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b50a86e449ed94971ccbcc0d1b32c4356a4c6cfb886195c23fee448fe8b704fe | Text | 4,724 | 96 | # <img src="docs/assets/EthoPy_logo.png" alt="EthoPy Logo" width="200" style="vertical-align: middle;">
[](https://pypi.python.org/pypi/ethopy)
[](https://pypi.org/project/ethopy/)
[ hardware and software.
## Installation
This package is currently available on [PyPi](https://test.pypi.org/project/fibp... |
a41f4afbae827e4d245874b7e899ef3bf79d916ec44a1be41d6f68069ae884a8 | Text | 4,835 | 108 | <p align="center">
<picture align="center">
<source media="(prefers-color-scheme: dark)" srcset="https://github.com/OpenFreeEnergy/kartograf/blob/0a2ecb10f1c5ede3842fd9b92ffb232ad726426f/docs/_static/img/kartograf_logo_style5.png">
<source media="(prefers-color-scheme: light)" srcset="https://github.com... |
a7373012c98b3f4960eb4f6a56310d5f5b337059aa7d22d77d0ba197766f23d0 | Text | 4,902 | 119 | <p align="center">
<picture align="center">
<source media="(prefers-color-scheme: dark)" srcset="https://github.com/OpenFreeEnergy/kartograf/blob/0a2ecb10f1c5ede3842fd9b92ffb232ad726426f/docs/_static/img/kartograf_logo_style5.png">
<source media="(prefers-color-scheme: light)" srcset="https://github.com... |
057d4fb0b2a65afeaad314c8d2a7d621a22cc2a64756eb6466d5986e25156cdf | Text | 4,949 | 169 | # rd_filters
This script provides a simple means of applying the
functional group filters from the ChEMBL database, as well as a number of
property filters from the RDKit, to a set
of compounds. As of ChEMBL 23, the database table **structural_alerts**
contains 8 sets of alerts. ChEMBL doesn't apper to have muc... |
89a22537db67632d1785f857ec04c153315e2a341635a58c3f1bee211b4ed817 | Text | 4,955 | 149 | # VaD_DTMR2025
Taylor-Bateman et al., 2025 - Repurposing drugs for the prevention of vascular dementia: Evidence from drug target Mendelian randomization
# MR & Colocalization Analysis Scripts
## File Descriptions
- **`Cis_DTMR.R`** – Runs MR for an exposure and outcome using instruments from the chosen cis-acting g... |
af973e1666450e10d31bba1c1cbc788143262058e5e2bd7296ec70b0d152319a | Text | 4,995 | 158 | # Reproducible analysis: tDCS effects on bimanual force control
This repository contains code and data to reproduce the analyses and figures for the Bioengineering submission:
**Effects of Transcranial Direct Current Stimulation over the Left Sensorimotor Cortex on Bimanual Force Control: A Computa-tional and Experim... |
cec167af18a1bf06789606771e216d236c4f310bb4c55b5c08860c8dcd35b05b | Text | 5,004 | 158 | # seg: tools for evaluating binary semantic image segmentation models
- Frameworks & Models:
- [torchvision](https://pytorch.org/vision/main/models.html)
- [segmentation_models.pytorch](https://github.com/qubvel-org/segmentation_models.pytorch)
- [Mask2Former](https://github.com/facebookresearch/Mask2Former)
-... |
6993d6d203267ce227af8190241d83f47087071bb407e23735bf48f073030b28 | Text | 5,028 | 48 | # INSPIRE
*INSPIRE: interpretable, flexible and spatially-aware integration of multiple spatial transcriptomics datasets from diverse sources*
An effective and efficient method for joint analyses of multiple spatial transcriptomics datasets.
We develop INSPIRE, a deep learnin... |
d2a9cb5ee14cd18414f296041ce0aa0ff2c6f66e0f80fcbc5c46e9d40b13dec4 | Text | 5,030 | 122 | 
ReKinDLe (Reconstruction of Kinetic models using Deep Learning) is a python package for training and generating with generative adversarial networks (GANs) to parametrize large-scale nonlinear kinetic models of cellular metab... |
fb692e660485f0f0b7ec4e1d6c1e88c9c61b0d0aebaeddb60c7df7b5994eff28 | Text | 5,030 | 122 | 
ReKinDLe (Reconstruction of Kinetic models using Deep Learning) is a python package for training and generating with generative adversarial networks (GANs) to parametrize large-scale nonlinear kinetic models of cellular metab... |
1090515b82c38c3fe87da65b6079ca49e54f35ed5f0a1cda15bd2dcee11f4b52 | Text | 5,060 | 101 | ## [Richer Convolutional Features for Edge Detection](http://mmcheng.net/rcfedge/)
We have released the code and data for plotting the edge PR curves of many existing edge detectors [here](https://github.com/yun-liu/plot-edge-pr-curves).
### Citation
If you are using the code/model/data provided here in a publicatio... |
3f4f6d9bdd6c79dff3dd9117258066356e198ac668eeebd2b09b8d9b63b88e90 | Text | 5,063 | 182 | # Oracle Upper Bounds on Clean-EEG Recoverability from Single-Channel Decompositions
MATLAB code for the **core oracle benchmark pipeline** used in the paper:
> **Oracle Upper Bounds on Clean-EEG Recoverability from Single-Channel Decompositions under EOG/EMG Contamination**
This repository contains the code needed ... |
c741e3552450fd57887fa6509f8b8afa2e1a0a5704f8e8c8a4f6312d84cb39d3 | Text | 5,080 | 114 | # ASHLAR: Alignment by Simultaneous Harmonization of Layer/Adjacency Registration
## Whole-slide microscopy image stitching and registration in Python
**Ashlar** performs fast, high-quality stitching of microscopy images. It also
co-registers multiple rounds of cyclic imaging for methods such as CyCIF and
CODEX. Ashl... |
2481103b013e5875cdc8c8fe97a888f89228cc7de726aeb48e58a108e394ff0d | Text | 5,083 | 79 | 
[](https://github.com/friendsofstrandseq/mosaicatcher-pipeline/actions/workflows/main.yaml)
[![Snakemake](https://img.shields.io/badge/... |
da7b7af5d9311890acb1eac08c22aa22a6d619af21aecfd39a60a03637a8f61c | Text | 5,103 | 146 | <div align="center">
# Raidionics Validation & Metrics Computation
**Backend for k-fold cross-validation and metrics computation over 2D-3D medical data.**
Part of the [Raidionics](https://github.com/raidionics) ecosystem.
[](https://opensou... |
72fbbc328ebecb4e88e40e8ca1d780432b3e8331b88ee7b427db1bb3b0c53048 | Text | 5,118 | 116 | # 🧠 Centralized brain networks controlling antennal grooming coordination
This repository provides the code for reproducing results from
[**Centralized brain networks controlling antennal grooming coordination**]([https://www.biorxiv.org/content/10.1101/2024.12.17.628844v1](https://www.nature.com/articles/s41467-026-... |
bf6138ca54428615d672ed9b24c2d4c00c2f5af84c5eb6540bd6edb1995c7c64 | Text | 5,151 | 114 | # Welcome to The nnU-Net for MRI-Perivascular Space Segmentation!
Our models are capable of PVS segmentation in the:
- White matter (WM)
- Basal ganglia (BG)
- Midbrain (MB)
- Hippocampus (HP)
There are five models based on different MRI sequences:
1. T1w = WM-PVS and BG-PVS
2. T1w = MB-PVS
3. T1w = HP-PVS... |
00757026eb390b895350650458fce112c306025bb291a7e6d3f7e72bef9e83ed | Text | 5,217 | 116 | HTGTS pipeline package (Wei, Pei-Chi group; DKFZ)
====================================================
High-throughput, genome-wide, translocation sequencing (HTGTS) pipeline. More documentation about the pipeline itself can be found [here](https://robinmeyers.github.io/transloc_pipeline)
Table of Contents
==========... |
fe4c82e4816753f4a51253e6e05c56545a276859cbb63ddb3f0c842c363acd73 | Text | 5,259 | 105 | # 🧠 CortPro: You cortical profiling toolbox
**CortPro** is an open-source toolbox for generating and analysing intracortical microstructure profiles. The only prerequisites for microstructure profiling are (i) an MRI suitable for cortical surface reconstruction (e.g. T1w) and (ii) a microstructure-sensitive volume (e... |
05f1edff0553cc4da71f1b4f6987883e86bd6299207ed6cf15b83bb32b86fbd4 | Text | 5,282 | 97 | cinnabar (formerly Arsenic)
==============================
[//]: # (Badges)
[](https://github.com/OpenFreeEnergy/cinnabar/actions/workflows/ci.yml)
[]... |
848d342b19d42666f9d9abd84107baf632af4e82ab57cf616d6a2f57257132fe | Text | 5,283 | 231 | <p align="justify">
<!-- README.md is generated from README.Rmd. Please edit that file -->
Fig. 1a: Cognitive effects of coffee.
``` r
source("scripts/fig_1_behav_cog_health_data.R")
```
``` r
(plot_cog <- (plot_cog_NCD | plot_cog_CD) +
plot_layout(guides = 'collect', widths = c(1,3)) &
theme(strip.text = el... |
ebd9f63defb5b4a990b7fbd1e81cce13b71b7b805fb339bfad4f742d3bc50436 | Text | 5,311 | 44 | # Virtual Epileptic Patient (VEP)
## Introduction / Objective
Success rates of Epilepsy surgery in patients with drug-resistant Epilepsy has remained about 60% for the past decade. In order to improve the success rates of the surgeries better methods are necessary for pre-surgical estimation of the pathological brain ... |
51bb97a039ec30c2245aa97c528bbfa614dba7e1bf26aa51081e266caeb9c67f | Text | 5,353 | 62 | # Cheese3D
[](https://hou-lab-cshl.github.io/cheese3d/)
[](https://labshare.cshl.edu/shares/houlab/www-data/cheese3d_paper_data/cheese3d_demo.tar.gz)
Cheese3D is a pipeline for tracking mouse fac... |
e5d9beafc05e3a605fa7ab1badf8f483466d99fdcd99300ec3cc18f2a6220a9d | Text | 5,442 | 79 | <div align="center">
<img src="assets/images/raidionics-logo.png" width="128">
<h1 align="center">Raidionics</h1>
<h3 align="center">Open software for AI-based pre- and postoperative brain tumor segmentation and standardized reporting</h3>
[ energy calculations, as used in "[Spatiotemporal asymmetries on brain energy landscape uncover system entra... |
6e0723478b99a82b2dc1e4273affffb77c1d1e6b47555fb1938eb0c7d310d0d7 | Text | 5,524 | 72 | # Surf Ice
##### About
Surf Ice is an open source surface render. It can be compiled for the Linux, Macintosh OSX, and Windows operating systems. For details and compiled versions visit the [NITRC wiki](https://www.nitrc.org/plugins/mwiki/index.php/surfice:MainPage). You can also get a compiled version from the [Gith... |
f0b0405f313f81bbb7c48e76eaeacdf4fc74743cecf9d8970adc91d6e4521ec8 | Text | 5,539 | 142 | # Flood-Filling Networks
Flood-Filling Networks (FFNs) are a class of neural networks designed for
instance segmentation of complex and large shapes, particularly in volume
EM datasets of brain tissue.
For more details, see the related publications:
* https://arxiv.org/abs/1611.00421
* https://doi.org/10.1101/2006... |
9521afd36fad2af5b02ce223cc7cc273715bf02aced70c432073ceab0d380a38 | Text | 5,555 | 107 | # E/I imbalance and internal noise cause weak neural representations and face recognition challenges in ASD
[](LICENSE)
[](https://doi.org/10.1038/s42003-026-10094-2)
[
📦 Data arc... |
fddb5ef44f89d709f8bb0b25533ca6e54ce99761a4af9fc7aeafbbbfb41434f6 | Text | 5,581 | 122 | # Neural BCI Performance Analysis Toolkit
This repository provides the full analysis pipeline used in the preprint:
**"Intracortical brain-computer interface for navigation in virtual reality in macaque monkeys"**
🧾 Available at: [bioRxiv](https://www.biorxiv.org/content/10.1101/2025.05.05.652199v1)
📦 Data arc... |
369d1740229afbe485b14b3d3d5406537b2b1be0355447e96061dff0723142a0 | Text | 5,626 | 172 | =======
Shapely
=======
.. Documentation at RTD — https://readthedocs.org
.. image:: https://readthedocs.org/projects/shapely/badge/?version=stable
:alt: Documentation Status
:target: https://shapely.readthedocs.io/en/stable/
.. Github Actions status — https://github.com/shapely/shapely/actions
.. |github-act... |
a46412ac62080a80f28a41334fa3e8f5d9a60eb4b207f04f7038ebfb6c4c5163 | Text | 5,631 | 109 | # **Visual-Startle Analysis Code**
This code was used in Weinschutz Mendes et al. (2023) to analyze visual-startle phenotypes in zebrafish mutants of autism genes. This method is described in the STAR Methods section of Weinschutz Mendes et al. (2023).
# **Required user input files**
1. ViewPoint file (.XLS)\*
1. ... |
91f348c2ee39a1f4b906f073ad1de5a4327999e5027579ca7c2b9d0b2a7cbd3f | Text | 5,645 | 42 | # Glial_Chimera_Maturation
Ordered scRNA-seq, scATAC-seq, CUT&Tag, and Xenium analyses of ESC/iPSCs, their differentiated GPCs, and their post-transplantation derivatives.
[Link to Preprint: Charting the transition from in vitro gliogenesis to the in vivo maturation of transplanted human glial progenitor cells](https:... |
db765d8434d7e18139cb6692afc457cb79dab9da117c9715c6ef62a4da2a391c | Text | 5,710 | 131 | # Ethopy Analysis
[](https://pypi.python.org/pypi/ethopy-analysis/)
[](https://pypi.org/project/ethopy-analysis/)
[](... |
72ae61852a5366bf2162df5b2fb80c379b067b079f1d0ce95b43eca0da685880 | Text | 5,746 | 229 | # KissSmoothing.jl
This package implements a denoising procedure, a Radial Basis Function estimation procedure and a Natural Cubic Splines estimation procedure.
## Denoising
denoise(V::Array; factor=1.0, rtol=1e-12, dims=ndims(V), verbose = false)
smooth data in `V` according to:
`V` : data to smooth
`... |
4c3c48ed21e0e43c5b0bd942edf22fb0524ed528733c23c39a251523da6ff70a | Text | 5,887 | 54 | # Embrace_Dataset
The EMBRACE dataset includes the multimodal dyadic recordings acquired during the final validation phase of the EMBRACE project (https://cordis.europa.eu/project/id/101007521) using the upgraded multimodal EMBRACE system during cooperative and competitive table tennis. In particular, the dataset incl... |
1eb2151d2e312e95260663fb13199d20d4a594e3b249d3d47550651768041fa4 | Text | 5,892 | 145 | # CORTADO: hill Climbing Optimization foR cell-Type specific mArker gene DiscOvery
  
 dataset. It characterises eac... |
1fad106d75465c566d9540a6da2bddb434e4194aec86fb18ca2a4c50deb4d3a2 | Text | 6,087 | 116 | # calcFD toolbox
A toolbox for MATLAB for calculating the fractal dimensionality of a 3D structure, designed to work with intermediate files from FreeSurfer analysis pipeline, but can also use other volumes.
To use the toolbox with data in NIfTI format, see `example_nii` in examples.
Current public version: build 31 ... |
38c1614b314e0bd748bc90fc3d33622af88a41107c0dff134d415c7b0edbac36 | Text | 6,113 | 81 | # GNOVA
GNOVA (GeNetic cOVariance Analyzer), a principled framework to estimate annotation-stratified genetic covariance using GWAS summary statistics.
## Requirements
1. Python 2.7
2. numpy
3. scipy
4. pandas
5. sklearn
6. bitarray
## Tutorial
Suppose you would like to calculate genetic covariance between Crohn's ... |
d50b9fe597177e0758f6577e5900a6c88b04d721feb86b5f81dd146821145cd9 | Text | 6,151 | 155 | [](https://doi.org/10.5281/zenodo.18752763)
# Introduction to WSL2 for Ubuntu 22.04 LTS
To ensure full compatibility with deep learning libraries and leverage the performance of NVIDIA GPUs, this project is developed in an environment based on Windows Su... |
1e4262ebc839f08a7923ad0dc17efef14a16fa0c0ef0932310a223ae058fd69a | Text | 6,232 | 99 | # NeXtSwin-X: Dual-Branch Cross-Attention Fusion for Brain Tumor Classification
This repository contains the official implementation of the paper **"NeXtSwin-X: Dual-Branch Cross-Attention Fusion of ConvNeXt and Swin Transformer for Accurate Brain Tumor Classification from MRI"**. We introduce a powerful hybrid deep l... |
b9c010bac830194d7d00fe93c7d96c44ea153ec8d6af702a0edac324f1387e1e | Text | 6,235 | 93 | # Variants_Tiers_Gene
## Getting started
To make it easy for you to get started with GitLab, here's a list of recommended next steps.
Already a pro? Just edit this README.md and make it your own. Want to make it easy? [Use the template at the bottom](#editing-this-readme)!
## Add your files
- [ ] [Create](https:... |
1b5c9624a16f9fbaf30c895194e37ac7b67d2d53d2691e1147b6733e0af2022d | Text | 6,419 | 140 | # Jx-EEGT : Electroencephalogram ( EEG ) Feature Extraction Toolbox
[](https://www.mathworks.com/matlabcentral/fileexchange/84235-eeg-feature-extraction-toolbox)
[![License](https://img.shiel... |
2d198a5b03b69aeaae8f601078d87b209429989e3e54ec7c7c32a9e0d80b6a48 | Text | 6,437 | 96 | # photometry_FLMM
Code to reproduce analyses and figures from the manuscript: "A Statistical Framework for Analysis of Trial-Level Temporal Dynamics in Fiber Photometry Experiments". This repository contains tutorials in both R and Python Jupyter notebooks.
## Installation
In order to run this tutorial the following ... |
95052d34735342d5be71ccdc0f891b627875a2a2a248744d2cac7b7913bfc09f | Text | 6,456 | 207 | # Subliminal Learning
[](https://arxiv.org/abs/2507.14805)
## Contents
- [Overview](#overview)
- [System Requirements](#system-requirements)
- [Installation Guide](#installation-guide)
- [Demo](#demo)
- [Instructions for Use](#instructions-for... |
d768c921d2cf88ee3f9fb5fbda33c6561791815b6eca632736131bf9e4fdcb3a | Text | 6,493 | 178 | # ProtoCloud
ProtoCloud is a prototype-based interpretable deep learning model for single-cell RNA sequence analysis. It combines variational autoencoder (VAE) architecture with prototype learning to provide both cell type classification and interpretable features.
## Installation
Dependencies:
- numpy>=1.26.... |
3e761d0c2e11b814fcaac7b9f88533eb662c8e610bccee0b3c6d4e6fd9caf557 | Text | 6,598 | 149 | GRO-seq pipeline package (Wei, Pei-Chi group; DKFZ)
====================================================
Global Run-On Sequencing (GRO-Seq) pipeline for analyzing transcription activity of genes from engaged RNA polymerase.
Table of Contents
=================
* Using GRO-seq docker image
* [Singularity](#sin... |
65c5a6e48c47556b8dd4bd3284d20dceb458d6291709a6a720d8ba59e62de1f0 | Text | 6,601 | 148 | <h1>
<picture>
<source media="(prefers-color-scheme: dark)" srcset="https://github.com/MultiQC/MultiQC/raw/main/docs/images/MultiQC_logo_darkbg.png">
<source media="(prefers-color-scheme: light)" srcset="https://github.com/MultiQC/MultiQC/raw/main/docs/images/MultiQC_logo.png">
<img src="https://github.com/MultiQ... |
e19b3e785e9cd9ac5f15d800ed60a64def2f6b155cc22fa26d668e6829e8f46d | Text | 6,615 | 133 | [](https://travis-ci.org/choderalab/pymbar)
[](https://anaconda.org/conda-forge/pymbar)
[](https://www.gnu.org/licenses/gpl-3.0)
Analysis of Repli-Seq data to study DNA replication timing program in R.
## Description:
An R package that features a set of functions to conduct Repli-seq data analysis.
We propose thi... |
147bb7d6f2b1e03ec08255271dc7e9d1b451ec9c1cb42d95ae79f013005e6138 | Text | 6,692 | 213 | # Subliminal Learning
[](https://arxiv.org/abs/2507.14805)
[](https://opensource.org/licenses/MIT)
## Contents
- [Overview](#overview)
- [System Requirements](#system-requirem... |
02596dbaa2d03cd62fd5010cdd4968edbe6b564fbc6997008d2c0b7928c9db26 | Text | 6,735 | 79 | # DEPRECATION NOTICE
This software is reaching its end of life, and we are in the process of consolidating and rearchitecting miniscope IO software as an SDK with minimal I/O functionality for all miniscopes - [`miniscope-io`](https://github.com/Aharoni-Lab/miniscope-io) and a yet-to-be-started GUI built on top of tha... |
82769539822bac8b7d1a881313e54ae20117bb37e40846107cabcc6bc634444c | Text | 6,770 | 103 | # Ubergraph [](https://doi.org/10.5281/zenodo.4641309)
Ubergraph paper presented at ICBO 2022: https://doi.org/10.5281/zenodo.7249759
## Integrated OBO ontology triplestore
- Merged set of mutually referentia... |
01b77a1a161574083f2f70eb2adc4c95181747ae8597e90fbbb016ea91447f3d | Text | 6,833 | 95 | # mp2rage
SPM implementation of https://github.com/JosePMarques/MP2RAGE-related-scripts
Based on:
* O'Brien KR, Kober T, Hagmann P, Maeder P, Marques J, Lazeyras F, et al. (2014) Robust T1-Weighted Structural Brain Imaging and Morphometry at 7T Using MP2RAGE. PLoS ONE 9(6): e99676. https://doi.org/10.1371/journal.pon... |
dcf59748c225e5ba64303aa6022422425db299dc97a112635015a83340f50a67 | Text | 6,857 | 154 | # PBupsModel
The `PBupsModel` package currently provides the Likelihood, Gradients, Hessian matrix of Evidence accumulation model for Poisson Clicks Task using Automatic Differentiation. This package was built based on code written by Brunton and Brody ([Brunton et al. 2013 Science][Bing]). This model also includes 4 ... |
06447b5601c8f9dba25c4589181ade032e920ef41a3b38252e2d3cfd9ef27517 | Text | 6,897 | 214 | <div align="center">
<picture>
<source media="(prefers-color-scheme: dark)" srcset="logo_dark_bg.png?v=3">
<source media="(prefers-color-scheme: light)" srcset="logo_white_bg.png?v=3">
<img alt="GenomeToWindows Logo" src="logo_white_bg.png?v=3" width="400">
</picture>
<p>
<strong>Automated Genome Downloading ... |
45c1708495c1b500b2748fd6cbe61f70a070a94f176fe243b26b022bb3827f34 | Text | 6,957 | 216 | # Ethopy Control
[](https://ef-lab.github.io/ethopy_control/)
[](https://opensource.org/licenses/MIT)
A Flask-based application for managing laboratory experiments and device... |
90da0f377bd381c295230b79b23b7e7afbfd977f6d20066a3cee45fcbc1c495a | Text | 7,008 | 77 | # **The Aging Epigenome: Integrative Analyses Reveal Functional Overlap with Alzheimer’s Disease**
Wei Zhang, David Lukacsovich, Juan I. Young, Lissette Gomez, Michael A. Schmidt, Brian W. Kunkle, Xi Chen, Eden R. Martin, Lily Wang
### Description
This github repository includes scripts used for the analyses in the a... |
ff1ba29be40835dc882dc419997e56e5c3fa489c6503fe7f5db9f76ab6106584 | Text | 7,030 | 154 | # Spinal cord structural-functional architecture and its shared organization with the brain across the adult lifespan
**Cite:**
> TBD
**📜 Preprint:**
> Landelle C, Kinany K, St-Onge S, Lungu O, Van De Ville D, Misic B, Marchand-Pauvert V, De Leener B, Doyon J.
Spinal cord structural and functional architecture and... |
46758ce84a62453ba69ee2713c6aa3772e479690d6469e28a323e52900e5b474 | Text | 7,136 | 154 | # Spinal cord structural-functional architecture and its shared organization with the brain across the adult lifespan
**Cite:**
> Landelle, C. CarolineLndl/Landelle_spinebrain_aging: v1.0.0. Zenodo https://doi.org/10.5281/ZENODO.18675164 (2026).
**📜 Related paper:**
> Landelle C, Kinany K, St-Onge S, Lungu O, Van D... |
1f17dc6905b787805442ef20bba006a561cc4e7a12c9e80f3a5d20b15e69bb31 | Text | 7,169 | 106 | # Kids First DRC Tumor Only Pipeline
This repository contains tools and workflows for processing of tumor-only
samples. The Kids First DRC recommends running the tumor only pipeline ONLY
when no matched normal sample is available. If your data has matched normals
we recommend running the [Kids First DRC Somatic Varian... |
314ebc2329723b5df47e17adf7ad7887e829b36e4cb700658885cdf876d104b0 | Text | 7,361 | 229 | # Ethopy Control
[](https://ef-lab.github.io/ethopy_control/)
[](https://opensource.org/licenses/MIT)
A Flask-based application for managing laboratory experiments and device... |
87826d135c37c901addff7a4e855075216abd1545fd92a3c29cb366158cb434d | Text | 7,378 | 50 | # MoCoProject
In this repo we host code for the work on the ongoing MoCo project at Neurobiology Research Unit, Copenhagen University Hospital (Denmark). Check out the project webpage [here](https://sites.google.com/view/melanieganz/research-projects/imaging-children-without-anesthesia)
Overall project abstract:
It i... |
c551b99b70a9a2a2934c2962d80823cbdbfea8be097501c467b0ffbfef3d06d9 | Text | 7,427 | 54 | BREAST MASSES DATASET WITH PRECISELY ANNOTATED SEQUENTIAL MAMMOGRAMS
General Information
This dataset consists of 100 pairs of mammograms, from two temporally sequential rounds. Specifically, this dataset includes the prior and recent mammograms with two mammographic views for each patient. This is a complete datas... |
25a9a83c54287247d18284fceee37cf73b521286cfea4f2e1c357063a9df6609 | Text | 7,442 | 180 | CellRDA-LS — mechanochemical cell motility simulations (C11)
============================================================
CellRDA-LS is a research code for simulating amoeboid cell motility by coupling
reaction–diffusion–advection (RDA) dynamics with a diffuse-interface level-set (LS)
description of cell shape and cyt... |
e22f9a18d567757aa27294672561183080cb7dde1ca146cc302a9c15df3b6858 | Text | 7,512 | 155 | [](https://travis-ci.org/choderalab/pymbar)
[](https://anaconda.org/conda-forge/pymbar)
[.
## Citation
Paper Citation will be added once available.
## Requirements
- ```PLINK V2.0``` (https://www.cog-genomics.org/plink2/)
- ```METAL``` (https://github.com/statgen/METAL?tab=readme-ov-f... |
8a5c59cbb3d164d5d377c9b52ce879e55d83938c64e90821c53b3686217bc804 | Text | 7,664 | 251 | # Favoring Flat Minima Improves Generalization of Transfer-Learned Models for Breast Ultrasound Tumor Classification
This repository contains the complete source code for reproducing the experiments presented in:
> **"Favoring Flat Minima Improves Generalization of Transfer-Learned Models for Breast Ultrasound Tu... |
219d91c9a8c7893a128253e4ef8b470fe3bf6c1712781af8676e3987de8fc11f | Text | 7,719 | 207 | # RBP Family Diversification and Neural Complexity
**Repository for:** Yasuda K. "RNA-Binding Protein Family Diversification Correlates with Neural Complexity Across Metazoan Evolution" (iScience, 2026)
---
## Overview
This repository contains all analysis scripts and processed data for a systematic comparative ana... |
28ad60a62b72c95dfa60b57976b3e3f16f19d7389c8a38b3248a17ace386459a | Text | 7,851 | 151 | # Drug Mechanism Database (DrugMechDB)
**DrugMechDB** is a curated database that captures mechanistic paths from a drug to a disease within a given indication. DrugMechDB provides:
- Mechanistic paths from drug to disease via biological entities.
- Expert curation of relationships supported by literature.
- Graph-based... |
8df8c5999a479b11fe1574c2d8eee9f30ebb01bf6c402da735460927f75fb4ac | Text | 8,015 | 151 | # CReM-pharm: enumeration of compounds based on 3D pharmacophores
Starting fragments matching a subset of pharmacophoree features are grown to match all remaining features. CReM generator is used for structure growing that provides flexible control over synthetic feasibility of generated structures. The search is desi... |
a8829ed659d3d1b1e6d3e2459a6b1080afee2cd6776b1c8300c9a7e89e512e04 | Text | 8,024 | 203 | SKiMpy: Symbolic Kinetic Models in Python
==========================================
|docs| |Build Status| |Codecov| |Codacy branch grade| |license|
SKiMpy is a python package bridging implementing an efficient kinetic model-ing toolbox to build and analyze large-scale kinetic models for various biological domains s... |
a819d0169e66155d48029338f86a27eadf1666527d9b79041a6399d018814d6a | Text | 8,108 | 193 | # TaskRest
Analysis for comparison of task-based and resting-state data
## Citation
If you use this code in your research, please cite:
```
Multi-task fMRI outperforms resting-state fMRI for revealing task-invariant organization of the human brain
Caroline Nettekoven, Ali Shahbazi, Bassel Arafat, Matea Skenderija, J... |
1e4e5de569fc9674a66f5b2f2a5a906be2b987fcc7d8f3b8a700fe4ef061ba2b | Text | 8,111 | 164 | # Mid-level feature representations
**If you want to use the updated version of the code, first edit the root dir in `Controls/create_config.py`, then create the `config.ini`file by running `python create_config.py`. If you used the same folder structure as me (see below), you should be able to easily reproduce all m... |
f703842cd3d216c881b8fd7329a422b1a8c59644b19c4f43716b1592968019c9 | Text | 8,334 | 188 | # Neural Quantum States Based on Selected Configurations
## Quick-Start Guide
The external dependencies of this program should be installed in a virtual environment:
```
[user@host Workspace]$ cd nqs/
[user@host nqs]$ python -m venv .venv
(.venv) [user@host nqs]$ pip install -e .
```
Once the external dependencies ... |
7a4302d26052e292f943250dabfbf5d6798d239b83203f73fe29989936a4c2c5 | Text | 8,669 | 149 | proteinbenchmark
==============================
[//]: # (Badges)
[](https://github.com/chapincavender/proteinbenchmark/actions?query=workflow%3ACI)
[ doi: 10.3389/fnagi.2026.1730265
---
## Overview
This is the full analysis pipeline I built for my study examining how... |
26bc992dff0fa4e1fa435977c943707485451de613242f0f554b719097037f13 | Text | 9,010 | 218 | # YAMMBS
Yet Another Molecular Mechanics Benchmarking Suite (YAMMBS, pronounced like "yams") is a tool for
benchmarking force fields.
YAMMBS is currently developed for internal use at Open Force Field. It is not currently recommended for external use. No guarantees are made about the stability of the API or the accur... |
1e4ff7cecc5a2b8c248282aa9eb16c682ddedf97561b7853fdd0e56cf2fa175c | Text | 9,266 | 153 | # Convergent and divergent functional topographies of individualized human brain networks and their developmental origins
E-mail: [zhaojianlong@mail.bnu.edu.cn](mailto:zhaojianlong@mail.bnu.edu.cn)
This repository provides code and source data that support the findings of the article entitled "*Convergent and diverge... |
224adb4bc7c38f2748892b27c566003690ee82763cb4fc1e65c161158b506b57 | Text | 9,387 | 131 | # Tunable Approach for Median Polish of Ratio -- Biological Abundance Batch Effect Removal
## (TAMPOR, v1.5), by Eric Dammer
For public use with citation of origin, and original author
####
## Purpose
####
#### - Robustly removes batch artifacts and batchwise variance from abundance data.
#### - Works well even if batc... |
951da103d271115c4a98a7bae9c916bb961e74e1a02e149b2b366d0ed0322fc8 | Text | 9,687 | 176 | # Woltka
[](https://opensource.org/licenses/BSD-3-Clause)
[](https://github.com/qiyunzhu/woltka/actions)
[
[](https://zenodo.org/badge/latestdoi/13996/obophenotype/cell-ontology)
[ is a toolbox for analysing anatomical variations at multiple spatial scales by using the fundamental, resonant modes—eigenmodes—of brain anatomy. The goal is to characterize a group average or group difference at multiple spatial scales by obtaining the spatial frequency spectrum, cal... |
a297619828e8f7a5c9d2ccbbd068181a6cde9645941d0230cb3e7d4be4641e21 | Text | 10,215 | 156 | # 
[](https://github.com/vanvalenlab/deepcell-tf/actions)
[](https://pypi.python.org/pypi/ethopy-analysis/)
[](https://pypi.org/project/ethopy-analysis/)
[](... |
f8feae31505f6fa48e00e524669f0baee5917517e4a3eb4cd3fd15d261ebc60b | Text | 10,582 | 120 | [](https://github.com/obophenotype/cell-ontology/actions/workflows/qc.yml?query=branch%3Amaster)
[](https://zenodo.org/badge/latestdoi/13996/obophenot... |
563a39f634f196b927a8c7e8527bd292c77b24eb48f7cfeedd0f2eb36d37bf47 | Text | 10,636 | 251 | # YAMMBS
Yet Another Molecular Mechanics Benchmarking Suite (YAMMBS, pronounced like "yams") is a tool for
benchmarking force fields.
YAMMBS is currently developed for internal use at Open Force Field. It is not currently recommended for external use. No guarantees are made about the stability of the API or the accur... |
e66ff98ab896c920aa1a97bdea2e0f78cfb6e3f37a8fc5dea0380fbbce6e508f | Text | 10,762 | 263 |
# MetGenX CLI Manual
MetGenX is a structure-informed generative model for metabolite annotation based on MS2 spectra. This command-line tool processes a single MS2 spectra file (.msp/.mgf) and outputs generated structures.
---
## Requirements
- Python >= 3.10
- Dependencies:
- `numpy==1.2... |
6fea190c4cc7d0bcd2a8b3f67eee81a603df597d04030e5aa23d52f1150e0f12 | Text | 10,939 | 201 | # MRI2PET
Code accompanying the paper:
> **Realistic PET image synthesis from MRI for automated inference of brain atrophy and Alzheimer's**
> Brandon Theodorou, Anant Dadu, Brian Avants, Mike Nalls, Jimeng Sun, Faraz Faghri.
> *iScience*, 2026. https://www.cell.com/iscience/fulltext/S2589-0042(26)01122-3
This repos... |
949e3629e641193e320cc008b4a5a438755ab39ca2b942d1667d8abd4373f92b | Text | 11,278 | 328 |
GSEApy
========
GSEApy: Gene Set Enrichment Analysis in Python.
------------------------------------------------
.. image:: https://badge.fury.io/py/gseapy.svg
:target: https://badge.fury.io/py/gseapy
.. image:: https://img.shields.io/conda/vn/bioconda/GSEApy.svg?style=plastic
:target: http://bioconda.githu... |
4b8252f82c391b3a277415c8c5dd8fca62f234691b4aeb19d373de220fb5dbdc | Text | 11,887 | 266 | <p align="center">
<a href="https://academic.oup.com/bioinformatics/article/28/18/i333/245403/DELLY-structural-variant-discovery-by-integrated">
<img height="150" src="https://raw.githubusercontent.com/dellytools/assets/main/delly-logo/delly-logo-539x600.png">
</a>
<h1 align="center">Delly</h1>
</p>
[![insta... |
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