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10f6ea4f1cee76ddf8861deba8805c4cb48ab9bf3b5d9758ca90b2826edd2913 | Text | 6,311 | 81 | # ENCODE ATAC-seq pipeline
[](https://doi.org/10.5281/zenodo.156534)[](https://circleci.com/gh/ENCODE-DCC/atac-seq-pipeline/tree/master)
## Introduction
This pipeli... |
eb46b8a54e60643ca0cd8cb375ede05b01dcbd2380ca17ce8027a92ba13cebbb | Text | 6,311 | 147 | <a href="https://scvi-tools.org/">
<img
src="https://github.com/scverse/scvi-tools/blob/main/docs/_static/scvi-tools-horizontal.svg?raw=true"
width="400"
alt="scvi-tools"
>
</a>
[![Stars][gh-stars-badge]][gh-stars-link]
[![PyPI][pypi-badge]][pypi-link]
[![PyPIDownloads][pepy-badge]][pepy-link]
[](https://doi.org/10.5281/zenodo.20341604)
This repository contains code and notebooks for forecasting ROI-level fMRI time
series and derived functional connectivity measures from Natural Scenes Dataset
(NSD) scans.
The ... |
abe69d9f61e881e91e87c53786c7b6e10b84b46197b642b47f9be7fe4d58a4ad | Text | 6,371 | 108 | # Mutual-information minimization in recurrent neural networks
This directory contains the public analysis and reproduction scripts for:
**Tomoda, Yamaguti, "Mutual-information minimization enhances noise robustness and induces fault containment in functionally differentiated recurrent neural networks"**
The scripts... |
3245a66f34804adef6a6dd1e0f3172a0f7ffa37291128d4a265796090b0fa06b | Text | 6,450 | 151 | # RegRegSEA: Regulatory Region Set Enrichment Analysis
RegRegSEA is an R package designed for Regulatory Region Set Enrichment Analysis of epigenomic data. By adapting the statistical approach of GSEA to the epigenetic landscape, our tool allows you to test for the enrichment of regulatory region sets in DNA methylati... |
fe1b8a23b315de66cae4af0845e69d2462741a111ca00d91d464bf2b0e7548ab | Text | 6,454 | 75 | # iapi
Instrument Application Programming Interface for the Thermo Fisher Scientific Tribrid, Exactive, and Exploris series Mass Spectrometers.
## News
Update (September 29 2025): there are now patches available for the [microscans issue](https://github.com/thermofisherlsms/iapi/issues/49) seen on Tune 4.2 and 4.3, ... |
740f40049accc897be91c00ebc587a4fd1795ae7c58c81157c20aeffb640e2a8 | Text | 6,473 | 60 | Code and data for our work modelling sharpness-specific tuning of neural entrainment to speech and speech tracking more generally.
## Julia version and packages
This code uses Julia 1.10.3, and the following packages: Arrow v2.8.0, CSV v0.10.15, ColorSchemes v3.29.0, Colors v0.13.0, ComponentArrays v0.15.25, DSP v0.8.... |
2b7706a330846d4cd461ff38df98b34994fe83c8dc91f8aae9a23fc060ff4881 | Text | 6,545 | 133 | # Simulation encoder repository
[](https://github.com/bagherilab/simulation-encoder/actions?query=workflow%3Abuild)
[](https://codec... |
517184d372958b773f85de55d847e290ad5ea20907dd9a34f201a97f7a92f908 | Text | 6,545 | 163 | # CrystalGRW: Generative Modeling of Crystal Structures with Targeted Properties via Geodesic Random Walks
[](https://arxiv.org/abs/2501.08998)
### Version
Current version: **1.1.1**
See the [CHANGELOG.md](./CHANGELOG.md) for details on updates.
### Train... |
3a5db68743837d5c9c3d791a457c0a91679ba5d59296c4a25e17b8fd09f5e09d | Text | 6,595 | 104 | <div class="title" align=center>
<h1>💊DrugGPT</h1>
<div>A GPT-based Strategy for Designing Potential Ligands Targeting Specific Proteins</div>
<br/>
<p>
<img src="https://img.shields.io/github/license/LIYUESEN/druggpt">
<img src="https://img.shields.io/badge/python-3.8-blue">
<a href="https:... |
35dfb6e3a6a23572ef118f195fa30351f750c6bffbe383c76f3a6e85c2584de5 | Text | 6,596 | 200 | # RAG-GNN: Retrieval-Augmented Graph Neural Networks for Protein Interaction Network Embeddings
[](https://www.python.org/downloads/)
[](https://opensource.org/licenses/MIT)
A framework... |
2170a2a844d062e1fda58769dfb6c6566e211c90282ea4a0cdb5a88be9928cd7 | Text | 6,701 | 241 | # CLRN1 Knockout Rabbit Retina snRNA-seq Analysis
[]()
## Overview
Complete analysis code and results for:
**"Müller Glia-Exclusive CLRN1 Expression Drives Non-Cell-Autonomous Photoreceptor Degeneration in Usher Syndrome Type 3A"**
Dongshan Yang, et al.
*xxx" (2026)
## Experimental De... |
1e5a30281519b174f43499d056820b672461f9dc4ce3fd2ed60e34ae0f58ccdf | Text | 6,811 | 200 | # TNF scRNA-seq neurogenesis analysis
Code to reproduce the scRNA-seq (Seurat) analyses and figures for the publication:
**"TNF-α induces type I IFN signalling to suppress neurogenesis and recruit T cells."**
This repository contains analysis code, metadata, and a reproducible R environment.
Processed input data a... |
3963c8dd2aa518c1fa443852c8bb817923205d2e099be9ea4b855fda4ce01730 | Text | 6,953 | 107 | [](https://doi.org/10.5281/zenodo.8172821)
[](https://github.com/Julie-Fabre/bombcell/blob/master/LICENSE)
[![View bombcell on File Exchange](https://www.mathworks.com/matlabcentral/images/matla... |
23bf31b17f3d2dcdf7b444e3e3167e681423f5bc4aaa555169465af983986797 | Text | 7,053 | 177 |
<div style="background-color: white; padding: 10px; display: inline-block;">
<img src="https://raw.githubusercontent.com/veitlab/moove/main/assets/logo_white_bg.png" alt="Moove Logo" width="250">
</div>
# Moove
Moove (Marking Online using Only the Onsets of Vocal Elements) is a novel tool for real-time syllable ... |
c525301b19ce3b620cb519b0761250244c7238c2b06cfa1235e2b4f1fd396419 | Text | 7,182 | 237 | # SegJointGene
## Overview
SegJointGene is a self-training framework for spatial cell-type segmentation that integrates **Computational Information Discarding (CID)** to constrain iterative label propagation. The method combines a segmentation network with attribution-guided label updates to progressively refine ... |
b37aa72c4d034698308cf434e7ad7f523ef3adeb32665d91c815b1f01f8c911e | Text | 7,226 | 149 | # Garfield — Reproducibility
Reproducibility resources for **Garfield** (*Graph-based Contrastive Learning
Enables Fast Single-Cell Embedding*), a geometric deep-learning framework that
co-embeds single-cell and spatial multi-omics data—transcriptomics, epigenomics
and proteomics—into a shared, spatially aware latent ... |
0312fb9646aef630a30cd3039337b31a48f4345f4dd1cdd71edcc483afd8b9d0 | Text | 7,250 | 143 | # GPN — Genomic Pretrained Network
[](https://github.com/songlab-cal/gpn/actions/workflows/ci.yml)
[](https://gpn.readthedocs.io/)
[ detection and threshold-free cluster enhancement (TFCE) analysis of infant fNIRS/HD-DOT data, developed for two related studies conducted in rural Gambia as part of the BRIGHT and INDiGO projects:
- **Beaton et al.**, *"Characterizing developmental changes in infant habi... |
4b0bc5e81743b5d9464521d56a5b7fbd6dc66260ba810fe3da695e4ad3559aae | Text | 7,427 | 128 | # Neural.Efficiency.2025
Analysis files and meta-data to accompany the manuscript "Reduced Threat-Related Neural Efficiency: A Possible Biomarker for Pediatric Anxiety Disorders", which has been accepted for publication by The American Journal of Psychiatry.
This repository contains analysis scripts (bash, Python, Mat... |
4cf7db05eaca831a2a5707ddbc31759987aeb8d0954850bea8767dd52093ab71 | Text | 7,467 | 99 | # GenomicSEM
R-package which allows the user to fit structural equation models
based on the summary statistics obtained from genome wide association studies (GWAS). Note that a recent update includes the ability to automatically obtain Q_SNP results without running a separate follow-up model. Until explicitly stated ... |
879fe53304a4df8d02250e543cc1a1a9571021bef65df2e8526ae446e07c45ac | Text | 7,500 | 130 | # UTR-LM: A Semi-supervised 5’ UTR Language Model for mRNA Translation and Expression Prediction
The untranslated region (UTR) of an RNA molecule plays a vital role in gene expression regulation. Specifically, the 5' UTR, located at the 5' end of an RNA molecule, is a critical determinant of the RNA’s translation effi... |
aa5de166342c33017262ad107c98aa05d025f877e5507023db2c27265a5c9f8c | Text | 7,500 | 69 | # S<sup>2</sup>ALM: Sequence-Structure Pre-trained Large Language Model for Comprehensive Antibody Representation Learning
The repository is an official code implementation of [S<sup>2</sup>ALM: Sequence-Structure Pre-trained Large Language Model for Comprehensive Antibody Representation Learning](https://spj.science.o... |
04f222ae3e005f575f45e8058e9755fa05d6a03592953ee597b9722c3fb47e19 | Text | 7,514 | 118 | # drosophila_body_orientation_predictor
Repo for [Mangat et al. (2026)](https://www.biorxiv.org/content/10.64898/2026.03.30.715335v1.full). Predicts *Drosophila* body heading angle from flight trajectory data using a neural network trained on data from [van Breugel et al. (2014)](https://www.sciencedirect.com/science/... |
55a802f28296c82a6c73b6cddf0cbbf6503ee654e6d76a1497632ffbce214b9b | Text | 7,557 | 202 | # brain-maintenance-lgcm
Reference implementation of the core analytical pipeline for
> Menze, I., Ziegler, G., Spottke, A., Jessen, F., Düzel, E., et al.
> *Joint trajectories of brain atrophy, white matter hyperintensities and
> cognition quantify brain maintenance*.
This repository accompanies the manuscript and ... |
62930497597473116088cbe6fd34ba7e115ec21912521ee0c5baeae3331239cb | Text | 7,561 | 64 | # Automated detection of neurofibrillary tangles in digitized whole slide images using deep learning
Welcome to the tangle-tracer repository! This repo is associated with the study [Ghandian et al. 2024](https://doi.org/10.1101/2024.05.15.594372). The repo offers a few key utilities:
- Reproducibility of the above st... |
afc4fa94a2dd7d735c45f23fe4e7a3d68f367567fb4281d1056a058c0e94d195 | Text | 7,572 | 140 | # ecephys spike sorting
https://github.com/AllenInstitute/ecephys_spike_sorting
Modules for processing **e**xtra**c**ellular **e**lectro**phys**iology data from Neuropixels probes.
... |
596accee0fde41fd577d4a22b6d42573a7e179bb1975315396454bb46a3f54c7 | Text | 7,711 | 92 | # Cell Counter
Processes microscopy images to count cells and identify which are pyknotic. This is internal/development-grade source code, provided as-is primarily for reference purposes. However, we hope this program will help other labs establish an automated method of analyzing histologic images, and we hope someon... |
c1c810ef1addd5c0459fc708832565c57592c9569da96a06e5bfbf7162454e6c | Text | 7,715 | 208 |
# NeuroSyncApp (Version 2.0.15)
**NeuroSyncApp**: A Photometry, Behavior, and Telemetry Alignment Tool
NeuroSyncApp is a Python tool designed for neuroscientists and researchers to align and analyze photometry, behavioral, and telemetry data in a single interface. This application facilitates visualization, AUC calc... |
dcf08602288350548b6a8e76b47a3b2e2ff8ae6259622a00031e8d99662ecd55 | Text | 7,747 | 168 | # **KCL_Neuromelanin-MRI**
### **King's College London (KCL) Neuromelanin-Sensitive MRI (NM-MRI) Analysis Pipeline & Midbrain Atlas**
---
## **Overview**
This repository provides code for generating **SN-VTA NM-MRI contrast-to-noise ratios (NM-CNRs)** from NM-MRI... |
3e723719936260323d606238d5b5d332d3bc2c74b03009316cbfeeb3752c96f3 | Text | 7,774 | 144 | # Knowledge-exploited Auto-encoder for Proteins (KeAP)
This repository contains an official implementation of KeAP, presented by our ICLR'23 paper titled [Protein Representation Learning via Knowledge Enhanced Primary Structure Reasoning](https://openreview.net/forum?id=VbCMhg7MRmj). KeAP effectively encodes knowledge... |
322831ed5ba1c0eb2881a4df03cee68e079920fcad1dd9ac53a59469c0e9a135 | Text | 7,802 | 135 | # FunBurd
[](https://doi.org/10.5281/zenodo.17369429)
[](https://doi.org/10.1038/s41467-026-76676-0)
[](https://... |
105bd86ef800afe494f56b5887d76fe4007e6f64147409adeadc2088fe32de53 | Text | 7,838 | 208 |
# 
## ⌛️ Data availability
[3UTRBERT_dataset](https://doi.org/10.6084/m9.figshare.26082916.v1)
## ⌛️ Download pre-trained 3UTRBERT model
[3UTRBERT-3mer](https://figshare.com/articles/software/Pre-trained_3mer_model/22847354)
[3UTRBERT-4mer](https:... |
7aafaab3986f63d822b703ff3aa90c7fa4ed008d4c997e6f55fa976d1ac6c8f4 | Text | 7,886 | 314 | # neural-ode-temperature-kinetics
## Brief description
This repository contains the source code and analysis scripts used in the study
"Machine Learning of Temperature-dependent Chemical Kinetics Using Parallel Droplet Microreactors"
by Mamoru Saita and Yutaka Hori.
The codes implement image processing, ... |
288fc998e0553ddeab3fea40b5a531e8222fac6145f1f1affed7641a254b004c | Text | 7,954 | 181 | # GRAPHYCS
This repository contains the open-source code for the paper:
**["Graph-based modeling of optical system enables adaptive optics on dynamic samples with self-calibration"](https://doi.org/10.1016/j.isci.2026.116769)**
*iScience* 29, 116769 (2026).
## About GRAPHYCS
Sensorless adaptive optics offers signi... |
96cd336bc308a8d9d0b79f59ce4b58e09f8b3cda6273b43d39452ac06435ce49 | Text | 8,034 | 142 | # TVSD
## THINGS Ventral stream Spiking Dataset (TVSD)
######
Large-scale electrophysiological recordings from V1, V4 and IT in two macaques in response to ~22k images from the THINGS image database.
**Paolo Papale, F... |
85ace71a3659a346ef81db6a8c88650a9bb9f9e171203df122524f04dcd33313 | Text | 8,054 | 360 | <h1 align="center">
<img src="puffin.png" height="40" style="vertical-align:-6px;"> PUFFIN: Protein Unit Discovery with Functional Supervision
</h1>
<p align="center">
<a href="https://doi.org/10.1093/bioinformatics/btag265">
<img src="https://img.shields.io/badge/DOI-10.1093/bioinformatics/btag265-blue">
... |
b287ba1934ff4b70906b183c9fed997696931bd24eb4fdc1c966b0d1cc1dc47e | Text | 8,058 | 138 | # CrossSim
CrossSim is a GPU-accelerated, Python-based crossbar simulator designed to model analog in-memory computing for any application that relies on matrix operations: neural networks, signal processing, solving linear systems, and many more. It is an accuracy simulator and co-design tool that was developed to ad... |
d50ebe7bedf993a49b13c595292416931a5b7effe60dd306e981c5227a53321b | Text | 8,227 | 159 | # A collection of various utilities for GWAS summary statistics.
## sumstats.py
sumstats.py is a collection of utilities that work with GWAS summary stats.
``csv`` utility reads raw summary statistics files
and convert them into a standardized format:
tab-separated file with standard
column names, standard chromosome... |
e5f726ce78bd9140df62c3a9849d89477e390261284cfc3ba6b137c31f9de211 | Text | 8,361 | 238 | # 🔬 Deep Learning-Enhanced Raman Microspectroscopy
This repository provides an implementation of the Raman imaging pipeline described in [Georgiev et al., Science Advances, 2026](https://doi.org/10.1126/sciadv.aec5080).
⚡ **Purpose:** Extract chemical components and their spatial maps from hyperspectral Raman imagin... |
ac4eefdd98c0c86de7731cf896cae5621cc43df4fcce413058a3b03c02e0860f | Text | 8,440 | 98 | ggrepel <img src="man/figures/logo.svg" width="181px" align="right" />
============================================
[![Build Status][bb]][githubactions] [![CRAN_Status_Badge][cb]][cran] [![CRAN_Downloads_Badge][db]][r-pkg]
[bb]: https://github.com/slowkow/ggrepel/workflows/R-CMD-check/badge.svg
[githubactions]: https... |
028023918ec02cab3947c86135b0cfe690f278f25f4eb9d60093eae7208d3d4c | Text | 8,444 | 146 | # Band gaps and densities of states of 1,784 halide perovskites (SIESTA-PBE/DZP)
Data and code supporting the manuscript *"Band gaps of halide perovskites from an
orbital cluster-expansion descriptor: mechanism, a localized failure in the iodides,
and a hybridization channel"* (D. L. Azevedo).
**Version 1.0.0**
---
... |
00cb9c2d1ea28b512f8ef0dfc77f6a07ea8b109777c5350a8c92a8d5ca5a2462 | Text | 8,508 | 189 |
# DrugReAlign: A Multisource Prompt Framework for Drug Repurposing Based on Large Language Models
<p align="center">
<img src="https://github.com/kkkayle/DrugReAlign/blob/master/DrugReAlign.png" width="400">
</p>
This repository contains the official implementation of the paper:
> **DrugReAlign: a multisource pro... |
b27a3fc9b62951993d72d920c73f7bc52f5f209eb51e7769f8dafe36b2974e5d | Text | 8,569 | 166 | # EIF2S1-PELO Co-Expression Architecture in Human Brain
[](LICENSE)
[](https://gtexportal.org/)
[](https://www.ncbi.nlm.nih.gov/... |
2a453b904b6fc1127be92197f34f0d2f14606491850cc40345c4855b6afe87c0 | Text | 8,658 | 110 | 
# A human lysosomal storage disorder toolkit for decoding proteome landscapes in cortical and dopaminergic-like induced neurons
[](https://www.bio... |
de3d60dd5aedc63c4f401a92876c2d1e053011e008773ce1be38511360463b63 | Text | 8,682 | 166 | # RiboNucleic Acid Language Model - RiNALMo
### [Paper](https://arxiv.org/abs/2403.00043) | [Weights](https://zenodo.org/records/15043668)
[Rafael Josip Penić](https://www.fer.unizg.hr/en/rafael_josip.penic)<sup>1</sup>,
[Tin Vlašić](https://sites.google.com/view/tinvlasic)<sup>2</sup>,
[Roland G. Huber](https://web.... |
bbcee42b5fdc6e0f0da0906fb8bb304ba941a3d75ff61f4710f4ca77e26d5fa1 | Text | 8,699 | 149 | # 🧬 BINND: Binding and Interaction Neural Network for DNA
[](https://doi.org/10.5281/zenodo.19488794)
This repository contains the official implementation of **BINND (Binding and Interaction Neural Network for DNA)**, a novel framework designed to predict interactions b... |
d3f524fabcb2c00ed737e37c692d4cda6c964b911fcc6200577a1459626d9c11 | Text | 8,733 | 192 | # BigStream
---
BigStream is a library of tools for 3D registration including images too large to fit into memory and/or too large to register in a single (multi-threaded) process. BigStream can automate chunking of the alignme... |
61ec235cae69cf8983b97c345c7c2aec66da610ce04ad4e31add5cd2539e3565 | Text | 8,752 | 206 | # README #
Parallel High Angular Resolution Diffusion Imaging (pHARDI) is a toolkit for the GPU/CPU-accelerated reconstruction of intra-voxel reconstruction methods from diffusion Magnetic Resonance Imaging (dMRI) data. It was designed to support multiple linear algebra accelerators in a wide range of devices, such as... |
eb244651b112d1cbf6ba5c91dcd7c64d9b702cac61527939852e98b6452afb1d | Text | 8,801 | 183 | # Garfield: G**raph-based Contrastive Le**ar**ning enable **F**ast S**i**ngle-C**el**l Embe**dding
[](https://github.com/zhou-1314/Garfield/blob/main/LICENSE)
[](https://pypi.org/project/garf... |
01a84248f24f64fe1a5b3d81a1a2aa84bf8a5379a6fbaeca24e925170147476f | Text | 8,821 | 220 | # Evo: DNA foundation modeling from molecular to genome scale
**We have developed a new model called Evo 2 that extends the Evo 1 model and its ideas to all domains of life. Please see [https://github.com/arcinstitute/evo2](https://github.com/arcinstitute/evo2) for more details.**
Evo is a biological... |
500e8f5670a3d9eeaa157afa389b9c75c97f961ee3a32c49183372f2582a21ca | Text | 8,873 | 156 | [](https://pepy.tech/project/aestetik)
[](https://opensource.org/licenses/MIT)
[](https://www.python.org/downloads/)
[ 2018 Othneil Drew
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish,... |
3a05d72d3dcea1437a8f12d622d3747a9abb63ec3df3ea290a1e9da78d16562e | Text | 8,907 | 163 | **MENTOR**: **M**echanistic **E**xploration of **N**etworks for **T**eam-based **O**mics **R**esearch
=======================
Installation
============
```sh
$ git clone <link>
$ cd MENTOR
$ conda env create -f ./environment.yml
$ conda activate mentor
$ make
```
Verify the installation:
```sh
$ mentor --help
```
... |
b0503e8ca789f19f1fc2350c5aaf57b1b323bbae43b354655231b5f4a1586c83 | Text | 8,908 | 113 | # scGPT
This is the official codebase for **scGPT: Towards Building a Foundation Model for Single-Cell Multi-omics Using Generative AI**.
[](https://www.biorxiv.org/content/10.1101/2023.04.30.538439)
[ is now published in *Nature Methods*.**
We developed a large-scale pretrained model scFoundation with 100M parameters. scFoundation was based on the **[xTrimoGene](https://pr... |
7a9a51b9606924bd404bfeabb8504d294624350254fe300aa26d810b75fd1cf8 | Text | 9,141 | 133 | # Kuzushiji-MNIST
[](https://creativecommons.org/licenses/by-sa/4.0/)
📚 [Read the paper](https://arxiv.org/abs/1812.01718) to learn more about Kuzushiji, the datasets and our motivations for making them!
## News and Updates
**... |
ded288b007a8f9ae2222f09dfeb715f46654af7964519fed9cefc3ce3aec7374 | Text | 9,320 | 191 | [](https://doi.org/10.5281/zenodo.1419527)
[](LICENSE)
[](https://github.com/NeuropsyOL/SENDA/releases/l... |
e39f004fac1efc7b94c9e9aea9c5f52cb884606e38c4797d6563f72ea7f36dbc | Text | 9,432 | 170 | <img src="https://raw.githubusercontent.com/broadinstitute/Tangram/master/figures/tangram_large.png" width="400">
[](https://badge.fury.io/py/tangram-sc)
Tangram is a Python package, written in [PyTorch](https://pytorch.org/) and based on [scanpy](https://scanp... |
40649aa6a58e5b0648f9ab0edbc757d51db516a1dc1324597cd34c8b8b0d26b7 | Text | 9,528 | 244 | # NeuroSyncApp
NeuroSyncApp is a PySide6 desktop app for processing raw photometry recordings and aligning photometry with coded behaviour, telemetry, and optogenetic recordings.
The app opens to a dashboard. The default first tool is **Analyse Raw Data**.
## Available Tools
| Tool | App ID | Purpose |
| --- | --- ... |
ab6a8b2c1afed0a4ea18a06e5d9f96471e8a44458b1a02aec21f23d033f80de0 | Text | 9,545 | 53 | ## fMRI Simulator
Designing an fMRI study is a daunting task. Note that with fMRI you have to tradeoff predictability with statistical efficiency. Completely random event related designs will inherently have low power, requiring long scanning sessions. While block designs offer optimal statistical power, but the parti... |
e61c562984f645cc0b27fdf4d5d638b51fa007a4b0ffd565189afe9a6c650a9f | Text | 9,568 | 188 | [](https://opensource.org/licenses/MIT)
# MSI-VISUAL: New visualization methods for mass spectrometry imaging and tools for interactive mapping and exploration of m/z values
`pip install msi-visual`
| Feature | De... |
2017e5a8a81980a1af7d4f984ddd5e548c2c2178c0c1852a36b3ffed70ceec91 | Text | 9,579 | 136 | [](https://doi.org/10.5281/zenodo.18269709)
# Population Morphology Implies a Common Developmental Blueprint for *Drosophila* Motion Detectors
Nikolas Drummond, Arthur Zhao, Alexander Borst
[BiorXiv](https://www.biorxiv.org/content/10.1101/2025.11.15.688637v1)
This is th... |
951f6a5b8247fe0838a32563647acddf2c273b8d2a940083c79bb52eb1cfad0d | Text | 9,710 | 224 | <h2><a href="https://github.com/NICALab/SUPPORT/blob/main/Beginner_guide.md"> 𝐅𝐨𝐫 𝐭𝐡𝐨𝐬𝐞 𝐰𝐡𝐨 𝐚𝐫𝐞 𝐧𝐞𝐰 𝐭𝐨 𝐏𝐲𝐭𝐡𝐨𝐧, 𝐩𝐥𝐞𝐚𝐬𝐞 𝐜𝐡𝐞𝐜𝐤 𝐭𝐡𝐞 𝐬𝐭𝐞𝐩-𝐛𝐲-𝐬𝐭𝐞𝐩 𝐢𝐧𝐬𝐭𝐫𝐮𝐜𝐭𝐢𝐨𝐧𝐬. 𝐂𝐥𝐢𝐜𝐤 𝐡𝐞𝐫𝐞.</a></h2>
#### We welcome discussions and collaborations! Try SUPPORT on your data,... |
a02f3fa7616a1131425fb17ebdede073fe2b828d2dd940cc45ba8b0721551edb | Text | 9,755 | 206 | # Glutamatergic signaling underlies brain structural organization for mathematical and reading abilities in children
© 2026 by The Board of Trustees of the Leland Stanford Junior University is licensed under [CC BY-NC 4.0](https://creativecommons.org/licenses/by-nc/4.0/)
For commercial license inquiries, contact the ... |
734a8cec5f667d74d421bf3b273ad7e256216109636da45aa7ceba21cd34de16 | Text | 9,791 | 278 | # DNABERT-2: Efficient Foundation Model and Benchmark for Multi-Species Genome
The repo contains:
1. The official implementation of [DNABERT-2: Efficient Foundation Model and Benchmark for Multi-Species Genome](https://arxiv.org/abs/2306.15006)
2. Genome Understanding Evaluation (GUE): a comprehensize benchmark cont... |
99299d80156a588c4b354f7771be9c78ad4f81d1780835cf74ca29a7d9eb4ed3 | Text | 9,972 | 177 | ## Neuroglancer: Web-based volumetric data visualization
[](https://opensource.org/licenses/Apache-2.0)
[](https://www.npmjs.com/package/neuroglancer)
[ if you were looking for the old one instead.
Coming from V1? Check out the [TLDR Migration Guide](documentation/tldr_migration_guide_from_v1.md). Reading the rest of the documentation is still strongly recommended ;-)
# What... |
97f0339e5bc7ccd150c54d3a01cb4de4aadf9c4cb70a0b33bffb5eeeccac8863 | Text | 10,043 | 186 | <div>
<a href="https://www.pgmpy.org"><img src="https://raw.githubusercontent.com/pgmpy/pgmpy/dev/logo/logo_color.png" width="175" align="left" /></a>
pgmpy provides the building blocks for causal and probabilistic reasoning using graphical models. It implements data structures for a range of causal and graphical mode... |
439b8b877ce39476722560d32676958a5229d60185a02bb4381eedd345723334 | Text | 10,119 | 192 | # SpliceBERT: RNA langauge model pre-trained on vertebrate primary RNA sequences
SpliceBERT ([manuscript](https://doi.org/10.1093/bib/bbae163), [preprint](https://www.biorxiv.org/content/10.1101/2023.01.31.526427v2)) is a primary RNA sequence language model pre-trained on over 2 million vertebrate RNA sequences.
It ca... |
3f779845b68bb66b9b1de799be43d056a8c8a2cae3715080569b70b35959302f | Text | 10,141 | 75 | ## This repository contains python notebooks, codes and data used to produce all the figures in the main manuscript and the supplementary material of the paper:
# High reelin expression can explain why the entorhinal cortex is a cradle for Alzheimer's disease [doi: https://doi.org/10.1101/2025.06.04.655278]
#... |
2aeb3e08e8e6b0ea8c321ec0440fc16165a819b000305c19c27adb54d9cbd1a6 | Text | 10,151 | 158 | # Official code repository for the original spike-based alignment learning paper
[](https://github.com/unibe-cns/sal-code/actions/workflows/ci.yml)
[](https:... |
e520842a36dfd0ddab0b6cfb8d3d17f5f9f72e091334cd4bf2dc6bb3493c104d | Text | 10,268 | 195 | # iDCF: Interpretable Deconvolution of Cell Fractions via Biologically-informed Deep Models Using scRNA-seq Data
**iDCF** is a deep learning framework designed for accurate and interpretable deconvolution of cell type fractions from bulk tissue gene expression data. By integrating prior biological knowledge, such as p... |
4f23faa276bdeef957a0f7c00088f913214bcaad93d79e7768accb9ab5d0f58e | Text | 10,287 | 271 | ---
language: en
tags:
- clip
- biology
- medical
license: mit
library_name: open_clip
widget:
- src: https://huggingface.co/microsoft/BiomedCLIP-PubMedBERT_256-vit_base_patch16_224/resolve/main/example_data/biomed_image_classification_example_data/squamous_cell_carcinoma_histopathology.jpeg
candidate_labels: ade... |
d2b2ca2f33c4d4d1dac63659cff494631732b7ec87ac07ad99a0826e55bfa603 | Text | 10,500 | 214 | # ERNIE-RNA
This repository contains codes and pre-trained models for **RNA feature extraction and secondary structure prediction model (ERNIE-RNA)**.
**ERNIE-RNA is superior to the tested RNA feature extraction models (including RNA-FM) in the feature extraction task, and its effect in the secondary structure predict... |
e6ac27033f0c37b67644f03103e3a1db8ba4c6b44604a9966e54b4f44a9bfc10 | Text | 10,534 | 212 | 
**Warning: Orbformer checkpoints are stored using `pickle`. Never read a checkpoint from an untrusted source.**
# OneQMC
This package provides an implementation of the [Orbformer wave function foundation model](https://arxiv.org/abs/2506.19960).
We also provide the following:
- the [Neural E... |
01122457fed05fe5b51e2393a0eaac1ca7e82194eb87e28bb9e7d590dbeca865 | Text | 10,625 | 214 | 
**Warning: Orbformer checkpoints are stored using `pickle`. Never read a checkpoint from an untrusted source.**
# OneQMC
[](https://doi.org/10.5281/zenodo.21160149)
This package provides an implementation of the [Orbformer wave function foundatio... |
a80df2724a3434264835d4f7bae337c34b5bc8bd26419f7e8adf5641fa17c706 | Text | 10,781 | 120 | # SANDI Matlab Toolbox: Latest Release
This repository contains the latest release of the SANDI Matlab Toolbox. <img align="right" src="https://github.com/palombom/SANDI-Matlab-Toolbox-Latest-Release/assets/33546086/c4995b93-6e41-45c0-ae96-1897b44ef301.png" width="220" height="200">
The "***SANDI (Soma And Neurite D... |
26284f3b6d7c77ac0fe2999f9d4f1895c485a4b7c355dc123c692bcae10dcee9 | Text | 10,848 | 227 | # Bio-inspired decision making in robot swarms under biases
Repo contains the code to run Gillespie simulation, the robot simulation code and the code to process Gillespie and robot simulation data to generate the figures. For all the installations, we assume a clean installation of Ubuntu20.04, Ubuntu22.04 or Mac OS.... |
b8f296398e21038f25634d5f4d9023150cc3b509d2baee088133820b4e7d4744 | Text | 10,904 | 196 | # ATAC-seq
**Institut Curie - Nextflow ATAC-seq analysis pipeline**
[](https://www.nextflow.io/)
[](https://multiqc.info/)
[](https://doi.org/10.5281/zenodo.20341604)
This repository contains code and notebooks for forecasting ROI-level fMRI time
series and derived functional connectivity measures from Natural Scenes Dataset
(NSD) scans.
The ... |
0140dd93a62e84d4e018dcd0043275d7dbbbf00b61032072d21aed57e9855069 | Text | 11,091 | 207 | # SPADCFR
SPAD-CFR (Spatial Point-cloud Attention-based Diffusion for CounterFactual Reprogramming) is a generative framework for in silico targeted reprogramming of tissue microenvironments. It unites structural causal modeling with point cloud diffusion to enable spatially resolved counterfactual inference from multi... |
d03dbb6ec72e162b00287ac39aa93a235ba3859b87dc86fb0b9e10259efc7464 | Text | 11,096 | 236 | <div align="center">
# 【Nucleic Acids Research 2024】🧬RNA-MSM
**Multiple sequence-alignment-based RNA language model and its application to structural inference** <br>
[RNA-MSM Web Server](https://aigene.cloudbastion.cn/#/rna-msm) | [Paper](https://academic.oup.com/nar/article/52/1/e3/7369930) | [Report Bug](https://g... |
a30d0c2d9e6c9fa32393a1defc2ef976ca047cedaddf674faa679a84d46f9965 | Text | 11,433 | 140 | # MS multi-omics re-analysis — analysis code
Analysis code for the study prioritising *ITGB2* and *IKZF1* in multiple sclerosis by
inverse-concordant DNA-methylation × transcription integration across four omic layers.
Every script ships with the placeholders `__MS_GEO_ROOT__` (project root) and `__PYTHON_BIN__`
(int... |
d6876ddba164151f5ff402f5d6b5a0072eaa7d087bbae415bb5f0ec1d5f13b9d | Text | 11,641 | 245 | # `folx` - Forward Laplacian for JAX
This submodule implements the forward laplacian from https://arxiv.org/abs/2307.08214. It is implemented as a [custom interpreter for Jaxprs](https://jax.readthedocs.io/en/latest/notebooks/Writing_custom_interpreters_in_Jax.html).
## Install
Install `folx` with your package manag... |
46b6385e1920d0bacc84fa4a1c79af9eb696576951945dee49c3290a435eda0d | Text | 11,687 | 191 | <h1 align="center">
<picture>
<source media="(prefers-color-scheme: dark)" srcset="https://raw.githubusercontent.com/FelixKrueger/TrimGalore/master/docs/public/logos/hero-dark.svg">
<img alt="Trim Galore" src="https://raw.githubusercontent.com/FelixKrueger/TrimGalore/master/docs/public/logos/hero-light.svg" w... |
035beb760a6cf4695d59fe42bff6e856f029cbc46edc3ffb53685dd77f9a3625 | Text | 11,704 | 211 | # EIF2S1 Translational Quality Control Hub in Human Brain
[](LICENSE)
[](https://gtexportal.org/)
[](https://www.python.o... |
4e6ebca086fe79aee992ff53151d4a605d53e874e844a9038bc983f175c6d1c7 | Text | 11,727 | 195 | ## TCRmodel2
To model TCR-pMHC complex structures, as well as unbound TCR and pMHC structures, with high fidelity.
While you have the option to download and install TCRmodel2 locally, we recommend utilizing our web server for generating predictions. The web server offers a user-friendly interface and eliminates the... |
da4153105affcc2b7e1426a249b1aed2847648bf35cae7c3f5d1853a1826cb4c | Text | 11,931 | 335 | # CC-NSIEA: Class-Contrast Evidence Audit for Reliable Cross-Subject Wearable Activity Recognition
This repository contains the source code for the final method reported in the manuscript:
> **Neuro-Symbolic Class-Contrast Evidence Audit for Reliable Cross-Subject Wearable Activity Recognition**
CC-NSIEA is a label-... |
a607c218860bb53e794c6ee0476db2afdb74630b5a9adec81796a9c68ea0ca68 | Text | 11,962 | 202 | [](https://www.nextflow.io/)
[](http://bioconda.github.io/)
[](https://github.com/NeuropsyOL/RECORDA/actions/workflows/android_build.yml)
[](LICENSE.md)
[](https://github.com/jonescompneurolab/SpectralEvents/actions/?query=branch:master+event:push)
[](https://mybinder.org/v2/gh/jonescompneurolab/SpectralEvents/HE... |
58d96261672e707affb50a6d025ef599eb16b2c30b0901621b9d00f9e63b0638 | Text | 12,537 | 389 | # GAMT-GINE
GAMT-GINE is a geometry-aware multi-task graph neural network for protein–ligand
binding-affinity prediction. A protein–ligand complex is represented as an
atom-level intermolecular graph. Atom types are encoded as node features, while
protein–ligand interatomic distances within 5.0 Å are expanded with Gau... |
68490c7b59d07b054ae8bebeb54337493859f006d26fe1d018a656c0a69bb39c | Text | 12,623 | 256 | <p align="center">
<img src="https://user-images.githubusercontent.com/19553554/71825144-2d568180-30d6-11ea-8ee0-63c849cfd934.png" alt="pyecharts logo" width=200 height=200 />
</p>
<h1 align="center">pyecharts</h1>
<p align="center">
<em>Python ❤️ ECharts = pyecharts</em>
</p>
<p align="center">
<a href="ht... |
1b008d1a833e68f957fe72f77661795c9b8a9b6f3830baa0b25a88eff25889d0 | Text | 12,694 | 189 | # HIPPIE benchmarking (release)
Repository for reproducing the results reported in
**HIPPIE: A Generative Model for Electrophysiological Analysis Across Species,
Technologies, and Modalities**. Contains HIPPIE's code, the three baseline
methods (PhysMAP, NEMO, WF-RF), and the cached results and processed datasets
used... |
9bc797972923d612dec378886101bc98f5c3ca4cd081bdb1a9f8db2d6cc88aa2 | Text | 12,734 | 213 | # Band gaps and densities of states of 1,784 halide perovskites (SIESTA-PBE/DZP)
Data and code supporting the manuscript *"Band Gaps of Halide Perovskites from an
Orbital Cluster Expansion: Mechanism, Iodide Bias, and a Hybridization Channel"*
(D. L. Azevedo, J. Phys. Chem. C, manuscript jp-2026-05221e, revised versio... |
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