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19f410c00b67213ac6efb8ca4ee7b8b5cfab030c0b59820181e385f8efa9fa2a | Text | 5,756 | 154 | # Synaptic Diversity: Bridging Biological and Artificial Neural Networks
## Introduction
Welcome to the reproduction repository for "Synaptic Diversity: Concept Transfer from Biological to Artificial Neural Networks" by Martin Hofmann, Moritz Franz Peter Becker, Christian Tetzlaff, and Patrick Mäder. This groundbreak... |
3d1a72128f43241b0e891ac57ee12026a41224c5da68e3e572f824621d771560 | Text | 5,769 | 164 | [](https://doi.org/10.5281/zenodo.13992707)
# PyMRItools
Toolbox for MRI sequence programming, reconstruction, simulation, processing, and analysis using Python.
## Installation
Clone the repository.
```shell
git clone https://github.com/schmidt-jo/PyMRItools.git
cd PyM... |
d712a5dbd5ae99504300e165f70cd9a2aeeb5fb981f495af1af5f7281d71a372 | Text | 5,799 | 116 | # Shifting dengue vector composition under warming in South and Southeast Asia
Analysis code and derived data for:
> Doeurk B, Ghosh A, Amiji MM, Ganguly AR, Sundaram R. *Shifting dengue
> vector composition under warming in South and Southeast Asia: a change
> routine surveillance cannot detect.* Submitted to ... |
29b0bdfabc0ae4cb52b380023531505288ef435f33d7998995b81903a695e607 | Text | 5,807 | 113 | # Escott-Price Lab Pipelines
[](https://github.com/seafloor/escott-price-lab-pipelines/actions/workflows/R-CMD-check.yaml)
[
## atlases
[atlases](atlases/) folder contains Glasser, DK, and various other maps/parcellations and co... |
7273aa952fca695d1eddc00c11b864e4f420182899df0a5373c593e3b4f454c5 | Text | 5,842 | 126 | GenomeComb
==========
A program for the analysis of genome and transcriptome sequencing data
Copyright VIB and University of Antwerp
Purpose
-------
Genomecomb is an integrated package designed to analyze, combine, annotate
and query genome as well as transcriptome sequencing data.
For the first step it provides pip... |
6783f8c3c8d1e1d838f7617896f852bd1d593663ddfbe6bfa0408890ea5bf8ed | Text | 5,848 | 85 | # Data-Augmentation
Code for manuscript titled:
Innovative Data Augmentation Strategy for Deep Learning on Biological Datasets with Limited Gene Representations Focused on Chloroplast Genomes
DOI:
https://doi.org/10.1038/s41598-025-12796-9
# Overview
In the current study, a novel and highly effective data augmentati... |
da16e4a8b56a643a6892b23eeecd2fe424f33d85e4c10f23b1e3252b12ebe46f | Text | 5,880 | 99 | # FANC_auto_recon
FANC (pronounced "fancy") is the Female Adult Nerve Cord, a GridTape-TEM dataset of an adult _Drosophila melanogaster_'s ventral nerve cord. The dataset was first published in [Phelps, Hildebrand, Graham et al. 2021 _Cell_](https://www.lee.hms.harvard.edu/phelps-hildebrand-graham-et-al-2021), after w... |
e79379f4fedfa2f8dcb228b19cdddc4d184e0f4a7c4f4e526dbb6e1f1f71ef77 | Text | 5,884 | 158 | ***User Support:***
For user questions please look for answers and ask first in the [GATK forum](https://gatk.broadinstitute.org/hc/en-us/community/topics).
----
[](https://github.com/broadinstitute/picard... |
835ae53aac2d5dc56deb84e6b6bb81bde0a3839a7a7cfa9ac7c7af28adc2accf | Text | 5,913 | 161 | # Always-on Mobile Multimodal Embedding
## Table of Contents
- [Environment Installation](#environment-installation)
- [ImageBind](#imagebind)
- [ImageBind Trainer with LoRA fine-tuning](#imagebind-trainer-with-lora-fine-tuning)
- [Code structure](#code-structure)
- [Usage](#usage)
- [Search](#search... |
bcee82e4f3a22851b23077de68146716281523ae2f1b551f3571d47690fc1727 | Text | 5,930 | 65 | ## Longitudinal-Trajectories-Early-Brain-Development-Language
This repository houses code (or links to code) used for the following study:
Turesky et al. Longitudinal trajectories of brain development from infancy to school age and their relationship to literacy development
Broadly, the study involved structural... |
f6cdeccd028893d2e8dfe8656add05cddddfe60ddefe0b1441f5e6b9c39cf795 | Text | 5,954 | 101 | =======
bonndit
=======
.. image:: https://badge.fury.io/py/bonndit.svg
:target: https://badge.fury.io/py/bonndit
.. image:: https://readthedocs.org/projects/bonndit/badge/?version=latest
:target: https://bonndit.readthedocs.io/en/latest/?badge=latest
:alt: Documentation Status
The bonndit packa... |
ebc518728e098a4c91c4bb3c4c1c7e36773aa86274d10fed0e7d0defbe93c987 | Text | 5,990 | 160 | # Analysis Code for Yaron et al. (2025) PLOS Biology
**"Auditory cortex neurons that encode negative prediction errors respond to omissions of sounds in a predictable sequence"**
[](https://www.mathworks.com/products/matlab.html)
[![License: MIT](h... |
4fcda2de0c982d5f424138ea5b81e8ced59f548c856297aa195c9f374c4901ae | Text | 6,014 | 35 | # IJOQ
This repository contains the Python scripts used in the paper, "Dynamic Python-based method provides robust analysis of intercellular junction organization during *S. pneumoniae* infection of the respiratory epithelium." In version 1.0.1, the calibration script ("IJOQ Calibration.py") was merged with the IJOQ sc... |
cfc853b791ee91ab9e963a04e3f73ae49491b2e9b1549ce3e8b38c35f1a7063f | Text | 6,026 | 160 | # Analysis Code for Yaron et al. (2025) PLOS Biology
**"Auditory cortex neurons that encode negative prediction errors respond to omissions of sounds in a predictable sequence"**
[](https://www.mathworks.com/products/matlab.html)
[
DeepAAI is an advanced deep learning-based tool for identifying antigen-antibody interactions, which was collected in Nature Machine Intelligence:
**Cite this article**
Zhang, J., Du, Y., Zhou, P. et al. Predicting unseen antibod... |
ec8f065765946c49278a1a5f9c15129e0841985cdaa2c1bf508bbd218e8d52ee | Text | 6,048 | 97 | # genexpsim – Gene expression simulation for circadian clock and coupled cells
[-e30613?logo=doi)](https://doi.org/10.1038/s42003-025-08128-2)
[-... |
4256fa9541f24dee80457a8a5e7c85dd0a6b42aaeeee9c53dd07d83f54df8159 | Text | 6,135 | 162 | [](https://github.com/acquire-project/acquire-python/actions/workflows/build.yml)
[](https://github.com/acquire-project/acqui... |
dae6fd9acceee0f4edcae602f7cd7f71096d43994a6ebc4843b5b14509625f74 | Text | 6,172 | 141 | # sickle - A windowed adaptive trimming tool for FASTQ files using quality
## About
Most modern sequencing technologies produce reads that have
deteriorating quality towards the 3'-end and some towards the 5'-end
as well. Incorrectly called bases in both regions negatively impact
assembles, mapping, and downstream bi... |
8e3fc39525d62669b79504e750b43ac9e5d11eaa6a5afcbd890c35e6e390c486 | Text | 6,174 | 163 | # GWASLab
<img width="600" alt="image" src="https://github.com/user-attachments/assets/109262c6-c870-4078-94b5-66cf8c6b13c4" />
[](https://pepy.tech/project/gwaslab)
![badge_pip](https://img.shields.io/pypi/dm/gw... |
e438a6d21884ea6896f06ecbd6ec0d3bae3739cbc9ee125105eca7ff1c427e66 | Text | 6,185 | 105 | # Rapid_IIIC_Labeling_GUI_MultipleEEGs
GUI for rapid labeling of segments from multiple EEGs, and instructions for preparing data for these labeling tasks
This repository describes a GUI developed by Dr. Jin Jing ("JJ"), PhD that enables rapid labeling of IIIC patterns. By following these instructions you can set up t... |
37ad50630ed8df85267f062336b9f87cb51b0a301e6325adbb009cabca53536a | Text | 6,237 | 51 | # 2Photon_Analysis
# Introduction #
This code is analgous to the 1P extraction code, published alongside [this](https://www.science.org/doi/full/10.1126/science.abg7277) paper and on [GithHub](https://github.com/fmi-basel/1Photon_Analysis). It is also a wrapper that is build around [CNMF](https://www.sciencedirect.com... |
ef15059a005ec6e34b626ee9c31b157f2a0ac2526e0876009c1baeaadd2f3b48 | Text | 6,286 | 76 | # BADASS - Designing diverse and high-performance proteins with a large language model in the loop
[](https://creativecommons.org/licenses/by-nc/4.0/)
## Introduction
BADASS package introduces a novel approach to protein engineering... |
64cba29f30b620983afafb1961232812c86a005deb855ca165e8e56e70de3404 | Text | 6,295 | 162 | # TransUnet-for-CFZ-Segmentation
TransUnet for Capillary Free Zones (CFZ) Segmentation using PyTorch.
## Overview
This GitHub repository hosts the implementation of a TransUnet model developed in PyTorch for segmenting capillary free zones (CFZ), arteries, and veins in optical coherence tomography angiography (OCTA)... |
a3ad7ae3be2c984e7571e5a33a7e1a35d53819a5137f7d6cd646a24b9d2ac8b2 | Text | 6,316 | 115 | [](https://pypi.org/project/brainprint/)
# BrainPrint
This is the `brainprint` python package, a derivative of the original
[BrainPrint-legacy](https://github.com/Deep-MI/BrainPrint-legacy) scripts,
with the primary goal to provide a Python-only version, to integ... |
d2fbde33cf1e10eccdc2d6690f2fdc684c68faefcdcdd883eafdb6e274591bee | Text | 6,332 | 91 | English | [简体中文](README_cn.md)
<p align="center">
<img src="./.github/paddlehelix_logo.png" align="middle" heigh="90%" width="90%" />
</p>
------
[](https://github.com/PaddlePaddle/PaddleHelix/releases)
- [Installation](#installation)
- [Usage](#usage)
- [Example calls](#example-calls)
- [Update figures used in review pape... |
874b880c0486740a657214a76f03e236ea15426f9d8e9fe8ff5a8ce14ff39110 | Text | 6,398 | 114 | # **ONTraC**
[](https://pypi.org/project/ONTraC/)
[](https://pypi.org/project/ONTraC/)
[](https://pepy.tech/project/ONTraC)
[
- [System Requirements](#system-requirements)
- [Installation Guide](#installation-guide)
- [Data Description](#data-descript... |
3d8096c3e5575bd55e16ef119685f69dfa8c5463c423ad30903383e246155ba3 | Text | 6,458 | 52 | [](https://zenodo.org/badge/latestdoi/687046158)
# minis-benchmarking
This repository contains benchmarking analysis Matlab code for [minis](https://github.com/dervinism/minis) software. It contains all the analysis code required to reproduce Figure 3, Figures 5-13, and... |
2deafb9aad0f8c8ddbc2ce396c7e4cd52f7ceedd52e470cc9f10e6f7ea236eb6 | Text | 6,505 | 103 | # DANCE: Dimensionality Analysis for protein Conformational Exploration [](https://doi.org/10.5281/zenodo.15617757)
DANCE is designed to process a set of input protein 3D structures provided in Crystallographic Information File (CIF) format and output protein or protein fa... |
b2faff51cec093919a20279af08e223449a033d5afdea9ebacbdf1489ffd45bf | Text | 6,527 | 155 | <h1>
<img src="voxel-logo.png" alt="Voxel Logo" width="40" height="40" align="center">
Voxel
</h1>
**Control, coordinate, and acquire with light-sheet microscopes.**
Voxel is an application-first microscopy platform built from reusable Python components. It brings local and
distributed hardware under one cont... |
12bf78e66cb3a0e9a76b7aa5abaccaf86b53d9f4ea49f24eb343abab41158f9e | Text | 6,587 | 130 | # Scikit-NeuroMSI
<!-- BODY -->
[](https://github.com/renatoparedes/scikit-neuromsi/actions/workflows/ci.yml)
[, where a more complete set of methods can be found. Data from GOSH D... |
0803667db4d533702f5e3172246ce1c25fce908cfc509e49a0b2aa774746f8af | Text | 6,588 | 175 | # GLN
Implementation of Retrosynthesis Prediction with Conditional Graph Logic Network
https://arxiv.org/abs/2001.01408
# Setup
- ## Install package
This package requires the **rdkit** and **pytorch**.
For rdkit, we tested with [2019_03_3](https://github.com/rdkit/rdkit/releases/tag/Release_2019_03_3). Please buil... |
ef1e2a7a082b6b4b9e7d672c19caf2484402453815c56d538f87b3ec20c34242 | Text | 6,591 | 161 | # DeepExDC
## 1. Introduction
DeepExDC is an interpretable one-dimensional convolutional neural network for differential analysis of A/B compartments in scHi-C data across multiple populations of individuals.
## 2. Installation & example
**2.1 OS**
- ubuntu 18.04
**2.2 Required Python Packages**
Make sure all th... |
2aba1f5d7f503c1f4bdd0b896e3c9bb7a98406994b5668ec0e6a9de5c71ccbce | Text | 6,762 | 185 | # HiCPlot
### HiCPlot can be used to plot square and triangle heatmaps from Hi-C matrices and tracks from bigwig files.
#### usage:
```
HiCPlot [-h] <tool> ...
```
#### Hi‑C plotting utility (wrapper for individual tools)
options:
-h, --help show this help message and exit
Available tools: ... |
2674b8d8e23fdc9ec9e7b19bb732c6707a5ec79e052e857e4b11ef13a7eaba5a | Text | 6,810 | 136 | # GSN (Generative Modeling of Signal and Noise)
-------------------------------------------------------------------------------------------
GSN is a toolbox for accurately modeling signal and noise distributions in neural da... |
6f148a43fcc3bf0da69930d9af7dee9d2a157256b5d572bb29b6794371cabd5d | Text | 6,884 | 99 | ### OSM4EO LULC classficaiton with deep residual convolutional neural networks
- Extract OSM objects download for https://doi.org/10.11588/data/IUTCDN and visualization at https://osmlanduse.org and here https://heigit.org/tag/osmlanduse-en/
- existing models: https://1drv.ms/f/s!AsaD57Gg8TWIlfFvgtTjDT6E0067Jg?e=kkme... |
1657ce44875a55e3ba6542a442b11896353c7ee263a0caee742cc8135e0fc63e | Text | 6,901 | 162 | # model-based-prediction
This repository provides tools for model-based prediction using machine learning techniques. Follow the steps below to set up the environment, train models, and generate figures.
## Install Dependent Python Modules
Ensure you have Python 3 installed. Then, install the required Python libraries... |
2965051aeed55c95635aca3da757c5cd0ce923e0e7c2dd048f10b53b0021d785 | Text | 6,920 | 117 | <div align="center">
<img src="https://github.com/NIMH-SCCN/callicog/blob/master/docs/images/callicog_logo.png" alt="callicog logo" width="635" height="184">
<br><br>
Open-source tools for automated behavioral training and testing, designed for the homecage environment.
</div>
## Summary ##
CalliCog is an automated... |
0e3cc6fbb6d33c56d0e1c9605aa44bde96f49a38e92c40862c6b970ad44b8855 | Text | 7,012 | 110 | # CountMatrix
Fully Automated RNAseq pipeline, goes from raw reads to count matrix. Includes quality control.
## What does it do?
This pipeline automates and parellizes Illumina NGS processing to produce a count matrix ready for differential expression analyses. It also automates all quality control for this process... |
af5f7abe247eb3177b3ae708fa80fc8d805a27e80e71488410a144bff95e53f3 | Text | 7,034 | 125 | # S3AI
The official code repository of ["Interpretable antibody-antigen interaction prediction by introducing route and priors guidance"](https://www.biorxiv.org/content/10.1101/2024.03.09.584264v1).
## Table of Contents
- [Overview](#overview)
- [Installation](#installation)
- [Data... |
61ad93466dbeef32154fcd4c1f67ea5627eca59fd90bbf66293dc3276b5c1759 | Text | 7,053 | 122 | <h1>
ExA-SPIM control
</h1>
- [Overview](#overview)
- [Getting Started](#getting-started)
- [Installation](#installation)
- [Finding Device IDs](#finding-device-ids)
- [Recommended Hardware](#recommended-hardware)
- [Documentation](#documentation)
- [Usage](#usage)
- [Support and Contribution](#support-a... |
4d87c82ab54b830ac63543222a615cb58cf5c6e44fed583a9045b2e24bbfe98f | Text | 7,085 | 142 | # DAXOS: Dask and XGBoost on SNPs
[](https://doi.org/10.5281/zenodo.15526395)
DAXOS is a Python library designed to efficiently run Dask and XGBoost on SNP data, particularly for use on high-performance computing (HPC) systems that use a SLURM management system. The code ... |
b62e236b6334991a9d997e4a97c71c6b094276eff7b12f8be2ce49d390d0044f | Text | 7,139 | 89 | # SPMCleanup
**WARNING**: This script is designed to delete data, and improper use may lead to accidental deletion of important data. Be sure to read this readme carefully before proceeding with this tool. We strong encourage that this tool is only used when you have a standard structure to your data (e.g., using BIDS... |
3489c0bd38dd212ecb9169ff410d571e2e7c6bd3efe379a17461a387316a138d | Text | 7,143 | 88 | # CorticalFoldingAnalysisTools
Matlab toolbox to extract features of cortical folding from Freesurfer folders. Current version 3.0
## What can this toolbox do?
The MATLAB toolbox is designed to extract various features of cortical folding derived/based on the universal scaling law of cortical morphology (see "Related ... |
dd5910a7539bece1345929108f3e466a20f7aefb2028bd47327b454ce6bd1915 | Text | 7,228 | 66 | [](https://matlab.mathworks.com/open/github/v1?repo=schnitzer-lab/EXTRACT-public) [](https://www.mathwork... |
6bc57f455b8bbb8c6fedc36b1f2398a99c62043ca3c5231eb7ca92dd43114e4a | Text | 7,315 | 107 | 
## Multimodal connectome processing with the `micapipe` ##
[](https://www.gnu.org/licenses/gpl-3.0)
[](ht... |
34a0424afb6f71e659dc7d1065ce832084a9d4f3b78337783b02166e2d7d4ec4 | Text | 7,343 | 121 | 
========
PANDASEQ is a program to align Illumina reads, optionally with PCR primers embedded in the sequence, and reconstruct an overlapping sequence.
INSTALLATION
------------
[](https://github.com/edf-hpc/verrou/actions/workflows/github-actions-travis.yml)
[](http://edf-hpc.github.io/verrou/vr-manual.html)
Verrou... |
80c9a25c05c759d3ebcb134d4bfc69341f686adcc492aafacd8dcece2f654226 | Text | 7,444 | 151 |
# Code repository for "Performance of deep-learning based approaches to improve polygenic scores"
DOI: 10.1101/2024.10.23.24315973
This respository represents the last snapshot of the bash, R and python scripts used to generate our results and is provided as-is. As the analysis involved a lot of input/output operati... |
ecb57a2887210c049b593ad6f737acb460661eb2b829992e489b83fb9ddb4d50 | Text | 7,464 | 145 | # PolyFun, PolyLoc and PolyPred
**PolyFun** (POLYgenic FUNctionally-informed fine-mapping)
<br>
**PolyLoc** (POLYgenic LOCalization of complex trait heritability)
<br>
**PolyPred** (POLYgenic Prediction of complex traits)
[](https://github.com/... |
0e6f125304779b8da8859c2991b5b99b5858dcfd207960d97d743469923d83eb | Text | 7,505 | 79 | <img src="plots/braincharts/dev_ct_brainchain.png">
---
# <a name="top"></a>Regional patterns of human cortex development correlate with underlying neurobiology
This repository accompanies the paper:
Leon D. Lotter, Amin Saberi, Justine Y. Hansen, Bratislav Misic, Casey Paquola, Gareth J. Barker, Arun L.W. Bokde, ... |
3abad17cc98209bdb4dade19e39c3d1f207f5a031c44ee03990d376511464d45 | Text | 7,509 | 97 | # CATS: **C**limate-**A**ware **T**ask **S**cheduler
| Category | Links (click badges) |
| ------------- | --------------------------------------------------------------------------------------------------------------------------------------... |
e0f3ac3c2a3e8d5a32e6cd2a09b4fca2df1737b71f038ca07589017cae5a5df6 | Text | 7,541 | 118 | # 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/axon-projection
# Axon Projection
A code that analyses long-range axons provided as input, and classifies them b... |
dd76dcac6c1b262df84b837e151a93a57d06ad85a11c83fa6bfbd78052140277 | Text | 7,602 | 118 | ### Prerequisites
- Python3.7+ (we need to be able to rely on dictionary item order preservation!)
### Dependencies
Build:
- wheel
Install (will be automatically installed if pip install is used as described below):
- intervaltree
- numpy
- pandas
### Installation
1. Obtain the source code `git clone h... |
b4bfa5c738de045ff1e717d7fb42fc94d957c41f7094822315b87a613d3f9c8f | Text | 7,620 | 210 | ### 1. Purpose of repository
This repository contains all R scripts used for performing data analysis for our project on neuronal vulnerability in Alzheimer's Disease (AD). A preprint of our study is available:
_Intra-cellular accumulation of amyloid is a marker of selective neuronal vulnerability in Alzheimer’s dise... |
c06e1a45926a356a0e288464d2092afad22eda041d1c192e15fdaf6209c91d5b | Text | 7,635 | 126 | # Welcome to the TACOS
## What is TACOS？
TACOS (Transform brAin COnnectomes across atlaSes) is a toolbox that converts network-based statistics from structural and functional brain connectomes across different atlases. Specifically, network-based t values (usually derived from group comparisons in case-control connecto... |
631f7f678765e406eb72d271a57066039e0843620bb71ead9f81f1f2b322d070 | Text | 7,652 | 96 | # isoCycle
[](https://www.biorxiv.org/content/10.1101/2023.11.20.563492)
[](https://colab.research.google.com/github/esiabri/isoCycle/blob/main/isoCycle_yourData_Colab.ipynb)
[![pip](https:/... |
93c4b4badf9a93ac1e482a4a1d7480b5983330555797aa61760ef8a67fa076b3 | Text | 7,661 | 132 | # UNAGI: virtual disease and drug perturbation
UNAGI is a data-driven virtual disease model powered by deep generative AI for reconstructing longitudial cell dynamics in disease progression and performing **unsupervised** in-silico drug perturbations for drug discovery/repurposing.
Full documentations and tutorials c... |
94466a94e26c2b5e3b15f1b1c3b7090f436ac111e35eece172206c36f1d59c40 | Text | 7,796 | 123 | <div align="center">
<h1>UltraLight VM-UNet </h1>
<h3>Parallel Vision Mamba Significantly Reduces Parameters for Skin Lesion Segmentation</h3>
Renkai Wu<sup>1</sup>, Yinghao Liu<sup>2</sup>, Pengchen Liang<sup>1</sup>\*, Qing Chang<sup>1</sup>\*
<sup>1</sup> Shanghai University, <sup>2</sup> University of Shanghai ... |
12408d80ff7914a0f92dc22da56396a830e47ce96b8e477fc32f2bd26738fb47 | Text | 7,876 | 89 | # Code for NKX2-1 Paper
Citation:
This repository includes the main pieces of code used to support the conclusions in the paper. The following code were used in a SLURM High Performance Computing environment, using a combination of bash scripting, R (4.0.3) and python >=3.6. Detailed versions of softwares used are lis... |
b20519acb9540abd14ba4e7ff2419e435c6bec19bcdb9ac65adcc846176943c3 | Text | 7,906 | 172 | <div align="center">
<img src="https://raw.githubusercontent.com/google/flax/main/images/flax_logo_250px.png" alt="logo"></img>
</div>
# Flax: A neural network library and ecosystem for JAX designed for flexibility
[](https://gith... |
c7715dd40c8b52b5edf4b1b793ea6e9caa9188d645dd12e09563ba1404ef6e61 | Text | 7,931 | 128 | <div align="center">
<h1>UltraLight VM-UNet </h1>
<h3>Parallel Vision Mamba Significantly Reduces Parameters for Skin Lesion Segmentation</h3>
Renkai Wu, Yinghao Liu, Guochen Ning, Pengchen Liang\*, Qing Chang\*
Cell Patterns ([j.patter.2025.101298](https://doi.org/10.1016/j.patter.2025.101298))
</div>
## 🔥🔥H... |
da9da8e196fab783205a4a9a0eb78c68502f1d730d795611716a1e0c409d90b5 | Text | 7,943 | 122 | # Anders MelBrM
Analyses of RNA and DNA sequencing data from melanoma brain metastases and extracranial tumor tissue.
## Data
### Duke dataset
* For a sample summary, see Figure 1: Consort diagram of MDACC and Duke dataset patients represented in RNA and DNA
* NCBI dbGaP accession: [phs003009.v1.p1](https://www.nc... |
6dd711f440ee7c313af3c8d46cbcee224c772f79e7bb3fbe587b723d5396dcb6 | Text | 7,977 | 187 | [](https://pypi.org/project/epyt-flow/)
[](https://opensource.org/licenses/MIT)
[![build](https://github.com/WaterFutures/EPy... |
3c0d3da662edc6c87cc43f6e96c5bbb91b75dc29f7a9303209a28ecd4013c3c0 | Text | 7,980 | 64 | # DySample: Learning to Upsample by Learning to Sample
<p align="center"><img src="complexity.jpg" width="500" title="Complexity"/></p>
Code for the ICCV 2023 paper [Learning to Upsample by Learning to Sample](https://arxiv.org/abs/2308.15085).
We present DySample, an ultra-lightweight and effective dynamic upsample... |
48dbdebff681b6d7d395f04f09f7b61c642d3f66a3522b64e8dcb85e59cd3fa1 | Text | 8,001 | 116 | # PCMCalculator
[](https://doi.org/10.5281/zenodo.18712355)
**PCMCalculator** (**P**hase **C**ontrast **M**apping Calculator) is a Python-based GUI for analyzing 2D phase-contrast MRI data and quantifying blood flow in vessels (ml/min).
The software offe... |
3d42b6129321fcd809b6eb2444f4bd7204fdb81d76c999a9a95bf8a7003d740f | Text | 8,035 | 128 | # In silico discovery of representational relationships across visual cortex
Here we provide the code to reproduce all results from the paper:</br>
"[In silico discovery of representational relationships across visual cortex][paper_doi]"</br>
Alessandro T. Gifford, Maya A. Jastrzębowska, Johannes J.D. Singer, Radoslaw... |
c8eed9da59d70794bf6cc2bbf39f2598582f4cb5008fd71bb593f970a51896bd | Text | 8,090 | 156 | # fBOSC
### fooof+BOSC: A repository for the robust detection of oscillations at the single-trial level
[](https://www.doi.org/10.1111/ejn.15829)
tl;dr: This repository contains MATLAB code for combining BOSC and FOOOF
Tutorial script **[HERE](./custom/te... |
16cbd7d8d2cbe07cc7319813d859104b10d28473b5eee971d6d1349000ed4a58 | Text | 8,141 | 123 | # scbiasnoise – Analysis of single-cell expression bias and genetic noise
[-e30613?logo=doi)](https://doi.org/10.1038/s42003-025-08128-2)
[-285... |
8f7fa594f66c61cab929f49b700d97ac80898a257d54eccb80885bd93672a574 | Text | 8,144 | 101 | #  CellNEST
Nature Methods: [CellNEST reveals cell–cell relay networks using attention mechanisms on spatial transcriptomics](https://www.nature.com/articles/s41592-025-02721-3)
### Singularity Image:
For users' convenience, we h... |
212429d3ea7ab39fc2ff39e2ecdaf70941721b24acb252f6d2d712d8990b79f0 | Text | 8,162 | 95 | # minis
'minis' is a software for electrophysiological data analysis.
It allows you to:\
(1) detect and analyse spontaneous postsynaptic potetnials/currents in whole-cell patch clamp recordings (Dervinis and Major, 2023);\
(2) estimate the quantal size in the central synapse (Dervinis and Major, in preparation).
'mini... |
1219dfa861b1a08b3248d87f98b2ef594bfcfbdf6ec6863b8188c0c9677c934e | Text | 8,206 | 280 | ## DiffCoRank: A Comprehensive Framework for Discovering Hub Genes and Differential Gene Co-expression in Brain Implant-Associated Tissue Responses
**Author**: Anirban Chakraborty<sup>1,3</sup> (chakra96@msu.edu), Erin K. Purcell<sup>1,2,3</sup>, Michael G. Moore<sup>3</sup>
**Affiliations**:
1. Department of Elec... |
e48d943bf5e496b668a343b6af4e6932ee0fdc86763085b4102cf8cf73410f73 | Text | 8,253 | 193 | [](https://doi.org/10.5281/zenodo.11506094)
# CryptoWakeupRNASeq
Cryptococcus neoformans H99 reactivation in different media and temperatures. Informally, "CryptoWakeup".
Data generated by Liz Ballou and Edward Wallace, 2017; Reanalyzed by Edward Wallace and Liz Hughes,... |
4e8bcb1830e868c62c5af34dfff56b06868adb8cacd7c1c4862c1ff940345095 | Text | 8,264 | 209 | # De-Identification of Medical Imaging Data: A Comprehensive Tool for Ensuring Patient Privacy
[](https://www.python.org/downloads/release/python-3120/)
[ of both noise... |
113b6f306ecb747b65497a87f04c2adf05d02ac9d80f18202f74c648256a16c2 | Text | 8,344 | 212 | .. image:: https://raw.githubusercontent.com/amnsbr/cubnm/main/docs/_static/logo_text.png
:align: center
:width: 350px
.. badges-start
.. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.12097797.svg
:target: https://zenodo.org/doi/10.5281/zenodo.12097797
.. image:: https://img.shields.io/pypi/v/cubnm
... |
a78340787ee4519e3557a46c3efad32b5561c1c89bdce3a8e6fac3aeff2504a0 | Text | 8,349 | 223 | # ShimNet
ShimNet is a data-driven AI solution to improve high-resolution nuclear magnetic resonance (NMR) spectra
distorted by the inhomogeneous magnetic field (less than optimal shimming). To use it, the experimental training data has to be collected (see **Data collection** below).
Example data can also be downloade... |
835d495b6aa756ed2f8f27320783a525f44b452c6cd81f9c5d172820f87cedfb | Text | 8,365 | 236 | # A generic non-invasive neuromotor interface for human-computer interaction
[ [`Paper`](https://www.nature.com/articles/s41586-025-09255-w) ] [ [`BibTeX`](#citation) ]
[](https://github.com/facebook... |
3c111c26c7780ad9e99108d001b29f89c87b8d8c3426d0219416135be2c7a05d | Text | 8,371 | 146 |
| **Authors** | **Project** | **License** |
|:------------:|:-----------:|:-----------:|
| [**T. Giacometti**](https://github.com/TommyGiak) | **pharmacoNODE**<br> | [](https://github.com/TommyGiak/pharmacoNODE/blob/main/LICENSE) |
<a href="... |
f59a5e0e885dd14d15371526d29d21560f3d7a52be88ade937eb47d8c7a5419f | Text | 8,503 | 90 | # SC-shapes-the-maturation-of-cortical-morphology
This repository provides core code and relevant toolboxes for data analysis in the article "Liang X, Sun L, Liao X, Lei T, Xia M, Duan D, Zeng Z, Li Q, Xu Z, Men W, Wang Y, Tan S, Gao J, Qin S, Tao S, Dong Q, Zhao T, He Y (2024) Structural connectome architecture sh... |
5590992af252b0ca5c1f5b25a252bc6cc5e6f66713b189a0e52fc8f63ca045c1 | Text | 8,510 | 172 | # DigCNV
[](https://badge.fury.io/py/digcnv)
](https://github.com/sparkainlp-x/quantum-claims-passport/actions/workflows/ci.yml)
[](LICENSE)
[!... |
f0eeb36713b2f53e39a1b08caf6dea9eea1edc8b38565391d9438d848e59ea50 | Text | 8,808 | 101 | # Transverse Relaxation
## Introduction
This repository includes the original analysis code used to compile the results presented in the scientific publication:
*Non-exponential transverse relaxation decay in subcortical grey matter*
*Rita Oliveira, Quentin Raynaud, Evgeniya Kirilina, Valerij Kiselev, Ileana Je... |
c65ffa489664ff91ea61de13b2682b9e3209bb8ca10439dc6c4470eb13e9dad1 | Text | 8,890 | 193 | # Cosyne Tutorial 2022
These are the exercises for the [COSYNE](https://www.cosyne.org/) 2022 Tutorial, _Spiking Neural Network Models in Neuroscience_, by Dan Goodman.
The exercises are in Python, in the Jupyter Notebook format.
You can run these notebooks either locally, or in the cloud (via Google Colab or Kaggle)... |
751b861e127702ee3f8cbc9f1363028609d734d3d842464b57560b11838c8f9f | Text | 9,011 | 238 | # Always-on Mobile Multimodal Embedding
## Table of Contents
- [Environment Installation](#environment-installation)
- [Code structure](#code-structure)
- [Usage](#usage)
- [Search Demo](#search-demo)
- [Fine-tuning](#fine-tuning)
- [End-to-end System Workflow](#end-to-end-experiments-instruction)
<... |
e1a419c626f733c73a95f14cc5a1b2a7055c6f3d9a1cc28c523ffc190e29543d | Text | 9,127 | 201 | # Cosyne Tutorial 2022
[](https://zenodo.org/badge/latestdoi/451483302)
These are the exercises for the [COSYNE](https://www.cosyne.org/) 2022 Tutorial, _Spiking Neural Network Models in Neuroscience_, by Dan Goodman.
The exercises are in Python, in the Jupyter Notebook ... |
07949c7398d6a7ab0f2e79fd57838a770577d075b5d11fc1d320cedcaa34b7f1 | Text | 9,155 | 173 | # Sosa_et_al_2024
Code for analyses and figures in: \
Sosa, Plitt, Giocomo. 2025. [A flexible hippocampal population code for experience relative to reward](https://www.nature.com/articles/s41593-025-01985-4). _Nature Neuroscience_. \
Repo by Mari Sosa with contributions from Mark Plitt and the resources listed below... |
0f17a24fded2404a3eb6080f06b21adf548ee4006be1c47ff0e2220afede7e58 | Text | 9,176 | 127 | # MORPHOVIEW
**M**ultispecies **O**ptimized **R**efractive index matched tissue **P**reparation for **H**igh-resolution **O**ptical imaging, **V**isualization, **I**mage segmentation, and **E**xploration of **W**hole tissues
The purpose of the enclosed Matlab files is to read cell segmented data output from software s... |
99a06c266fd89603bc34ad821a8920ff238e17d8e32d6858fdffdd1d32081538 | Text | 9,206 | 205 | # Neural Jacobian Fields
**Sizhe Lester Li, Annan Zhang, Boyuan Chen, Hanna Matusik, Chao Liu, Daniela Rus, Vincent Sitzmann**
📄 [**Paper** (Nature, 2025)](https://www.nature.com/articles/s41586-025-09170-0) | 🌐 [**Project Website**](https://sizhe-li.github.io/publication/neural_jacobian_field/) | 📖 [**Tutorial**... |
7301882d54399c5b276b2fbd26132f9eb9a0ddfc2b6d13f03ed47d2cdaef1379 | Text | 9,240 | 121 | # QuipuNet: a convolutional neural network for single-molecule nanopore sensing
## Abstract
Nanopore sensing is a versatile technique for the analysis of molecules on the single-molecule level. However, extracting information from data with established algorithms usually requires time-consuming checks by an experien... |
a63d4d01a419ea7ebabcab49ad142f7088712721a6096df044899ed8a7a89089 | Text | 9,300 | 179 | # Implementation of HABiC and Wass-NN
## Installation
Before using HABiC, it is necessary to install requirements presented in [`requirements.yml`](requirements.yml) file.
If you are using `conda`, you can install an environment called `HABiCenv`. First, clone this repository ([Cloning a repository](https://docs.gith... |
4eb14ae4715f8e7068c9f42847d16918859781a40fd77d1ba82168c3abddcd70 | Text | 9,310 | 223 | # Parrot
 <br>
Implementation of reaction condition prediction with Parrot<br><br>
## Contents
- [Publication](#publication)
- [Quickly Start From Gitpod](#quickly-start-from-gitpod)
- [OS Req... |
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