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a891da3d58bd5ec82ccef33b143fa880ca4dd24c4680c65081722d41155b21be | Text | 9,314 | 215 | # Building-a-Neural-Network-Model-to-Define-DNA-Sequence-Specificity-in-V-D-J-Recombination
A sequence-based dense neural network, with DNA sequence one-hot encoded inputs to predict recombination efficiencies. The models are optimized and trained on the H4S2 region and the other trained on the H4S2 and the partial non... |
4bc79ff26536e046030cd6acfc48e65551434cf5f3d76086a35b26bb33d01ae1 | Text | 9,323 | 193 | [](http://bioconda.github.io/recipes/sccaf/README.html)
# SCCAF: Single Cell Clustering Assessment Framework
Single Cell Clustering Assessment Framework (SCCAF) is a novel method for automated identification of p... |
c46f8d153fac84da369cc009d69a5147aa5eb703fddb45345f1bf7d4f6025c40 | Text | 9,360 | 102 | # Code for Multimodal Head Direction Cue Integration
This repository contains the code for network simulations and figure generation in
Melanie A. Basnak, Anna Kutschireiter, Tatsuo S. Okubo, Albert Chen, Pavel Gorelik, Jan Drugowitsch, and Rachel I. Wilson (2024). Multimodal cue integration and learning in a neural ... |
4d12a387e2c1d67fe3c2a0895a976bcb933c39ecb85381c58d61ee31621ff368 | Text | 9,370 | 94 | # Epidemic Model for COVIDAnalytics Research Effort
The repository contains code for a epidemiological model utilized in the research effort of our group called COVIDAnalytics, with projections on the website:
http://www.covidanalytics.io/
This repository contains multiple models, most of them being archived in the ... |
1acbcd71f36b55b73fe5d79645bc7c8b685a9d5b0d68da19cf01444a2278b4dc | Text | 9,375 | 211 | ## Verificarlo v2.6.0
A tool for debugging and assessing floating point precision and reproducibility.
![Build Status](https://github.com/verificarlo/verificarlo/a... |
7f0e7f3bf823c0739f2311aa05d34023a95c3782459012ade9715a2966dbf205 | Text | 9,489 | 231 | # DEPRECATION
We are deprecating this library. We plan to drop support on 2024-08-01 and will archive the repository on 2024-09-01. In particular, we are:
- Moving modality specific transformation ETL jobs into their own repositories. This will make dependency conflicts less likely.
- Each modality specific transform... |
76f45f235a7a858df7cdb081bf255de4a4440f1e8c079d42ab331cf04b9f1dc0 | Text | 9,541 | 166 | # ginjax
<a href="https://ginjax.readthedocs.io/en/latest/">
<img src="https://badgen.net/badge/Read/the doc/blue" alt="doc"/>
</a>
<a href="https://github.com/WilsonGregory/ginjax/blob/main/LICENSE">
<img src="https://badgen.net/badge/License/MIT/blue" alt="doc"/>
</a>
<a style="border-width:0" href="https://doi.org/... |
7c5789bc88b6ba947626d7b26e2dc9909de151a499bca2fa54a79cc700de701a | Text | 9,547 | 381 | # Motor Assisted Commutator to Harness Electronics in Tethered Experiments (MACHETE)
Designed by members of the [Pégard](https://www.nicolaspegard.com/) and [Rodríguez-Romaguera](https://www.rodriguezromagueralab.org/) Labs at the University of North Carolina at Chapel Hill, **MACHETE** is a motor assisted commutator ... |
91df6e4173425ef89451fb07f6e0129051efaba39a3cdc6be50f3888b0a1c958 | Text | 9,580 | 191 | # Herbify Dataset
This repository contains the dataset for herb classification and recognition, named **Herbify**. The dataset is derived from two datasets and is manually cleaned, with further improvements and processing. The dataset is designed to facilitate research in the field of herb (plant) classification and r... |
2f5f477955e00f88defe0c8f552efb4b7e1153972d9b05c3e4caf22ea99e7f1c | Text | 9,675 | 243 | # 3D ResNets for Action Recognition
## Update (2020/4/13)
We published a paper on arXiv.
[
Hirokatsu Kataoka, Tenga Wakamiya, Kensho Hara, and Yutaka Satoh,
"Would Mega-scale Datasets Further Enhance Spatiotemporal 3D CNNs",
arXiv preprint, arXiv:2004.04968, 2020.
](https://arxiv.org/abs/2004.04968)
We uploaded... |
b845f4a81ff4d47a5b8c5547854dab177daafd7fff8b40ccc1d61022236211cc | Text | 9,838 | 241 | ==============
neuroHarmonize
==============
Harmonization tools for multi-site neuroimaging analysis. Part of the work
reported in our paper with data from the ISTAGING consoritum [1]_.
contact: raymond (dot) pomponio (at) outlook (dot) com
Overview
---------
This package extends the functionality of the package d... |
e819f814802c01a4f44f66fe6637ff5bb07f2be1d48a632b6875ae50d463c3ef | Text | 9,847 | 287 | # SlidebookObj
SlidebookObj is a Matlab class for processing and analyzing Tiff files generated by the Frye lab 3i 2-photon system.
The class contains some basic tools for exploring data using ROIs (similar to the Slidebook software), making use of the accompanying DAQ file saved with each experiment to make it easy ... |
e71bd36a45474861bb677268f4b7e2562802cd96b6c7be107c6b4779634a434f | Text | 10,118 | 246 | # ARMBR: Artifact-reference multivariate backward regression
Version 2.0.12
Artifact-reference multivariate backward regression (ARMBR): a novel method for EEG blink artifact removal with minimal data requirements
ARMBR is a lightweight and easy-to-use method for blink artifact removal from EEG signals using multivar... |
0ce4ff49add5f188929d445a124c6cec45a9cecf412f5323bdb89cdc8740781d | Text | 10,229 | 157 | # ChildFER
This repository contains data and scripts as part of the following paper: Huang, S., Pollak S.,& Xie, W. (2025). The Contributions of Spontaneous Discrimination and Conceptual Knowledge to Children's Understanding of Emotion.
# Background
The folders provided here contain shared code, data, and materials... |
4edb2d3e37f06453ae149cd928624644aeb2a3501d33376e94473fc0575cb291 | Text | 10,229 | 126 | # A Benchmark for Physics-informed Machine Learning of Chlorine States in Water Distribution Networks
This repository contains the benchmark and the implementation of the experiments from the paper [A Benchmark for Physics-informed Machine Learning of Chlorine States in Water Distribution Networks](https://doi.org/10.... |
a8c3413c4714589afcb2ae8465955cbdb43ca176de4cb364f92bceb6d75846ff | Text | 10,267 | 255 | 
[](https://github.com/BlueBrain/morphology-workflows/releases)
[](https://g... |
75b9a4b87a52507ab948ff1c3685e33faf63e9e2ddcd2f6732c227e4dc03a714 | Text | 10,287 | 148 |
# Overview
DENTIST (Detecting Errors iN analyses of summary staTISTics) is a quality control (QC) tool for summary-level data from genome-wide association studies (GWASs). It leverages the difference between the observed GWAS test-statistic of a variant and its predicted value (using the neighbouring variants and link... |
851b888cc49e406ad31545afedc00d2c5673b4bcd071881ef413d37fdeab7fa2 | Text | 10,396 | 200 | STITCH
=========
STITCH assembles a graph manifold from time series single-cell RNA sequencing data. STITCH acknowledges that the gene expression signatures defining a complex biological process (e.g. embryonic development) can change dramatically over time. Rather than projecting data from several timepoints into a... |
0d9c5deb4333e6d0c5bb188a094e32836e5a3941781ea2adf2ce05423dfc9b48 | Text | 10,433 | 152 | <p align="center">
<picture>
<source srcset="img/pyspi_logo_darkmode.png" media="(prefers-color-scheme: dark)">
<img src="img/pyspi_logo.png" alt="pyspi logo" height="200"/>
</picture>
</p>
<h1 align="center"><em>pyspi</em>: Python Toolkit of Statistics for Pairwise Interactions</h1>
<p align="center">
... |
ae6e4d59e07bfeed465a8f9fef483eada68194ed82c0b396a847d2d2852e0c39 | Text | 10,521 | 192 | # Important Note
This is MemBrain v1 -- you might be actually looking for MemBrain v2, which adds more capabilities, including segmentation of membranes.
If this is the case, please check out [MemBrain-seg](https://github.com/teamtomo/membrain-seg) on the #TeamTomo Github.
# MemBrain
### Automated detection of membran... |
f0d1904484e069438d6350277eed1a3e15cb951de2cf3f5e0dbb9097e70e48d1 | Text | 10,524 | 298 | # Pytorch-YOLOv4
[](./License.txt)
A minimal PyTorch implementation of YOLOv4.
- Pa... |
be2cb8f9065682e1ef419c499460f5bec1f6910813a6c75454adfae2ae26448a | Text | 10,641 | 177 | # varKoder
A tool that uses **var**iation in **K**-mer frequecies as DNA barc**ode**s.
This python program can generate varKodes from raw reads, which are images encoding the relative frequecies of different k-mers in a genome. It can also train a convolutional neural network to recognize species based on these image... |
83b6f0ab4f3b1aa6c346ab0425c16a28f5b26ea4098a2cde2e91e0be22133f0e | Text | 10,645 | 199 | ### Overview
These scripts have been used to conduct the data-analysis in the publication:
Machine learning-based meta-analysis reveals gut microbiome alterations associated with Parkinson’s disease
Stefano Romano, Jakob Wirbel, Rebecca Ansorge, Christian Schudoma, Quinten Raymond Ducarmon, Arjan Narbad, Georg Zelle... |
f49f9529eee6e2606ec0a20070d0a170665f6fde4e367680c7b7a0553da30783 | Text | 10,652 | 275 | # MRI-labeling: label human brain MRI image by AAL/BA system
- ##### Under the R program environment,input an MNI coordinate, output the corresponding AAL(Automated Anatomical Labeling) and BA (Brodmann area) brain region name. More importantly, if the coordinate does not match a brain region defined by AAL/BA (e.g., w... |
a52128301975d9666b3d39897763e0bff64d489829850271aa766b965642dd01 | Text | 10,756 | 202 |
### Overview [](https://doi.org/10.5281/zenodo.14698367)
These scripts have been used to conduct the data-analysis in the publication:
Machine learning-based meta-analysis reveals gut microbiome alterations associated with Parkinson’s disease
Stefano... |
ae08cceee453467c516b4bc891b84c1883e5c097406934ab74afb673298f9a0f | Text | 10,761 | 155 | # PanCollection
## Pansharpening Datasets from WorldView 2, WorldView 3, QuickBird, Gaofen 2 sensors
* [[Chinese Webpage](https://liangjiandeng.github.io/PanCollection.html)]
* ``Recommendation:`` Use the code-toolbox [[DLPan-Toolbox](https://github.com/liangjiandeng/DLPan-Toolbox)] + the dataset [[PanCollectio... |
6abbeb12c8cd91608b09b1089d2e66b7a5921042943e7a649b0d76e4bce06b4e | Text | 10,815 | 269 | # IMPORTANT NOTICE
The WALT mapper is *deprecated and no longer maintained*. We created a novel WGBS
mapper that adds various improvements to WALT called [abismal](https://github.com/smithlabcode/abismal).
Please use this program instead
## WALT v1.0 ##
***WALT*** (Wildcard ALignment Tool) is a read mapping program ... |
0f825f6908b8b361fd5c3c8937e4f2c2a7c7e780735c87e3011d85a67ffac5cf | Text | 10,883 | 246 | <p align="center" style="margin-bottom: 1em;">
<img alt="Aeneas logo for the project" src="images/logo.svg" width="33%">
</p>
# Contextualising ancient texts with generative neural networks
Yannis Assael<sup>1,\*</sup>, Thea Sommerschield<sup>2,\*</sup>, Alison Cooley<sup>3</sup>, Brendan Shillingford<sup>1</sup>, ... |
0dac4c51eb9bc6ee9effb939122a6d8bbcf504f2f2e60a844b7ed97c5deacc77 | Text | 10,919 | 256 | # Geometric Convolutions
This package implements the GeometricImageNet which allows for writing general functions from geometric images to geometric images. Also, with an easy restriction to group invariant CNN filters, we can write CNNs that are equivariant to those groups for geometric images.
See the paper for mor... |
64f377c348f2b7637d8d8aeff5ef2c04fd254cac001abb41415f0279751a82da | Text | 10,942 | 264 | 
[](https://github.com/BlueBrain/morphology-workflows/releases)
[](https://g... |
dff00146eff0b3a4dc369ab6f3dd61dc14e87d520e842e5cae3696768c24cb8f | Text | 11,005 | 207 | # Lifespan Brain Charts from the Chinese Population
E-mail: lianglongsun@mail.bnu.edu.cn
This repository provides code and data that support the findings of the article entitled "**Population-specific brain charts reveal differences between Chinese and predominantly white participants from Europe, North America and ... |
c64caef74e0cb1bc488fb31fb6cda71cd5bac37e9fde498d7daa7f590ac3eb4e | Text | 11,047 | 205 | # AI4Green Installation Guide
___
AI4Green is an Electronic Laboratory Notebook which combines data storage and sharing while promoting green and sustainable chemistry.
**We highly recommend using Chromium-based browsers such as Google Chrome for accessing AI4Green.**
See the [video tutorials](https://youtube.com/pl... |
5566b688b47b59876bac584e2db596421daae5cf56592372303826cac2c606a5 | Text | 11,190 | 139 | SeqPrep is a program to merge paired end Illumina reads that are overlapping into a single longer read. It may also just be used for its adapter trimming feature without doing any paired end overlap. When an adapter sequence is present, that means that the two reads must overlap (in most cases) so they are forcefully m... |
0c6faa8fcc501f29ac164948f32a7a2d9204c1955d2474f429967ae702c8069b | Text | 11,273 | 215 | <div align="center">
<img src="resources/mmrotate-logo.png" width="450"/>
<div> </div>
<div align="center">
<b><font size="5">OpenMMLab website</font></b>
<sup>
<a href="https://openmmlab.com">
<i><font size="4">HOT</font></i>
</a>
</sup>
<b><f... |
c1e69c81d86c6f8277b2fe696865a29773c851af5dac637dd7008836f2e78095 | Text | 11,303 | 313 | # VPR Datasets Downloader
This repo is made to automatically download Visual Place Recognition (VPR) datasets in a simple and standardized way.
This is useful because all VPR datasets use different ways of storing the labels (some in csv files, some in matlab files, some in the filename), making it very inconvenient t... |
6654a53f6e5013f91da4f2111967473c48a5eed1bba6b86ebd3a4d6814ef1abe | Text | 11,355 | 116 | # fMRIPrepCleanup
IMPROPER USE OF THIS SCRIPT COULD RESULT IN THE UNINTENDED DELETION OF IMPORTANT FILES. PLEASE READ THIS DOCUMENT IN FULL BEFORE EXECUTING.
As well as reading this file, consider watching the following video, which provides an overview of how the tool works, and some examples of usage.
[
- [Re... |
e3e7cfaa22e1069b83ba9b177f14a7d3e82fef0c6cb9164fcde156ba33c0af17 | Text | 11,488 | 318 | # STABLE: Spatial and Quantitative Information Preserving Biomedical Image-to-Image Translation
This repository contains the open-source code for the paper:
**"Preserving Spatial and Quantitative Information in Unpaired Biomedical Image-to-Image Translation"**
Published in Cell Reports Methods. https://doi.org/10.10... |
f6f1ae2a0e7575924a6ef31ddde0d1c50b6f7c89c2e403c3d519873ca6a9d86c | Text | 11,528 | 215 | # Reverse engineering splicing-regulatory networks using diverse cellular transcriptomes
## Summary
This pipeline is composed of two workflows that can be run independently depending on your starting materials:
- The “Mapping and quantification” workflow takes single- or paired-end fastq files as input and applies the... |
88bf62ee7c9c7eb8d776b889923cf13dab132b4300d3a494df19ab28ed369d12 | Text | 11,604 | 140 | # ETL workflow for quantitative analysis of inscriptions from the EDCS dataset
* ETL
[](https://creativecommons.org/licenses/by-nc-sa/4.0/)
 CellNEST
Preprint: [NEST: Spatially-mapped cell-cell communication patterns using a deep learning-based attention mechanism](https://www.biorxiv.org/content/10.1101/2024.03.19.585796v1)
### Singularity Image:
For users' conven... |
05b0ac93095a3c99b9639b9bdb278f8b7fb3150871d4abe7d95a5194a820a623 | Text | 11,615 | 162 | <div align="center">
# Tucano: Advancing Neural Text Generation for Portuguese
<a href="https://doi.org/10.1016/j.patter.2025.101325" target="_blank">
<img src="https://img.shields.io/badge/Patterns-10.1016/j.patter.2025.101325-blue" alt="Patterns">
</a><br>
<a href="https://arxiv.org/abs/2411.07854" target="_b... |
c8362dae407680c2214e1abb623b83be2f06c382c6b829499ff965773f9b8b2d | Text | 11,657 | 144 | <h1 align="center"> PAK-KTM</h1>
<p align="justify">
PAK-KTM (Program for Structural Analysis - <strong>Kojic Transport Model</strong>) is a high-performance software for finite element analysis (FEA) of gradient-driven smeared physical fields, developed at the University of Kragujevac and the Research and Developmen... |
00ac8aa3f62053db42a95923d8783ffcd33a78d083e47f09091ffe516e37c9fc | Text | 11,683 | 236 |
# Automatic High Frequency Oscillation Detection (AHFOD)
**This code is still in development and as such welcomes suggestions.**
---
This code is intended to be used for the detection of High Frequency Oscillations (HFO) in the following data:
* Electroencephalogram EEG (Untested)
* Electrocorticography ECoG (T... |
ca0333e441fd39413e771727547af75aaa3a1ba51d84fed7b6ef45895d668c73 | Text | 11,791 | 222 | # Scaff10X v5.0
Pipeline for scaffolding and breaking a genome assembly using 10x genomics linked-reads.
Pipeline steps:
Scaffolding with scaff10x:
1 Barcoded tags are extracted from 10Xg raw sequencing reads and appended
to read names for further processing
2 The reads are mapped t... |
2820bbdd6bb5397213688811350e35e152deb3350356ee62ffc18f0512d4a744 | Text | 11,846 | 186 | 
[Paper](https://doi.org/10.1038/s41565-025-01955-8) | [Data availability](https://doi.org/10.18742/c.7711667) | [Additional source code](https://github.com/ChiappiniLab/Nanoneedle-Lipidomics)
# Nanoneedles Enable Spatiotemporal Lipidomics of Living Tissues
Chenlei Gu<sup>1,2*</sup>, Da... |
90a19afb91f87b7376a6cb2c28e2d4d5d7035a0e18b9652102025e834386ca95 | Text | 12,254 | 132 | # FlySeg
## 1. Setting up the conda environment
FlySeg is a Python-based package. The installation can be done by installing all the required dependencies manually or by using the provided file environment file issuing the command: `conda env create -f environment.yml`. Once the environment has been created, it shoul... |
8d1ef036933225e9c344ce53da38f61e6cbca42c6a94252ee0b43c4bbd5d5e3a | Text | 12,296 | 167 | # nanoDx pipeline
nanoDx is an open-source, end-to-end bioinformatics pipeline for DNA methylation-based classification of tumours using nanopore low-pass whole genome sequencing data.
# News and updates
## Major release (v1.0rc3)
**IMPORTANT NOTE:** Starting with version 1.0, nanoDx uses **crossNN**, a pre-train... |
1ecb5d2acc5996a02541b72226ad6bda43f5bf5b98d908b6648613af69991ceb | Text | 12,336 | 198 | # Synapse_Boundary_Simulation
Calculating synaptic weights during sleep-wake cycle under synaptic learning rules
## Outline
These codes search synaptic learning rules and calculate synaptic efficacy during sleep-like or wake-like firing patterns under synaptic learning rules.
## Getting Started
### Requirements
Py... |
a2a9f21cf5bce8e3942d9b32abad47087ecfc68ebbe3140df7654b5451d447d8 | Text | 12,362 | 254 | [](https://anaconda.org/warpem/warp)
[](https://doi.org/10.5281/zenodo.13982246)
# Warp?
Warp is a set of tools for cryo-EM and cryo-ET data processing including, among other tools:... |
fef4b5d881cedc6f87ee9cb0f9c9e592078b4b5512bf6e78edf022ac8ac26565 | Text | 12,402 | 225 | # RNA-seq
**Institut Curie - Nextflow rna-seq analysis pipeline**
[](https://www.nextflow.io/)
[](https://multiqc.info/)
[ | English
[](https://pypi.org/project/spikingjelly)
[](https://pypi.org/project/spikingjelly)
[
[](https://coveralls.io/github/tommasocarraro/LTNtorch?branch=main)
[](h... |
42424d19d7875a522fe8021661e1fd76db8a564d70c0227c62f67e01ddf65b4d | Text | 12,512 | 172 | # DRIADA
**D**imensionality **R**eduction for **I**ntegrated **A**ctivity **D**ata **A**nalysis — a Python framework for cross-scale analysis of neural population activity.
[](https://www.python.org/downloads/)
[ or assembled sequences (FASTA format), which are images encoding the relative frequencies of different k-mers in a genome. It can also train a convo... |
63d829c45b9f76de2de521579ae821ed415131e5a3b02ad1681b71206709defa | Text | 13,348 | 267 | # Rate of brain aging associates with future executive function in Asian children and older adults
## Summary (eLife assessment)
This valuable study marks a significant advancement in brain aging research by centering on Asian populations (Chinese, Malay, and Indian Singaporeans), a group frequently underrepresented i... |
e23473672e376829e22ff16801a69ba2c27b3d8c4ed2cfcbed6a3a33c62880cf | Text | 13,578 | 266 | [](https://zenodo.org/doi/10.5281/zenodo.10568795)
# deconvo_lute-paper
Supplementary materials to prepare data and run analyses for the paper "lute: estimating the cell composition of heterogeneous tissue with varying cell sizes using gene expression" (1). The `lute` R/B... |
59c8449ec42672def6ba04fdfbebe52cda2b0037736b0e576f83b27c0cd980f1 | Text | 13,621 | 235 | # Chainer Chemistry: A Library for Deep Learning in Biology and Chemistry
[](https://pypi.python.org/pypi/chainer-chemistry)
[](https://github.com/pfnet-research/chai... |
d8ab0db63c7b34c47c01047e6b36e017743e3aa8d8b0590bdd45b3b498d48e3f | Text | 13,735 | 330 | <p align="center">
<img style="width: 35%; height: 35%" src="https://raw.githubusercontent.com/resurfemg-org/ReSurfEMG/8ef19f7013553bd3dbdabf994781f0d612114336/Logo_rond_tekst.svg">
</p>
[](https://doi.org/10.5281/zenodo.6811553)
[
## About the Project
SimOpt is a testbed of simulation-optimization problems and solvers. Its purpose is to encourage the development and constructive comparison of simulation-optimization (SO)... |
90720da2c1085ca451ecfe79b561825f94eae2685ca001b448084278198f5f08 | Text | 14,310 | 374 | # Robust MRI reconstruction via self-supervised denoising | MRM 2025
Official implementation for "[Robust multi-coil MRI reconstruction via self-supervised denoising](https://onlinelibrary.wiley.com/doi/full/10.1002/mrm.30591)" (Magnetic Resonance in Medicine, 2025).
This repository contains the FastMRI implementatio... |
09a9d9d55a80643c29fe1a1b7e899545f56fb7efdd496d8d4631bb32dc271994 | Text | 14,338 | 288 | # In silico labeling: Predicting fluorescent labels in unlabeled images
This is the code for
<a href="http://www.cell.com/cell/fulltext/S0092-8674(18)30364-7">In silico labeling: Predicting fluorescent labels in
unlabeled images</a>. It is the result of a collaboration between [Google Accelerated
Science](https://rese... |
ce0b726fedd1198ebd841093b53ff5490672ffb2264479d8be044b5826a791c6 | Text | 14,379 | 190 | # LoRA: Low-Rank Adaptation of Large Language Models
This repo contains the source code of the Python package `loralib` and several examples of how to integrate it with PyTorch models, such as those in Hugging Face.
We only support PyTorch for now.
See our paper for a detailed description of LoRA.
**LoRA: Low-Rank Ad... |
55cbf126554e909113255f4171154dcc2183b57c9164e065b130a565a2cff5e3 | Text | 14,500 | 211 | # MedMNIST: [medmnist.com](https://medmnist.github.io/)
## Data ([Zenodo](https://doi.org/10.5281/zenodo.10519652)) | Publication ([Nature Scientific Data'23](https://doi.org/10.1038/s41597-022-01721-8) / [ISBI'21](https://doi.org/10.1109/ISBI48211.2021.9434062)) | Preprint ([arXiv](https://arxiv.org/abs/2110.14795)) ... |
9767d8f58f5967f675ceb5ea14ac75a9f5a1af20d12c4f3dbe6f57d6570e82fb | Text | 14,875 | 175 | README
Mengjun Sheng, Di Lu, Jun Ding (2025)
Activity-Dependent Remodeling of Corticostriatal Axonal Boutons During Motor Learning
Overview
This document summarizes the datasets associated with the study byMengjun Sheng, Di Lu, Jun Ding (2025) . Each figure panel (including extended data figures) has correspondin... |
561c658c6997542bea8395cb5ec96ad1931fb27de8d11388c09df510acbb6493 | Text | 15,064 | 339 | # CellPhoneDB
| :warning: We have updated CellPhoneDB to v3 and migted CellPhoneDB to a new repository. <br> Please refer to [ventolab/CellphoneDB](https://github.com/ventolab/CellphoneDB) for the most up to date version. |
| -------- |
## What is CellPhoneDB?
CellPhoneDB is a publicly available repository of curate... |
6b0efd77b09ed084e8dbaf76788126783bd0e3b4fcef894c9b877fd79a18b8f8 | Text | 15,123 | 307 | # miniMDS
miniMDS is a tool for inferring and plotting 3D structures from normalized Hi-C data, using a novel approximation to multidimensional scaling (MDS). It produces a single 3D structure from a Hi-C BED file, representing an ensemble average of chromosome conformations within the population of cells. Using paral... |
909d2f5ec4c2a7a7323422d2c1e0476b51d73ecd0ece25caa15ca95adad39793 | Text | 15,311 | 227 | domb-napari
===========
[](https://stand-with-ukraine.pp.ua)
[](https://napari-hub.org/plugins/domb-napari... |
fe3f28c872d379fdca0aefce0cf2a28d1a9f62cf1823ed2fc9cc99bb349897de | Text | 15,383 | 206 | # Hiera: A Hierarchical Vision Transformer without the Bells-and-Whistles
[](#torch-hub)
[](#hugging-face-hub)
[ within the [Skeide Lab](https://www.skeidelab.com/) at the [Max Planck Institute for Human Co... |
6a4d077bf3bd6f3c7c09251a0273a185149b6a0a30caad60297b4c4d1044cff2 | Text | 16,125 | 331 | AntiFold
==============================
AntiFold predicts sequences which fit into antibody variable domain structures. The tool outputs residue log-likelihoods in [CSV format](https://github.com/oxpig/AntiFold/blob/master/output/single_pdb/6y1l_imgt.csv), and can sample sequences to a [FASTA format](https://github.co... |
42f153fb53af7472a68c5839554c3559fe63b78f5011b1dc4e30eb11c13744d9 | Text | 16,155 | 155 | # 3D Cell and Pixel Quantification Pipeline for the Whole Mouse Brain
- Created by the [Yongsoo Kim Lab](https://kimlab.io/)
- README written and updated on 20250415 by J. Liwang and S. Manjila
## Overview
This code package is designed for comprehensive 3D cell counting and pixel counting using whole mouse brain imag... |
c4b5dd76ca005fd545cbf5c42b7ceb66ee2705a33bfac46b264508c21be8e769 | Text | 16,292 | 314 | # eyetrack-bird
Dual-camera video oculography plus rigid-body head tracking for freely moving birds.
Two calibrated cameras and two IR lights give the 3D pupil center and the center of
corneal curvature on every frame (Barsingerhorn, Boonstra & Goossens 2018, *Behav Res
Meth*). A Qualisys (QTM) rigid body on the head... |
93dbe31113d3701d918377271aba67b677a005f8fe81abac37eb5e50949e535c | Text | 18,149 | 490 | [](https://opensource.org/licenses/mit)
[](https://github.com/CeadeS/pytorch_bio_transformations... |
b256a379669ee8e72cee79aa2925566faab7368af02110f36e2ba56cf5bb9376 | Text | 18,653 | 353 | # Fuzzy v2.6.0
[](https://zenodo.org/badge/latestdoi/218554957)
[](https://github.com/verificarlo/fuzzy/actions/workflows/bui... |
ba8ca22790d5265355298d4ca2adc7b5a01290d5bd07e45fac332b7dc57f31f5 | Text | 18,673 | 377 | <left><img src="img/scaLR_logo.png" width="150" height="180"></left>
# Single-cell analysis using Low Resource (scaLR)
[](https://github.com/infocusp/scaLR?tab=GPL-3.0-1-ov-file#)
[](https... |
e0cdf1669bc6d2d8b6c5d9fe562111816113325f284dc74147a0f8cc2233e310 | Text | 18,687 | 424 | # Integrating physics and topology in neural networks for learning rigid body dynamics
This repository contains the code used to develop `HOPNet`, part of the publication
titled "Integrating physics and topology in neural networks for learning rigid body dynamics".
This work was published in Nature Communications 16... |
754fd84313ee62cbc95d39e453d3664e74ffa85fcdc8a37f2881a792b1c7ab56 | Text | 18,742 | 200 | # P-sort: an open-source software for cerebellar neurophysiology
P-sort has been developed in [Shadmehr Lab](http://www.shadmehrlab.org), [Department of Biomedical Engineering](https://www.bme.jhu.edu), [Johns Hopkins University](https://www.jhu.edu) and in collaboration with colleagues from University of Washington an... |
694c0264e4f19ba4b389b3a7c92a42438b9bbd5ea83560ac17348160a8aa24c3 | Text | 18,966 | 474 | <p align="center">
<img style="width: 35%; height: 35%" src="https://github.com/resurfemg/resurfemg/blob/main/Logo_rond_tekst.svg">
</p>
[](https://doi.org/10.5281/zenodo.6811554)
[](https://pypi.pyth... |
ed6df9b2dc5eee086fa8e6fe19aaa0a8531cb0853136231d0dc34f9bed043c8d | Text | 19,298 | 496 | <div align="center">
# ncpi: neural circuit parameter inference
___
<img src="https://raw.githubusercontent.com/necolab-ugr/ncpi/main/img/ncpi_logo.svg" alt="ncpi logo" width="150">
</div>
[Documentation](https://necolab-ugr.github.io/ncpi/)
`ncpi` is a Python package for model-based inference of neural circuit pa... |
09e18de9448ddee470be56ed9003383d6a530e8a36f39830e247a564d3f840b7 | Text | 19,581 | 397 |
.. image:: https://badge.fury.io/py/sequana-rnaseq.svg
:target: https://pypi.python.org/pypi/sequana_rnaseq
.. image:: http://joss.theoj.org/papers/10.21105/joss.00352/status.svg
:target: http://joss.theoj.org/papers/10.21105/joss.00352
:alt: JOSS (journal of open source software) DOI
.. image:: https:... |
a3ef57431b65fc7c6c5879a0e7e3ed372e21904d3ae73b26b17195f865dfc99a | Text | 19,842 | 514 | # singleCellNet
## Table of content
1. [Introduction](#introduction)
2. [Data](#data)
3. [Train SCN claissfier](#train)
4. [Assess SCN claissfier with heldout data](#assess)
5. [Query](#query)
6. [Visualization](#visualization)
7. [Train cross-species SCN classifier](#cs_train)
8. [Query for cross-species data](#cs_qu... |
01ffa11080ca0922830c9f40329686ab329d53e2adcfa36459d246b926b25101 | Text | 20,416 | 300 | # FLAMINGO: **F**ast **L**ow-r**A**nk **M**atrix completion algorithm for reconstruct**IN**g high-resolution 3D **G**enome **O**rganizations
## !UPDATE (04/22/2024): FLAMINGOrLite
Lite version of FLAMINGO, high-resolution 3D chromosome structures reconstruction based on Hi-C.
https://github.com/JiaxinYangJX/FLAMINGOr... |
3b369279eb47fd36bebc6d111da82bbaaba3a5a11452d050cf10c2dea0ae1bf8 | Text | 20,755 | 354 |
We have released a new version 1.0.0 (on March 15, 2022). It has substantial computation efficiency improvements for both Step 1 and Step 2 for single-variant and set-based tests. We have created a new program github page https://github.com/saigegit/SAIGE with the documentation provided https://saigegit.github.io/SAIG... |
86f69ac29a29464d3aedaa480d8bfd7d88d8869fc8bd48a4862a01a1ffdcceb2 | Text | 20,867 | 364 |
# Net2Brain 🧠
<p align="center">
<img src="docs/source/Net2Brain_Logo.png" alt="Net2Brain Logo" width="48%"/>
<img src="docs/img/ARENA_text.jpg" alt="ARENA" width="48%"/>
</p>
Welcome to [__Net2Brain__](https://www.frontiersin.org/journals/neuroinformatics/articles/10.3389/fninf.2025.1515873/full), a powerful... |
b2381a5fc75561e9c979ab977559a1d5c9ee9b0cc8304f51c9f38d82fb9fa856 | Text | 21,190 | 283 | # krakencoder
[](https://zenodo.org/doi/10.5281/zenodo.11106894)
<img align="right" src="images/krakencoder_squid.png" alt="krakencoder cartoon" width=20%>
The Krakencoder is a joint connectome mapping tool that simultaneously, bidirectionally translates between structura... |
d6c9fe661be6c589c3f9bb1181b41ef837fe16945356479ed0e0c077d59f2388 | Text | 21,811 | 324 | # Transfer Learning for Drug-Target Interaction Prediction
## Abstract
Utilizing AI-driven approaches for drug–target interaction (DTI) prediction require large volumes of training data which are not available for the majority of target proteins. In this study, we investigate the use of deep transfer learning for the... |
d2366976cea96ad1e8f0b3e9579987ace7e6bbb745106aa87a3e8a56c599ea3a | Text | 23,529 | 497 | domb-napari
===========
[](https://stand-with-ukraine.pp.ua)
[](https://napari-hub.org/plugins/domb-napari... |
50eb6a71957b204ed3cc857cdae1143b295b5f039b155c6eac9579ef489836ed | Text | 25,018 | 245 | # ArtSeg and VasMorph
## *Applying Machine Learning to Assist in the Morphometric Assessment of Brain Arteriosclerosis Through Automation*
Jerry J. Lou*, Peter Chang, Kiana D. Nava, Chanon Chantaduly, Hsin-Pei Wang, William H. Yong, Viharkumar Patel, Ajinkya J. Chaudhari, La Rissa Vasquez, Edwin Monuki, Elizabeth Hea... |
481799f531f1ea2306837b38c3253ed6ee70b8ff8f4996b84d06996939024cfc | Text | 25,214 | 227 | # What is Image-Based Meta- & Mega-Analysis (IBMMA)?
**IBMMA** is a powerful and versatile free software package designed for meta- and mega-analysis on neuroimaging datasets aggregated from multiple study sites, such as ENIGMA (Enhancing NeuroImaging Genetics through Meta Analysis) Consortium and NCANDA (National Con... |
a3b450a75ea3c21791acdc474f305710b27a38f858d409f0dba801b19885e63e | Text | 26,211 | 455 | <div align="center">
<img src="resources/mmdet-logo.png" width="600"/>
<div> </div>
<div align="center">
<b><font size="5">OpenMMLab website</font></b>
<sup>
<a href="https://openmmlab.com">
<i><font size="4">HOT</font></i>
</a>
</sup>
<b><font... |
255a19ff6c361b5895ecc51a2c0b96f8b8702b55caf81f02d6805bb7e9ba2365 | Text | 29,714 | 465 | <h1 align="center">
mllm
</h1>
<div align="center">
**Fast and lightweight multimodal LLM inference engine for mobile and edge devices**
[](https://opensource.org/licenses/MIT)
[](https... |
1a4ee70d498e58dc182dc05f38908d13fb69e907a039b591fb20cde6ab10d0fe | Text | 31,352 | 613 | # Mass Spectrum Predictors
**Update 7/7/2026:**
- Introducing ICEBERG 2.1! It has a substantial GPU speedup, and we provide pretrained NIST'23 model. Checkout to the [ICEBERG 2.0 branch](https://github.com/coleygroup/ms-pred/tree/iceberg_2.0) if you want to run the earlier 2.0 model.
- Introducing GLACIER! GLACIER i... |
ac865afae67cc54f0823b42b87f2a4f8b52d7984b2e2199955562c04d5775969 | Text | 33,160 | 580 | Repository of the paper entitled: "Fidelity Agnostic Synthetic Data Generation Improves Utility Whilst Retaining Privacy".
Experiments from the paper can be reproduced through the main.py script in the FASD_experiments folder.
Names of the datasets can be found in the datasets.json file.
When reproducing experiments... |
bdb64be215fdfba4aa40fa68c27bbf8b05a045474d85e5b7de31e1fd030fec3e | Text | 33,354 | 474 | <style>body {text-align: justify}</style>
## Replication Package for "DeepCrime: Mutation Testing of Deep Learning Systems based on Real Faults" paper
<!--
1. [Getting Started](#Getting-Started)
2. [Detailed Description](#Detailed-Description)
2.1. [On the feasibility of full replication](#On-the-feasibility-of... |
f9130a9938bd60a7cc10a75627c0a459cd26c0587b7f96339a3e1e5eee0a3bc0 | Text | 33,676 | 593 | Repository of the paper entitled: "Fidelity Agnostic Synthetic Data Generation Improves Utility Whilst Retaining Privacy", published in Cell Patterns.
Experiments from the paper can be reproduced through the main.py script in the FASD_experiments folder.
Names of the datasets can be found in the datasets.json file. ... |
c37d87b73395b6d341b52b3abfb92dd1990a937ffb13563c78302b2fe6441cf7 | Text | 37,314 | 470 | # PhysiCell Studio: User Guide
<!-- [[full images](README.md)]
[[small images](README-small-images.md)] -->
[[Dependencies](#dependencies)] [[Installing and Running](#installing-and-running)] [[Support](#support)] [[Overview](#studio-overview)]
[[Config Basics](#config-basics)] [[Microenvironment](#microenvironment)... |
7ef79dade63d546b7f9c32864440519fe152aa4201155ab0f746050be8e481fb | Text | 37,651 | 484 |
# An end-to-end attention-based approach for learning on graphs
This source code archive accompanies the [An end-to-end attention-based approach for learning on graphs](https://www.nature.com/articles/s41467-025-60252-z) paper, out now in Nature Communications. It includes the code required to run experiments inv... |
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