45 | # gusto_microbiome_brain_internalizingsx
Analysis scripts used for the manuscript "Childhood gut microbiome is linked to internalizing symptoms at school age via the functional connectome", accepted at Nature Communications.
DOI (from Zenudo): <img width="191" height="20" alt="image" src="https://github.com/user-at... |
28a76a790055e4010d9781ce311884cc747fe80582f8ef03fe3b23e2437489d1 | Text | 3,494 | 74 | # psgScore
[](https://www.repostatus.org/#wip)
**psgScore** i... |
7880fd6d3ca1e31404d515d7d7ced982e92ce26516736be943bf6c9508ff2122 | Text | 3,497 | 87 | # PyMARE: Python Meta-Analysis & Regression Engine
A Python library for mixed-effects meta-regression (including meta-analysis).
[](https://pypi.python.org/pypi/pymare/)
[](https://pypi... |
a0084491c6cda3c62ec45c8606d9fe0dd086cebcb3fd51c1c24331ada797d996 | Text | 3,507 | 113 | # # Transcriptomic and Gene Length Analysis in Parkinson's Disease by Severity
This repository contains R scripts for RNA-seq and gene length analysis in differential expression studies related to Parkinson's Disease (PD).
## Description
Script Overview
1. 1_deseq2_analysis.R
Purpose: Load Salmon quantifications, p... |
e5e44171a34be68297ad6d9895a2fbf3e966d1d6064cf1e97214c24ef038cb50 | Text | 3,513 | 79 | # Evaluating LLM-Generated Brain MRI Protocols
Official implementation by the [HAIM Lab (Human-Centered AI in Medicine)](https://www.neurokopfzentrum.med.tum.de/neuroradiologie/forschung_projekt_haim.html) of the Technical University of Munich (TUM).
## Overview
- Study Title: "Evaluating Large Language Model-Generat... |
4e224f8cbc321ea3531847798af9bbded59d3b22d3c28fd751e1581896d861e9 | Text | 3,514 | 82 | # ScaNER-01: A Multi-Tiered Natural Language Processing Framework for Acute Cerebrovascular Event Labeling
Welcome to the **ScaNER-01** repository! This project provides the code for **ScaNER-01**, a multi-tiered natural language processing (NLP) framework designed to automate the labeling of acute cerebrovascular eve... |
71e10525cdc757a7ec6f316df6fb8dec76d2bbe44e8e1f8d52dd1bafe164c018 | Text | 3,538 | 68 | # Ultrasound system for precise neuromodulation of human deep brain circuits
## MR and CT image processing tools for targeting and registration
[](https://doi.org/10.1101/2024.06.08.597305) [![License: GPL v3](https://img.shields.io/badge/L... |
c0d79040d736f41454133b51cb7575aaf5d1ce4a585be0856d35de22703850d1 | Text | 3,543 | 69 | # rV2_bifurcation
This is code and metadata repository for manuscript "Gene regulatory mechanisms guiding bifurcation of inhibitory and excitatory neuron lineages in the mouse anterior brainstem" (Kilpinen Sami, Virtanen Lassi, Bodington-Celma Silvana, Bonsdorff Amos, Heliölä Heidi, Achim Kaia, Partanen Juha (2025) Ge... |
edbf67c7584bead8956ebc6be96d42fa9e89aeff3426d7cc3314e2c9b7d94441 | Text | 3,555 | 71 | # Prior Localization
The repository provides the code associated with the manuscript
[*Brain-wide representations of prior information in mouse decision-making*](https://doi.org/10.1101/2023.07.04.547684) (Findling, Hubert et al, 2023).
## Dependencies
The code has been tested on Ubuntu 20.04 and 22.04, Rocky Linux 8... |
668806b05ca8668daaf80c6410732e08361689efc80c8d5967a00b454b274cf4 | Text | 3,561 | 90 | # ABBA-QuPath Registration Exporter
[](https://github.com/nickdelgrosso/ABBA-QuPath-RegistrationAnalysis/actions/workflows/python-app.yml)
[ cortex for fast and slow presentations, as described in the paper:
**"The Spatial Frequency Representation Predicts Category Coding in the Inferior Tempo... |
5fd20c4037f44bae1ef9b164727793e67e800fff3144864997923f78127ae914 | Text | 3,591 | 90 | # BamSlam
This script was written for long-read Oxford Nanopore Technologies direct RNA/cDNA sequencing data. It uses BAM files produced after mapping with minimap2 to the reference transcriptome. It will output a summary file and plots from your aligned reads. This script was used in: https://doi.org/10.1093/nar/gkab1... |
c8c71f965978511468fdbf6513740538572b100713733b4321e13267632416bd | Text | 3,594 | 107 | # ClusterMate
ClusterMate is an open-source data clustering and visualization tool designed for easy analysis of multi-dimensional datasets.
## Features
- Import and merge multiple datasets
- Apply various clustering algorithms (K-means, DBSCAN, Hierarchical)
- Visualize clustering results with interactive plots
- ... |
be78a401e23fec900e9a11be4f2eda28c258312077fbb1a7f4a42c608a901273 | Text | 3,604 | 69 | > [!WARNING]
> The Blue Brain Project concluded in December 2024, so development has ceased under the BlueBrain GitHub organization.
> Future development will take place at: https://github.com/openbraininstitute/emodel-generalisation
[](https://zenodo.org/badge/latestdoi/6... |
ee06179c9363f76ffd98920f80bea87b58971365c76efec2b5b4a89c55d0269a | Text | 3,628 | 68 | # Ultrasound system for precise neuromodulation of human deep brain circuits
## MR and CT image processing tools for targeting and registration
[](https://doi.org/10.1101/2024.06.08.597305) [](https://github.com/openforcefield/openff-recharge/actions?query=branch%3Amain+workflow%3Aci) | [![pre-commit.ci status](https://results.pre-commit.ci/badge/github/openforcefield/openff-recharg... |
e1f91d0c31f40226e13037197513654594087878733315819dfe053257433aa0 | Text | 3,632 | 85 | # Diff-AdaNAG
The official implementation of "The strength of Nesterov’s Accelerated Gradient in boosting transferability of stealthy adversarial attacks"
## Introduction
Diff-AdaNAG, a novel framework that introduces Nesterov’s Accelerated Gradient (NAG) into diffusion-based adversarial example generation. Specific... |
961cb5f784ebe09bb9241c014d9815aa97651024ffe2555013657833d77f7237 | Text | 3,633 | 78 | # MR to pCT for TUS
This script produces a pseudo-CT image from a T1-weighted MR image for use in acoustic simulations of transcranial ultrasound stimulation (TUS).
## Platform
Tested on Linux (Ubuntu 20.04.4 LTS) and on macOS Catalina (10.15.7; Intel i5) and Monterey (12.4; Apple M1 Pro).
Works with both NVIDIA ... |
e5dafb0ebd344a7c2c0cb9a9ff263c6eb6372683efcf9474cc466981eeb93fa9 | Text | 3,638 | 49 | # Non-invasive Finger Movement Decoding with LF-CNN
Welcome to the GitHub repository for our project on non-invasive finger movement decoding using a Linear Finite Impulse Response Convolutional Neural Network (LF-CNN). In this repository, you will find the code and resources related to our research on accurately clas... |
79c88863eb76c08b88471d33da97a5a244bdd648dfe95a590a407ebe0001d47f | Text | 3,644 | 54 | # snrnaseq-step2-cell-typing
Code used to perform likelihood-based cell typing on single-nucleus RNA sequencing data.
This is the second code step in a series that was used to study impacts of substance use disorders (SUDs) and HIV infection on cellular transcription in human ventral midbrain ([Wilson et al. 2025](ht... |
ba36188d837a873daf274049cfb4ade3b8297ac3d230e94f8d655e3f45b13cbe | Text | 3,675 | 59 | 
# Visit [Lenia portal](https://chakazul.github.io/lenia.html) for more information
* [2020-10-13] Update Python version with multi-kernel and multi-channel extensions (v3.4 LeniaNDK.py, v3.5 LeniaNDKC.py). To see the most advanced Lenia patterns, ... |
d36f21d46f504fcab07564dc8ac0b2edc67e5a39a90e98c349d80ad8e00fa244 | Text | 3,688 | 53 | # snrnaseq-step4-run-deseq2
Code used to run differential expression analysis (DEA) using DESeq2 ([Love et al. 2014](https://doi.org/10.1186/s13059-014-0550-8), [Van den Berge et al. 2018](https://doi.org/10.1186/s13059-018-1406-4)).
This is the fourth code step in a series that was used to study impacts of substance ... |
ad8034d45460704a2339f3a57689ab2d4e1fa6b45efb4057b29e87c10df7e5bb | Text | 3,697 | 36 | RMS synaptic plasticity simulation demonstration
Nicholas Hananeia
------------------------------------------------
Requirements:
* Recent version (R2019b to R2024b, note that TREES Toolbox, and thus this code, is currently UNSUPPORTED on R2025a onwards) of MATLAB & Statistics and Machine Learning toolbox (ht... |
f1bfaa1a5402c571f80effd90b56751e14d6c290b10c7a9366cdd27a3416d526 | Text | 3,715 | 112 | # Kovacheva_et_al_2025
This repository provides analysis scripts and example datasets accompanying the manuscript:
**"Recovery of the full in vivo firing range in post-lesion surviving DA SN neurons associated with Kv4.3-mediated pacemaker plasticity"**
Kovacheva et al., 2025
The dataset includes MATLAB and Python... |
2da7afeb79e5a7367bc9afd0e46d1cedd6cc8a840e4fd52dc52c48611ee959fe | Text | 3,724 | 45 | ### xQTLbiolinks: a comprehensive and scalable tool for integrative analysis of molecular QTLs
**`xQTLbiolinks`** is a end-to-end bioinformatic tool for efficient mining and analyzing public and user-customized xQTLs data for the discovery of disease susceptibility genes. xQTLbiolinks consists of tailored functions th... |
71386a6b2c15728d408e63ee229e20c710e31c4bd99e7772048b181eec1a4d9c | Text | 3,724 | 58 | # Code for cryptic polydenylation manuscript
Analysis code for cryptic polyadenylation manuscript, currently on biorxiv:
> **TDP-43 loss induces extensive cryptic polyadenylation in ALS/FTD**
>
>*Sam Bryce-Smith, Anna-Leigh Brown, Puja R. Mehta, Francesca Mattedi, Alla Mikheenko, Simone Barattucci, Matteo Zanovello, ... |
47a918cf2ea153f63e002a4da636f54bc1879c169d97efe61f157c4cd8f3bfba | Text | 3,727 | 43 | <h1 align="center">
<a href="https://anbai106.github.io/mlni/">
<img src="https://anbai106.github.io/mlni/images/mlni.png" alt="mlni Logo">
</a>
<br/>
MLNI
</h1>
<p align="center"><strong>Machine Learning in NeuroImaging</strong></p>
<p align="center">
<a href="https://anbai106.github.io/mlni/">Document... |
16068ad4536bf24f7d6fa547467751b4b1107cbaa124511e1f7259d887d3b829 | Text | 3,732 | 41 | # NematodeMovementAnalysis_v1
A pipeline to extract and analyze body postures from recordings of crawling C. elegans worms.
## Introduction
This is a compilation of MATLAB scripts to identify individual C. elegans worms in recordings and analyze the posture dynamics.
This script has been used in the publication ... |
81054e2cd01e35ca35c5e5b486adbb95c00ab693afa5f3ba683fd8d29f0651ba | Text | 3,733 | 60 | # Mutational Effect Transfer Learning
This repository contains the Mutational Effect Transfer Learning (METL) framework for pretraining and finetuning biophysics-informed protein language models.
You can use it to train models on your own data or recreate the results from our manuscript.
This framework uses [PyTorch L... |
c45057f49ec7b1faa9e5544ad924b43394efa7eddc43e2830d7e97589b06a63a | Text | 3,756 | 61 | # SPatial ECdna Intratumor Evolution Simulation (SPECIES)
This repository contains the code for simulating the spatial patterns of ecDNA content within expanding tumour cell populations. The program generates an output file tissue.csv containing a list of the (x,y)-coordinates of all cells in the system, and the numbe... |
ba387bd1e5cb6887b17420cddf6b0c911efb3cc90bf6304c89fe446bda29010a | Text | 3,757 | 52 | # snrnaseq-step3-dea-setup
Code used to prepare single-nucleus RNA sequencing (snRNA-seq) data for differential expression analysis (DEA) using DESeq2 ([Love et al. 2014](https://doi.org/10.1186/s13059-014-0550-8), [Van den Berge et al. 2018](https://doi.org/10.1186/s13059-018-1406-4)).
This is the third code step in ... |
41f45441c1cfe437f319a6889ecae14f101805924b329fc40c9f9c54c82b11e8 | Text | 3,776 | 59 | # SpaBalance: Balanced Learning for Efficient Spatial Multi-Omics Decoding
This repository contains the necessary SpaBalance scripts to reproduce the benchmark results presented in the paper. We also provide experimental data, which can be found in the data folder. All experiments can be reproduced using the provided T... |
7d5886e554da774ea53ae66a989f1f9e3078a3dbd3721a9b59ea6e5526743970 | Text | 3,783 | 65 | <div align="center">
IRK-SINDy: Implicit Runge-Kutta based sparse identification of governing equations in biologically motivated systems
[Mehrdad Anvari](https://github.com/anvari94)<sup>1</sup>, [Hamidreza Marasi](https://scholar.google.com/citations?user=4zn2HB4AAAAJ&hl=en)<sup>1</sup>, and [Hossein Kheiri](https:/... |
0d6131d714c8f5e2ee7e96e81543cf6978726c91c4555a433d46a5ff59491e0d | Text | 3,792 | 65 | # SegDecon
AI-powered nuclei segmentation enhances histological image process and Spatial Transcriptomics deconvolution
Spatial transcriptomics (ST) enables spatially resolved gene expression profiling but is often limited by low resolution. To address this, we introduce SegDecon, an AI-powered pipeline that enhances t... |
a20f0d8c319b926074f780ced8edddee16ac3e03dcc29789384fb9a5fe7baec3 | Text | 3,792 | 62 | 
## Overview
This repository contains a Python-based model that simulates the dynamics of the bladder, sphincter, and kidney, using normalised neural signals to predict pressure and volume of the bladder.
For more detailed mathematical explanations, please refer to... |
d355ff379f32984bf5670477fbbf50fa14c1fe7fa39e99d3ddf938bdbb56a4ee | Text | 3,800 | 77 | # Imbalanced Dataset Sampler
<a name="Introduction"/>
## Introduction
In many machine learning applications, we often come across datasets where some types of data may be seen more than other types. Take identification of rare di... |
2f72e805f68bbf4775a90e779e992e67c32f83274e2bb9e64a400fc79b7e9136 | Text | 3,815 | 77 | # CBAM-Keras
This is a Keras implementation of ["CBAM: Convolutional Block Attention Module"](https://arxiv.org/pdf/1807.06521).
This repository includes the implementation of ["Squeeze-and-Excitation Networks"](https://arxiv.org/pdf/1709.01507) as well, so that you can train and compare among base CNN model, base mode... |
a74cde443fb246810591cc7137cf7d47241dac997fe487653cab7f9bbac2bd7e | Text | 3,816 | 61 | # Code for cryptic polydenylation manuscript
[](https://doi.org/10.5281/zenodo.15210469)
Analysis code for cryptic polyadenylation manuscript, currently on biorxiv:
> **TDP-43 loss induces extensive cryptic polyadenylation in ALS/FTD**
>
>*Sam Bryce-Smith, Anna-Leigh Br... |
38db75043da2096973c36f56ce12ec38a792d5512e0aec76113e8a56a011bf20 | Text | 3,827 | 103 | 
[](https://coveralls.io/github/ggseg/python-ggseg?branch=main)
[](http... |
b146ebd65aeb10824fbda3f627addeee98e56717357d3dda0327a007059de5cc | Text | 3,830 | 57 | # 2PiLNet jGCaMP8f Pipelines
This repository provides the official pipelines for processing jGCaMP8f light-field videos using the LISTA-based net ("2PiLnet", or just "LNet") described in this [paper](https://www.biorxiv.org/content/10.1101/2025.03.17.643718).
## Abstract
Light field microscopy (LFM) enables high throu... |
d45cd960a3d7ded3b618b97deae9e502ddbe73ca7599ce3062250658b12c2ff8 | Text | 3,840 | 136 | # Thin Plate Spline (TPS)
[](https://github.com/raphaelreme/tps/raw/main/LICENSE)
[](https://pypi.org/project/thin-plate-spline/)
[... |
632726de6642616f34faeae412e8ca71b511ab2bca943cd2f45f33f6a9e88cf8 | Text | 3,864 | 61 | # **DROSOPHILA TRANSPOSON CANONICAL SEQUENCES**
This repository contains 'canonical' DNA sequences of the transposable
elements from species in the genus Drosophila.
History: These sequences were originally compiled by Takis Benos (EBI),
Leyla Bayraktaroglu (Harvard) and Michael Ashburner (EBI & Cambridge)
with help... |
b6ad12999b3acd9bd15a441f23c870ddf244eab5e79fc1ee15025f946a9a4698 | Text | 3,879 | 47 | # TL for Post-Surgical Mortality Prediction
## Description
Project for evaluating transfer learning on an in-house dataset containing patient data from major visceral surgery.
This code was used for our paper _Winter, Axel MD; Pfitzner, Bjarne MSc; van de Water, Robin P. MSc; Faraj, Lara; Riepe, Christoph; Hahn, Wolf-... |
6f5ad4d156c935d7d808634a860adcd90475a2f19b83c6f6a307410bdb6ae01b | Text | 3,885 | 29 | # Laminar Column Model for Bistable Perception
This repository provides the dynamic mean field implementation of the Laminar Column Model described in:
Layered Structure of Cortex Explains Reversal Dynamics in Bistable Perception ... [full reference once available]
## Abstract
Bistable perception involves the spontan... |
1e8419ad474be66c8f42d991a7172b900db55660b98d02e71bd2fd14949b527d | Text | 3,891 | 59 | # 
[](https://travis-ci.com/nf-core/smrnaseq)
[](https://www.nextflow.io/)
[![install with bioconda](https://img.... |
87f03920e97af987eff187edc8e6067cb9fa51b5bfe8517728f78d5cd85de147 | Text | 3,899 | 88 |
<!-- README.md is generated from README.Rmd. Please edit that file -->
# compareRhythms <img src='man/figures/logo.png' align="right" height="138.5" />
<!-- badges: start -->
[](https://github.com/bharathananth/compareRhythms)
[![License:
GPL-3](https... |
23fe9b3c5024608e3e6ad3c5197b63d5a7cf134f73391df8c2e4962eb553504f | Text | 3,906 | 32 | # DICOM2OMOP
This project builds on a published work, ["Development of Medical Imaging Data Standardization for Imaging-Based Observational Research: OMOP Common Data Model Extension"](https://pubmed.ncbi.nlm.nih.gov/38315345/). A copy of the full paper can also be found in the files folder.
This project aims to create... |
8d90c6524128387ef4035642854ca16dfd84d9b448ba276e701e8c5b34d6383f | Text | 3,919 | 92 | ## Parallels between NMT and CMR
This package provides scripts and tools for training and evaluating a seq2seq model of free recall, fitting models to individual subject data, and analyzing results using visualizations for the paper *Sequence-to-Sequence Models with Attention Mechanistically Map to the Architecture of... |
4eac93287cf0c65575240d4dc18464a60a4d2427458aadd87ef23e2a20f7605f | Text | 3,920 | 39 | # COVID-19-Arabic-Tweets-Dataset
The repository contains a collection of Arabic tweets IDs related to novel coronavirus COVID-19. The dataset contains Tweets ids starting from January ,2020 . The Twitter search API was used to gather real-time tweets that contained specific keywords in the Arabic language. To comply w... |
ca67b1494bad0688917199767cc48010241a99210f063ee271a747932bb637f6 | Text | 3,944 | 30 | # seg_cul_astro_app
## How to run seg_astro.mlapp
1. Install the latest version of MATLAB
1. Go to the folder ‘seg_cul_astrocyte_app’ and double click ‘seg_astro.mlapp’
1. A new window will pop-out, the first row of the left panel is for input the image data (Input the two channels separately), the second row and the ... |
ce491bb2d686145e0773c685d0d02e8a5fabc7daaea60eef07cf54298561fba7 | Text | 3,947 | 49 | # MetaPhlAn: Metagenomic Phylogenetic Analysis
[](http://bioconda.github.io/recipes/metaphlan/README.html) [](https://pypi.or... |
56bce347884f61f5c08fe9217ffc710330b79d71e89967e66b454ac26497ae8a | Text | 3,952 | 87 | # Spatial joint profiling of DNA methylome and transcriptome (Spatial-DMT)
## Introduction
This repository is for raw data processing and downstream data analysis & visualization code in the **"Spatial joint profiling of DNA methylome and transcriptome in mammalian tissues"** manuscript.
### Computational workflow fo... |
27751ecff9d2c622c51930edd17429463f698c34e018b967ff8567f7e9421a1d | Text | 3,953 | 78 | [](https://zenodo.org/badge/latestdoi/245546149)
## BrkRaw: A comprehensive tool to access raw Bruker Biospin MRI data
#### Version: 0.3.3
### Description
The ‘BrkRaw’ is a python module designed to provide a comprehensive tool to access raw data acquired from
Bruker Bi... |
75f48cb0e50fe26c07ecf434ad43309e5e062695b60c17bf8d645ebf1fdb54ba | Text | 3,959 | 94 | # paper-brain-wide-map
Code related to the brainwide map paper:
International Brain Laboratory., Angelaki, D., Benson, B. et al. A brain-wide map of neural activity during complex behaviour. Nature 645, 177–191 (2025). https://doi.org/10.1038/s41586-025-09235-0
Find editable figures and latex text here: https://gith... |
c3698af47ae7917f7bfe65486119480abf4be5b8069232b9bc54379cd2d3f9be | Text | 3,966 | 65 | # Bioinformatic pipeline for processing 16S rRNA amplicon data with exact Amplicon Sequence Variants (ASV's)
The `ASVpipeline.sh` script is a complete linux `BASH` script performing the essential steps in amplicon sequence data processing using only [usearch](http://drive5.com/usearch/).
**The script processes forward... |
f9ad5e745e39fcdc625b6b854e250a40dca6ba90c843d3b4d3d48743d46083a9 | Text | 4,003 | 85 | [](https://github.com/pog87/PtitPrince/actions/workflows/python_tests.yml)
[](https://www.python.org/downloads/)
[. https://doi.org/10.1038/s41398-025-03617-8.
R scripts were run in R version 4.0.2, MATLAB scripts were run ... |
ac0cdcad50d4174b4ffd137c327e3e129377f806c074bd00e5b0f3b1dedc8164 | Text | 4,069 | 55 | # snrnaseq-step5-process-dea-results
Code used to identify k-fold cross-validated differentially expressed genes (DEGs) and coordinated DEG subclusters resulting from differential expression analysis (DEA) using DESeq2 ([Love et al. 2014](https://doi.org/10.1186/s13059-014-0550-8), [Van den Berge et al. 2018](https://d... |
f3719100e4acc8fcd7d7919c14b5e70c830e4097cbad18f8dd306a0c64988c75 | Text | 4,102 | 124 | <!DOCTYPE html>
<html lang="en">
<head>
<meta charset="UTF-8">
</head>
<body>
<h1>ED_OverCrowding_Predictions</h1>
<h2>Project Overview</h2>
<p>
This project develops a deep learning approach to predict Emergency Department (ED) patient flow metrics, such as waiting count, using a complete machine learning pipel... |
e933431484de83e2d1366276f2ed78e91b9228577fc454eda833b91192570ae4 | Text | 4,126 | 114 | npTDMS
======
.. image:: https://img.shields.io/pypi/v/npTDMS.svg
:alt: PyPI Version
:target: https://pypi.org/project/npTDMS/
.. image:: https://github.com/adamreeve/npTDMS/actions/workflows/ci-cd.yml/badge.svg?branch=master&event=push
:alt: Build status
:target: https://github.com/adamreeve/npTDMS/ac... |
eb583f2e6ffb9513ed18cbf3a7ef3d2c4af46de07309f81887ff4272922262c3 | Text | 4,136 | 91 | # Code for Computing BOLD Estimates on Real-Data for Manuscript: "Unintended bias in the pursuit of collinearity solutions in fMRI analysis"
This code contains the analyses used for the Monetary Incentive Delay (MID) task for fMRI data.
As described in the [simulations code provided by Jeanette Mumford & Russ Poldra... |
fcdf2ecdc9a8244fbe74f6b36a63e073679d48dfed0344dd249c3d776e71031e | Text | 4,160 | 105 | # sabre - A barcode demultiplexing and trimming tool for FastQ files
## About
Next-generation sequencing can currently produce hundreds of millions of reads
per lane of sample and that number increases at a dizzying rate. Barcoding
individual sequences for multiple lines or multiple species is a cost-efficient
metho... |
6f9e34c49fc7cf10164c0137e8286994c5f145dff9a885ba33cefcd3f8314184 | Text | 4,163 | 91 | # Anatomy-guided, modality-agnostic segmentation of neuroimaging abnormalities
**Authors:** Diala Lteif, Divya Appapogu, Sarah A. Bargal, Bryan A. Plummer, Vijaya B. Kolachalama
This work is published in _Human Brain Mapping_ (https://doi.org/10.1002/hbm.70329).
---
## Overview
This reposit... |
26a9695e5b040c5d1e6bb009dd2946040d984c5754fea89153c04bb4b92cf6c6 | Text | 4,183 | 102 | # Code for Modeling Macroscopic Brain Dynamics with Brain-inspired Computing Architecture
This code implements the low-precision macroscopic brain dynamics. We present the curves (2-D distribution) of the commonly used indicators.
## files and folders:
```text
- exps/
- data/: group-average empirical data
- e... |
9a71ea4c61e7f3b962e98fcf3fe596493a05103c58df06f872c44fb6d29dfeb2 | Text | 4,207 | 130 | <img height=40 src='http://my5C.umassmed.edu/images/3DG.png' title='3D-Genome' />
<img height=30 src='http://my5C.umassmed.edu/images/dekkerlabbioinformatics.gif' />
<img height=30 src='http://my5C.umassmed.edu/images/umasslogo.gif' />
# crane-nature-2015
Publisher: NPG;
Journal: Nature;
A... |
126ec3cba114b231545e32a6b06bb33e36573f0be5c929d35e84bcf45bce74e7 | Text | 4,214 | 90 | # Predicting Cellular Responses to Novel Drug Perturbations at a Single-Cell Resolution
Code accompanying the [NeurIPS 2022 paper](https://neurips.cc/virtual/2022/poster/53227) ([PDF](https://openreview.net/pdf?id=vRrFVHxFiXJ)).
Our talk on chemCPA at the M2D2 reading club i... |
4f90543b4e3bd1bd4ad0633d1f81da0cee643f10fb06622b25b6898582d0d42d | Text | 4,215 | 101 | # Resample
## Usage
The resampler is containerized. In order to use it:
1. Configure
The file `docker-compose.yml` allows to configure:
- the target samplerate `SAMPLERATE`
- define the data to be resampled:
- from its start `TIME_START`
- to its end `TIME_END`
2. place the original files in the ... |
62cfd68366c83a4dc5d92d5c6a788325f95dd189d792b35016045e1ed7e3febf | Text | 4,220 | 54 | # Multiplexing microfluidic droplets - Deep Learning
### Research Group Applied Systems Biology
**Contributions:** Arjun Sarkar, Carl-Magnus Svensson
**Head:** Prof. Dr. Marc Thilo Figge
**Department:** Applied Systems Biology
**Institute:** Leibniz Institute for Natural Product Research and Infection Biology (Ha... |
b53cbff2a260415672765838919b7b0da0febe4737467d75fe0e19582bb80a28 | Text | 4,221 | 65 | Introduction
ImplantoMetrics is a comprehensive plugin for Fiji (an ImageJ distribution), specifically designed to facilitate the quantitative analysis of implantation processes using a 3D in vitro model. The plugin leverages advanced image processing, machine learning algorithms, and statistical methods to offer deep ... |
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