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ef9b1aab050086948b929a55901d3f1207ae9215c0052c98cf1d4a4ae639033b | Text | 8,186 | 255 | # NEMO: a NEural network model for mapping MOdifications in nanopore Long-read
<p align="left">
<img src="./img/nemo_logo.png" width="200"/>
</p>
# 🚀 Overview
NEMO is a deep learning tool designed to predict DNA modifications using nanopore long-read chromatin accessibility data. It allows users to train neural net... |
ee2bd89d8675b9cb45d74e4587fe0aa4d1b2275d3f8dbd3f334f9e946ae2ac87 | Text | 8,189 | 207 | # A-OKVQA
Official repository for **A-OKVQA: A Benchmark for Visual Question Answering using World Knowledge**.
Links: [[Paper]](https://www.ecva.net/papers/eccv_2022/papers_ECCV/papers/136680141.pdf) [[Website]](http://a-okvqa.allenai.org) [[Leaderboard]](https://leaderboard.allenai.org/a-okvqa/submissions/public)
... |
190afa53c91ccf7bc4621933ef79654214a9f3d9d079a60e1935a6c16d7a391c | Text | 8,303 | 153 | [. Keras-Prov integrates traditional retrospective provenance data (r-prov) with typical DNN software data, e.g. hyperparameters, DNN architecture attributes, etc. using W3C ... |
56b2253408fb1023adbef62b26ac2feba94f43258497734e887377a5eecc9c55 | Text | 8,328 | 177 | # NF Meta-Analysis: Data
Datasets for the meta-analysis published as:
> Galang EV, Velásquez MA, Elcin D, O'Connell S, Wieck J, McNair S and Colombo PJ (2025)
> *Systematic review and meta-analysis of the relationships between real-time neurofeedback
> training parameters and acquisition of neural modulation.*
> Fron... |
35301505299e12472d7012729a4c02bc682a51a0faf16e3f425108d88908e273 | Text | 8,430 | 125 | 
# GrID-Net
**GrID-Net** (**Gr**anger **I**nference on **D**AGs) is a graph neural network framework for Granger causal inference on directed acyclic graph (DAG)-structured dynamical systems, as d... |
96a6c96e4c66e9e025913739e4a090836c6f67277636e8f3e56f92618db88eca | Text | 8,498 | 127 | ## Note: this is a mirror of https://github.com/alexw16/gridnet ##
# GrID-Net
**GrID-Net** (**Gr**anger **I**nference on **D**AGs) is a graph neural network framework for Granger causal inferenc... |
34f300247f7161d1e4c0ff9708c5bf335ca3a3858301e11d0061b5bd10bd574b | Text | 8,507 | 291 | # HiScanner (HIgh-resolution Single-Cell Allelic copy Number callER)
[](https://badge.fury.io/py/hiscanner)
[](https://opensource.org/licenses/MIT)
HiScanner is a python package for high-resolutio... |
7299a1774f589908d0327152d825f46526ad468df0a664393ea96566ad2a81db | Text | 8,630 | 166 | # Codes used in Resolving out of Africa event for Papua New Guinean population using neural network
## 1. Variant Calling
### 1.1 Variant SNPs only
The VCF file containing only variant SNPs was not generated specifically for this manuscript. Instead, we reused a
dataset from our previous work ([Andre et al. 2024](htt... |
fdcb7cdf568a7dd35ff9a0b010f687514ff9f3c0228bde2b44c0d7b892fde109 | Text | 8,632 | 281 | # HiScanner (HIgh-resolution Single-Cell Allelic copy Number callER)
[](https://badge.fury.io/py/hiscanner)
[](https://opensource.org/licenses/MIT)
HiScanner is a python package for high-resolutio... |
dbe8ade35a5f088fca54c3962b25570291b82c0c3afab22cd67d61c8b2a2002b | Text | 8,672 | 229 | <div align="center">
[![zincware](https://img.shields.io/b... |
17e7255cd45c273daa40f8c33b9a4c3ea118db50a3249042d71d235776a5bcfa | Text | 8,674 | 195 | # iONMF
Integrative orthogonal non-negative matrix factorization
An integrative approach to model and predict multiple data sources based on orthogonal matrix factorization.
For details of the model, please refer to
Stražar M., Žitnik M., Zupan B., Ule. J, Curk. T: Orthogonal matrix factorization enables integrative... |
50e2ae7adf9666f434cff606459209dc3b032ec8ff946ad4c017ea9404717f78 | Text | 8,731 | 158 |
<div align="center">
<img src="assets/radiologynet_logo.jpg" alt="RadiologyNET Logo"/>
<span> </span>
<img src="assets/ai_lab.png" alt="RITEH AI Lab Logo"/>
</div>
# RadiologyNET Foundation Models
Welcome to the official repository of RadiologyNET fou... |
7b3dcfdbaaeb338f58854b996cae984f8dcb59af1d882361e55c4824d3e3be5b | Text | 8,755 | 173 | # Babel
[](https://doi.org/10.5281/zenodo.18489042)
[](https://arxiv.org/abs/2601.10008)
<!--
Because this document is written like an FAQ, I want to allow headers to
end with punctuation,... |
2c8b7a7111f9e5b5be5b520be2df2198bfabc73dad260a2366ca6121c534efe7 | Text | 8,773 | 180 | # How EEG preprocessing shapes decoding performance
Working title: Multiverse 4 Decoding (m4d)
**Kessler et al., 2025**, How EEG preprocessing shapes decoding performance. *Communications Biology*. [https://rdcu.be/evH5m](https://rdcu.be/evH5m)
- Read article [here](https://rdcu.be/evH5m)
- [Supplementary Informatio... |
c36d7a7683fc4de73c3e1b752f7e3e6648638f1fdbafb1bd92ee181b69d51a0f | Text | 8,959 | 154 | # MLSPred-Bench
MLSPred-Bench: Reference EEG Benchmark for Prediction of Epileptic Seizures
MLSPred-Bench will create 12 different benchmarks based on different values of the seizure prediction horizon ($SPH$) and the seizure occurr(ence) period ($SOP$). The benchmarks are for patient-independent epileptic seizure pre... |
0d4a692cbec2b446d8b7877e9d6e15f7291eb2bf3aeeb90a370ae1bd3e785b7d | Text | 9,028 | 168 | # Axonal-Injury
This resource provides the R code to reproduce key results described in Clements, Tang, Baronik, Simpson Ragdale et al. "Axonal injury is a targetable driver of glioblastoma progression".
## Getting started
1. Load all R code/RData from ./utils;
2. ./RData contains RData files needed for reproducing co... |
2c0b42e2506a5b044e172cb72993d4ed26a9339217d302080bad48d6e43a3c66 | Text | 9,069 | 249 | # Adversarial Observation
A framework for black-box adversarial poisoning attacks using **Particle Swarm Optimization (PSO)**, with analysis of attack resilience across model architectures and adversarial training regimes.
The current manuscript (in preparation) evaluates PSO-based poisoning attacks against models tr... |
9ebe352aa105c73074881b62417ce20cc4c5de041fbc2b6ee606a359a173d5ca | Text | 9,271 | 139 | # TrimNN: Characterizing cellular community motifs for studying multicellular topological organization in complex tissues
<img src="https://img.shields.io/badge/TrimNN-v0.0.1-blue"> <img src="https://img.shields.io/badge/Platform-Linux-blue"> <img src="https://img.shields.io/badge/Language-python3-blue"> <img src="htt... |
65c7b14d39f96ed21f5c0ec19fd870fc018dea8b1ca72c2046136bfe23c56c73 | Text | 9,315 | 213 | # Slice-to-Volume Registration Network (SVRnet)
This repository is the accumulation of the following works:
* [P1]: Predicting slice-to-volume transformation in presence of arbitrary subject motion
([Springer](https://link.springer.com/chapter/10.1007/978-3-030-00928-1_85) |
[ArXiv](https://arxiv.org/abs/1702.0889... |
09b46f3801d28dbe13dc8ec358b28d73254f5d49d158bfed1a79fa0d3e90f489 | Text | 9,374 | 143 | # TrimNN: Characterizing cellular community motifs for studying multicellular topological organization in complex tissues
<img src="https://img.shields.io/badge/TrimNN-v0.0.1-blue"> <img src="https://img.shields.io/badge/Platform-Linux-blue"> <img src="https://img.shields.io/badge/Language-python3-blue"> <img src="htt... |
6a1ce0d30f78378ac64347840bf22985b0da75751442f55dd1ba7b14e7426d3e | Text | 9,620 | 162 |
# Restormer: Efficient Transformer for High-Resolution Image Restoration (CVPR 2022 -- Oral)
[Syed Waqas Zamir](https://scholar.google.ae/citations?hl=en&user=POoai-QAAAAJ), [Aditya Arora](https://adityac8.github.io/), [Salman Khan](https://salman-h-khan.github.io/), [Munawar Hayat](https://scholar.google.com/citatio... |
932a445d3df8dfd58b591139f00b5371bfb2b49f515df4bdd5ab95d64c9b595b | Text | 9,809 | 85 | [](https://doi.org/10.5281/zenodo.15310934)
# dcm_validate
The `dcm_validate` repository serves as a centralized collection of all `dcm_qa` repositories. Each `dcm_qa` repository provides concise, illustrative examples of specific DICOM image file featur... |
99840dcf648e4e642ae0538bcd26635e734a3678b03f117024a59e14a4847e93 | Text | 9,813 | 111 | # Distributionally Robust Neural Networks for Group Shifts: On the Importance of Regularization for Worst-Case Generalization
This code implements the group DRO algorithm from the following paper:
> Shiori Sagawa\*, Pang Wei Koh\*, Tatsunori Hashimoto, and Percy Liang
>
> [Distributionally Robust Neural Network... |
8ecd8db821cbeb54cafae30690c4fcdc38fcd777c1dd15316f732ff90b299d42 | Text | 9,817 | 152 | # ROCKETSHIP v1.3
ROCKETSHIP is a toolbox for processing and analyzing parametric MRI and DCE-MRI data. It was developed at the Biological Imaging Center at the California Institute of Technology and Loma Linda University.
If you use ROCKETSHIP in your project, please cite:
Ng, T.S.C., et al. [ROCKETSHIP: a flexible... |
3be173aeff44232c4a656f861ed10f199db38a47723c6f9cdf825aac62b88570 | Text | 9,922 | 81 | # Pipelines + statistical and visualization scripts
This repository presents analyses for the manuscript
*LINE-1 transposable elements regulate the exit of human pluripotency and early brain
development*
## Organization
- `bulk` - Containing all scripts for bulk RNA sequencing CUT&RUN analysis.
- `10X` - Containing... |
4685a4f47be407282756c701222c5808e71768cf3ea1251af02b5b754cf6e7d1 | Text | 9,928 | 275 | # GNODEVAE: A Graph-Based ODE-VAE Enhances Clustering of Single-Cell Data
## Graphical Abstract
## Introduction
GNODEVAE is a computational framework that integrates Graph Attention Networks (GAT), Neural Ordinary Differential Equations (NODE), and Variational Autoe... |
d00c20a7af6b8700ec905e27778e5d8c20ed21423cda1ef4c23d8c753e27a638 | Text | 10,005 | 234 | |banner|
BluePyOpt
=========
.. raw:: html
<table>
<tr>
<td>Latest Release</td>
<td>
<a href="https://pypi.org/project/bluepyopt/">
<img src="https://img.shields.io/pypi/v/bluepyopt.svg" alt="latest release" />
</a>
</td>
</tr>
<tr>
<td>Documentation</td>
<td>
<a href="https://... |
67eba558bf7283761c4e43ecaf89104c0e4c7bb4dc0838d4aefe1bb5ae506ae4 | Text | 10,133 | 201 | > [!WARNING]
> After years of success, we are slowly dropping support for the `n2v` package. But no panic, we are providing you with an alternative: [CAREamics](https://careamics.github.io/)! The reason is that most of the recent development in the field happens in PyTorch, and maintaining TensorFlow code has become cu... |
0674af69fa366731d2c8bd3dba42125466254b09fa63e3283f73932ccc76a1bc | Text | 10,329 | 135 | # scikit-ribo-ext
Extended and improved scikit-ribo (https://github.com/schatzlab/scikit-ribo) for accurate estimation and robust modelling of translation dynamics at codon resolution
[](http://scikit-ribo.readthedocs.io/en/late... |
372c4794c5246bf6b9ad48b881173a1d486091994f5684819325234630f5b23c | Text | 10,350 | 174 | # TockyPrep: Data Preprocessing Methods for Fluorescent Timer Reporter Data
<a href="https://monotockylab.github.io/TockyPrep/">
<img src="vignettes/assets/bannar.jpg" align="center" width=75%>
</a>
**Author:** Dr. Masahiro Ono
**Date:** 6 November 2024
## Introduction - The R Package for Fluorescent Timer Data... |
c2917f1a3301570749b5b4ace3617c13e7e1384072a46466ee886a334d67b048 | Text | 10,607 | 131 | This is the **XLM-T** repository, which includes data, code and pre-trained multilingual language models for Twitter.
# XLM-T - A Multilingual Language Model Toolkit for Twitter
As explained in the [reference paper](https://arxiv.org/abs/2104.12250), we make start from [XLM-Roberta base](https://huggingface.co/docs/t... |
40e67b6e0d4f9590967f174fbabc15e9579a69d9c109494b17c8127e2e23cc40 | Text | 10,683 | 228 | .. 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/BluePyOpt
|banner|
BluePyOpt
=========
+----------------+------------+
| Latest Release | |pypi| |... |
4d75a7183c0aa39f5a1d0dabe4a5a123a5566797a6e3381adb20d9925517f567 | Text | 10,809 | 123 | <img src="lib/theme/icons/maia_logo_v3_small.png" alt="maia_logo" width="100" style="display: block; margin: auto" />
# Maia
Maia is a custom software tool for biomedical signal processing, especially optical determination of cardiomyocyte contractility.
## Installation
### On Windows
* Download and install the [Pyth... |
bd27671a6af4cf6baa07069197a62bb935e7b8af06895c2438120d0e91c613fd | Text | 10,925 | 114 | # Prerau Lab Multitaper Spectrogram Code
### Matlab, Python, Rust, and R implementations
---
## Table of Contents
* [General Information](#general-information)
* [Matlab Implementation](#matlab-implementation)
* [Python Implementation](#python-implementation)
* [Rust Implementation](#rust-implementation)
* [R Implemen... |
2706d50b280062debfb2476819688b9de869ad1b15f65e85e75cdcefc3a55406 | Text | 10,940 | 186 | **About PyTorch 1.2.0**
* Now the master branch supports PyTorch 1.2.0 by default.
* Due to the serious version problem (especially torch.utils.data.dataloader), MDSR functions are temporarily disabled. If you have to train/evaluate the MDSR model, please use legacy branches.
# EDSR-PyTorch
**About PyTorch 1.1.0*... |
e173619a5cb1f24060205ac96e1cdcaba03991792510c9a31d0f3310b929a928 | Text | 10,981 | 130 | # Unpacking the Biology of Psychiatric Genetics using Cell Painting
**Here, we propose to adapt the Cell Painting assay to interrogate traits in neuronal cells, and apply it to a cohort of 48 cell lines carrying the 22q11.2 deletion, a genetic variant strongly associated with psychiatric disease, to test the utility o... |
845fe19c1a4168432ac4d417b703e04b172083159046aa866165dadd5687e0e8 | Text | 11,145 | 297 |
----
[](https://zenodo.org/badge/latestdoi/273074387)
[](https://github.com/ALebrun-108/BoxSERS/blob/master/LICENSE.txt)
[](https://doi.org/10.5281/zenodo.15598540)
This repo is a RNA-seq pipeline that can quantify TERRA expression level from different RNA-seq datasets downloaded from GEO database.
## Description
This pipeline is a combination of various bioinfomatic tools fo... |
3e3799e09335541e7e8a3c5bc9442f20da3e47362691f506f870d68af63b46bb | Text | 11,399 | 307 | # TERRA-QUANT
This repo is a RNA-seq pipeline that can quantify TERRA expression level from different RNA-seq datasets downloaded from GEO database.
## Description
This pipeline is a combination of various bioinfomatic tools for performing reads dump, reads QC, alignment, total gene count and TERRA count. This pipeli... |
b85808c984542b12839f2611af212b4f78926a88f379977f0118e4673f94a31b | Text | 11,476 | 242 | # A 2-compartment poromechanical approach to account for the vascular network in human skin: Theoretical developments and comparison to a *in vivo* Laser Doppler Flowmetry measurement.
This repository contains the codes used to generate the results presented in *Lavigne et al.*[^1]. This paper proposes a proof of conc... |
0de8bc18d350493d179b404c6aececd847f74aa9c92eec8fce3ebd1924db7c92 | Text | 11,524 | 171 | Influences of diet quality, nursery-habitat complexity and sex on brain development and cognitive performance of brown trout (Salmo trutta, L.)
Short summary: In an experiment on captive-raised juvenile brown trout subjected to contrasting low and high long-chain
polyunsaturated fatty acid (LC-PUFA) diets and simp,e ... |
8c5dc91618c2f9609f90b543865fae3d71328d8ac5e0cde5e99252297179faf4 | Text | 11,731 | 292 | <img src="./equiformer.png" width="450px"></img>
## Equiformer - Pytorch (wip)
Implementation of the <a href="https://arxiv.org/abs/2206.11990">Equiformer</a>, SE3/E3 equivariant attention network that reaches new SOTA, and adopted for use by <a href="https://www.biorxiv.org/content/10.1101/2022.10.07.511322v1">EquiF... |
ea4415bc873f8fd763e879018900814e8b37a85989573cd72d9c00ac3c307fac | Text | 11,959 | 157 | # GDP-HMM Challenge at AAPM 2025
[](https://www.aapm.org/GrandChallenge/GDP-HMM/) [](https://qtim-challenges.southcentralus.cloudapp.azure.com/competitions/38/) [
# MedPerf
Medperf is an open benchmarking platform for medical artificial intelligence using Federated Evaluation.
## What's included here
Inside this repo you can find all important pieces for running Me... |
4cd5ef5375e26cb701d8d044f1ca0dfb9110c2d43e0c43b19ee2fc428b31f203 | Text | 12,339 | 208 | # RNA-seq Pipeline
## Contents
- [Overview](#overview)
- [Repo Contents](#repo-contents)
- [System Requirements](#system-requirements)
- [Installation Guide](#installation-guide)
- [Demo](#demo)
- [Instructions for use](#instructions-for-use)
- [License](./LICENSE)
# Overview
This is a Package to perform a typical ... |
c01aec583a8a7b258a433ca7689720547b919f952e101d6aead2a3e8fd0379a4 | Text | 13,127 | 186 | # HuatuoGPT (华佗GPT), Towards Taming Language Models To Be a Doctor.
## ✨ Latest News
- [12/11/2023]: 🎉🎉🎉 Our paper is accepted for EMNLP 2023! Check it out [here](https://aclanthology.org/2023.findings-emnlp.725/).
- [11/25/2023]: We realeased **[HuatuoGPT-II](https://github.com/FreedomIntelligence/HuatuoGPT-II)**,... |
1b1541aad6cce94c57d95239a52d391c6550f312fdab2c666d3824a403ff68e4 | Text | 13,487 | 283 | 
[](https://ww... |
d2bf6bc71b0b83f2d1466a68e2e638236c11735481fe8404e3b06a0ca1c2e9e3 | Text | 13,631 | 150 | # CalciPy: A Python script for processing ratiometric calcium fluorescence data
One of the primary challenges in processing ratiometric data is that the two signals which make up the ratiometric data are actually captured separately, and it is not known which is which. CalciPy processes interlaced calcium fluorescence ... |
c1aa5dd57849b57cd88293e0ddd37348d69710a1a01aac1ac16bd21b6b4db7a6 | Text | 13,734 | 93 |
[](./examples)
[](https://colab.research.google.com/github/genera... |
240550040d9bef1f296d6ff6fb3e779ee6a1344279da5bd27ea5d0ba6f95bbc3 | Text | 13,877 | 171 | # HybriDetector
HybriDetector is an automatic bioinformatics tool for the chimeric interactions detection between variety of noncoding RNAs and their genomic targets. HybriDetector allows to obtain hybrid interactions from binding NGS experiments namely CLASH (crosslinking, ligation and sequencing of hybrids), CLEAR-CL... |
c12efdc2759654840c9b2f8fe1cd9a6716be218b831c27056e13e3ec5cd3d663 | Text | 13,959 | 189 | ## Flickr-Faces-HQ Dataset (FFHQ)
](https://travis-ci.org/biod/sambamba) [](https://anaconda.org/bioconda/sambamba) [](https://github... |
6da2616b4e118fe361deb455a31fb49121885d9f647dff563d7627ba58dc9a43 | Text | 15,647 | 308 | <a id="top"></a>
<div align="center">
<img src="https://github.com/alireza-kr/NuRBiM/raw/main/Files/Numerosity.jpg" alt="NuRBiM banner — a numerosity dot-array display beside a silhouette with an activated brain overlay" width="640">
*A numerosity display (left) and the brain activity it evokes — the two signals this... |
eac0957dcbb5fc215d40cb9abfcc10cc8b10c4972f07fbd0f1b2e6376204062e | Text | 15,679 | 412 | # QTools: Toolbox for training siamese and quartet networks for inferring phylogenetic features
If you are mainly interested in exploring the training results, check out how to use the [Dashboard](#explore-the-results-with-dashboard).
If you want to use the training code start with the [Installation instructions](#in... |
b6c591a763bf99c027857385f0e87ce5aa96caeaa74d71afd1fcec449eadb3d7 | Text | 15,949 | 159 | # MMseqs2: ultra fast and sensitive sequence search and clustering suite
MMseqs2 (Many-against-Many sequence searching) is a software suite to search and cluster huge protein and nucleotide sequence sets. MMseqs2 is free and open source software implemented in C++ for Linux, MacOS, and (as beta version, via cygwin) Win... |
bda7ee80b309bc47c6aa1d420493b2972e1723f7492b353f8189ea579cb6d1c5 | Text | 16,144 | 371 | # DLProv
This project, called DLProv, is part of my DSc research in the Program of Systems and Computer Science (PESC), COPPE, at the Federal University of Rio de Janeiro (UFRJ).
DLProv is a service that evolved from [DNNProv](https://github.com/dbpina/dnnprov). Originally rooted in DNNProv, DLProv has expanded its s... |
3e05b1f0dde58cd2e69f5ada2cf03ca959f884d03ebab44b4f1cf21dc1c4c3df | Text | 16,478 | 262 | <h1 align="center">CHGNet</h1>
<h4 align="center">
[](https://github.com/CederGroupHub/chgnet/actions/workflows/test.yml)
[](https://app.... |
c0564bdf90a8f0e068ad9a635a86eeba51fb20b316ca5236447d879c83450960 | Text | 16,480 | 335 | # YOLOv9
Implementation of paper - [YOLOv9: Learning What You Want to Learn Using Programmable Gradient Information](https://arxiv.org/abs/2402.13616)
[](https://arxiv.org/abs/2402.13616)
[](https://travis-ci.org/ReproNim/containers)
[](h... |
28577acb62f753f9c4ef046b3fa93f0044fb994a209be4682a440ddc3d34c446 | Text | 17,088 | 207 | # PerCell ChIP-seq Pipeline
<br>
<img src="https://github.com/lextallan/PerCell/blob/main/subway.png" width="1250">
<br>
***PerCell ChIP-seq assays and their analysis using our pipeline are expected to generate similar qualitative readouts of protein:DNA interactions or histone modification localization to conventiona... |
e167dfaee05b3f86bdc66929e77c90c6b0a01541248e0981da6bea833949b27a | Text | 17,329 | 432 | # VIRTUS2 : VIRal Transcript Usage Sensor v2.0.2 <img src="https://github.com/yyoshiaki/VIRTUS/raw/master/img/VIRTUS.jpg" width="20%" align="right" />
**!!Note : We updated VIRTUS to version2. In this version, we removed the gene quantification step by Salmon and single virus mode, and added coverage on viral genomes ... |
c2b87610c806cf23926d0b37c6dee41183709d7675ab0111dce35991e4d7e66c | Text | 17,393 | 219 | # Scout - The Liu Lab
Welcome to the Liu Lab’s version of **_Scout_**, a powerful tool for analyzing mass spectrometry data generated from cleavable cross-linking reagents.
P.s.: This Scout version is publicly available but still under active development. Features and documentation may change. Use with caution and c... |
98686cfc241a6803557aa36536ea3f33c026775eed731bfa4f27eff55df24d46 | Text | 17,461 | 326 | # IsoRefiner
IsoRefiner is a refinement tool to identify exon-intron structures of transcript (RNA) isoforms using long reads. It employs multiple transcript-identification tools, filters erroneous structures, merges results from the tools, and constructs the final dataset including novel transcript structures. Its inp... |
781bdb1134a6f24358f0353bfb1cfca80733e2f41cd886395df72ae815ad7807 | Text | 18,059 | 273 | <div align="center">
<img src="https://github.com/AlexanderVNikitin/tsgm/raw/main/docs/_static/logo.png">
</div>
<h3 align="center">
Time Series Generative Modeling (TSGM)
</h3>
<p align="center">
Create and evaluate synthetic time series datasets effortlessly
</p>
<div align="center">
[![Open in Colab](https://col... |
815177cfabb1b4cdbb68c5c0e3454f37d5d2264378f46f3802db103c0a236626 | Text | 18,743 | 281 | <h1><img src="./README_files/icon.cluster.png" align="center" height="120"/> ClusterFoldSimilarity</h1>
Calculate similarities between cell-groups/clusters from any number of independent single-cell experiments, without data integration or batch correction.
### Citation
> Oscar González-Velasco, Malte Simon, Rüstem ... |
5afd970411dac8db4b25cf18fb321769e042fdf5a045cbdb196421bb76aca878 | Text | 19,311 | 304 | # RNA-SeqEZPZ: A Point-and-Click Pipeline for Comprehensive Transcriptomics Analysis with Interactive Visualizations
<br />
<br />
RNA-SeqEZPZ is a pipeline to run analysis of RNA-Seq experiments from raw FASTQ files all the way to differential genes analysis.
The pipeline is accessible through a graphical user interf... |
9a86f69529f405082d582bc1a5ebc16cbdc2689870b052b7b62ced07cd1f013e | Text | 19,627 | 461 | [](https://github.com/ReproNim/containers)
[](https://zenodo.org/badge/latestdoi/182005926)
[ life-cycle workflow analyses. DLProv captures provenance data during the execution and exports provenance graphs for DL model reproducibility.
**This repository provides a Docker container for DLProv, which can be found in step [Running exa... |
2479a704fe57fe53725f871ffacce05db31c763161181d1b85403546443dc122 | Text | 21,129 | 339 | [**中文**](./README.md) | [**English**](./README_en.md)
<p align="center">
<a href="./LICENSE"><img src="https://img.shields.io/badge/license-Apache%202-dfd.svg"></a>
<a href=""><img src="https://img.shields.io/badge/python-3.7+-aff.svg"></a>
<a href=""><img src="https://img.shields.io/badge/os-linux%2C%20wi... |
976260ec33bbbc53676262c609cc79ea36f8e06070359168a57b1329c2e4b16f | Text | 21,447 | 207 | # Deep Learning for Time Series Classification
This is the companion repository for [our paper](https://link.springer.com/article/10.1007%2Fs10618-019-00619-1) titled "Deep learning for time series classification: a review" published in [Data Mining and Knowledge Discovery](https://link.springer.com/journal/10618), als... |
b5a737b8a62e0165343ce90b005d8a8fd400b8bf54dd112462e9eee232ca149a | Text | 24,643 | 566 | # Battenberg
This repository contains code for the whole genome sequencing subclonal copy number caller Battenberg, as described in [Nik-Zainal, Van Loo, Wedge, et al. (2012), Cell](https://www.ncbi.nlm.nih.gov/pubmed/22608083).
## Installation instructions
The instructions below will install the latest stable Batte... |
b06e6edb4cf6cb44d036ac0188336da67358cb3c844450c8b3052b6e3d13bdd0 | Text | 24,796 | 270 | # CHISEL <br/> <sub><u>C</u>opy-number <u>H</u>aplotype <u>I</u>nference in <u>S</u>ingle-cell by <u>E</u>volutionary <u>L</u>inks</sub> #
CHISEL is an algorithm to infer allele- and haplotype-specific copy numbers in individual cells from low-coverage single-cell DNA sequencing data (e.g., those generated by Direct L... |
3327fa0aed817726a9447542aaadc73309b9e9507de7f5a4c27ff7535de0b30f | Text | 24,861 | 237 | # EmoEEG-MC: A Multi-Context Emotional EEG Dataset for Cross-Context Emotion Decoding
## Abstract
EEG-basedemotion decoding is essential for unveiling neural mechanisms underlying emotion and enabling artificial intelligence to understand human emotions. However, existing datasets for EEG-based emotion decoding a... |
28878eab8405acca90bc0720a653cd2ae612b7c32b02bf0d599128e6cbf7d5b2 | Text | 26,159 | 420 | <div align="center">
<img src="resources/mmseg-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... |
ec5c1cb5f47391ac9ddfc81f0e981d526992ed2e20937e9cfdab7394b80bc1b2 | Text | 26,421 | 207 | # FreeSolv: Experimental and Calculated Small Molecule Hydration Free Energies
This repository provides an issue tracker and revision control for the FreeSolv
database, initially described in JCAMD (10): http://dx.doi.org/10.1007/s10822-014-9747-x. If you find any issues, please raise an issue in the issue tracker or... |
21a552743f92c5861c787eec4aa0187095eb6727bba1315d91db0f1ef2ba3ab7 | Text | 28,171 | 245 | # Clonal_hematopoiesis
This repository contains code to reproduce analysis in Körber et al., Detecting and quantifying clonal selection in somatic stem cells. It consists of the following parts:
- [Before you start](#before-you-start)
This section gives an overview of the software and data used for the analysis.
- [... |
c37072919507ea0465e63f574fdfb9f6085a80a4ff51252c8dfe2c4ff332b3c9 | Text | 30,985 | 299 | <!--- SPDX-License-Identifier: Apache-2.0 -->
> **Deprecation Notice**: We sincerely thank the community for participating in the ONNX Model Zoo effort. As the machine learning ecosystem has evolved, much of the novel model sharing has successfully transitioned to Hugging Face, which maintains a vibrant and healthy st... |
c725da2f8f60a47ee1d765dee2d6ab349cd9c971112df3b39430a63f3e0bb595 | Text | 34,482 | 307 | # TTCP CAGE Challenge 4: Challenge Details
## Published Results
The results of this challenge were published at the 39th Annual AAAI Conference on Artificial Intelligence [Exploring the Efficacy of... |
5167adf4f62b4092f3a42d86e7650350bce9f95164c8f6bb599495ad4fa80ad1 | Text | 36,765 | 258 | # BUSCO_Phylogenomics
[](http://bioconda.github.io/recipes/busco_phylogenomics/README.html)
[Jamie McGowan, 2026](https://jamiemcgowan.ie)
This is a simple, easy-to-use pipeline to construct species phylogenies... |
4a622aeb68ac67a837a99be9d2f789ae5b73680624b43d5fc491d4bf8f2deffe | Text | 36,960 | 470 | # **README on Retinotopy**
<div align="right">
Created : "2013-11-25 10:25:05 ban"<br>
Last Update: "2023-10-26 16:21:43 ban"
</div>
<br>
<div align="center">
<img src="https://img.shields.io/badge/LANGUAGE-MATLAB-brightgreen" />
<img src="https://img.shields.io/badge/DEPENDENCY-Psychtoolbox3-green" />
<img src="h... |
8cb59ddecae46c848e162ca2551724700c61e172ba002651a59b514283b61ba2 | Text | 39,756 | 950 | #############################################################################################
``cwltool``: The reference implementation of the Common Workflow Language standards
#############################################################################################
|Linux Status| |Coverage Status| |Docs Status|
... |
d898ace6b070dfd921e045ff2927571aab56c9f23c42837a19e7502a7af76dde | Text | 78,090 | 1,135 | # MetaWIBELE User Manual
**MetaWIBELE** (**W**orkflow to **I**dentify novel **B**ioactive **Ele**ments in the microbiome) is a workflow to efficiently and systematically identify and prioritize potentially bioactive (and often uncharacterized) gene products in microbial communities. It prioritizes candidate gene produ... |
93e5707a7a3d648cdf1eb1a01c254e6ac1fdad55ca26fb8353cdb88ae66eb769 | TypeScript | 30 | 1 | export const prerender = true
|
4efb7c7f2fc0d15fe4038288fbbcebb422b08798b8a27f9c6cacacd621400a13 | TypeScript | 108 | 2 | export const composeRoomAddress = (ownerId: string, roomName: string): string =>
`${ownerId}/${roomName}`;
|
dbe312eaf66878b14554f57dfcdf980e9c87086e64d2b23f2865a120252bf757 | TypeScript | 135 | 5 | /// <reference types="@sveltejs/kit" />
/// <reference types="mdsvex/globals" />
declare module '*.md'
declare module '*package.json'
|
679b4d3f44385759870f2c95acdff1ab3a2be3aa2404b04a2f1fad53348f11ad | TypeScript | 190 | 6 | import { keyframes } from "@mui/system";
export const shimmer = keyframes`
0%, 100% { background-color: rgba(25, 118, 210, 0.12); }
50% { background-color: rgba(25, 118, 210, 0.28); }
`;
|
184c832302ef0ed5ebefa9da0b3c9205d653da88ea0b315922e4b464e6a48929 | TypeScript | 202 | 4 | export { FilesystemSelector } from "./FilesystemSelector";
export { FileBreadcrumbs } from "./FileBreadcrumbs";
export { FileList } from "./FileList";
export { LoadFileDialog } from "./LoadFileDialog";
|
047df4c42cf16c56470f9cc22ad26b36f21e6881d93c48926d5e014a51d23466 | TypeScript | 283 | 15 | import { sveltekit } from '@sveltejs/kit/vite'
import type { UserConfig } from 'vite'
export default {
plugins: [sveltekit()],
server: {
fs: { allow: [`../..`] }, // needed to import from $root
port: 3000,
},
preview: {
port: 3000,
},
} satisfies UserConfig
|
fa8f38426343de152a3fc58289ada10d112601b1f8f1a1d954b438a6b7552496 | TypeScript | 292 | 3 | /** File extensions accepted for trajectory upload. */
export const TRAJECTORY_ACCEPT =
".xyz,.extxyz,.pdb,.cif,.h5,.h5md,.hdf5,.gro,.mol,.sdf,.db,.json,.traj,.nc,.car,.xsf,.cube,.vasp,.poscar,.contcar,.xdatcar,.outcar,.xml,.pwi,.pwo,.out,.castep,.cell,.geom,.md,.gjf,.com,.log,.arc,.dmol";
|
4804189c196180792ba3ace1536472fbaafc44a9f2dc231eb4d3ca5b1f5a7f4f | TypeScript | 304 | 12 | import type { DockviewApi } from "dockview-react";
import { create } from "zustand";
interface DockviewApiStore {
api: DockviewApi | null;
setApi: (api: DockviewApi | null) => void;
}
export const useDockviewApi = create<DockviewApiStore>((set) => ({
api: null,
setApi: (api) => set({ api }),
}));
|
7b255a245f24155dc37eca759a70a60921018bf952faa75a8ca62390483b12d7 | TypeScript | 311 | 10 | import { useFilesystemProviders } from "./useFilesystemProviders";
/**
* Returns ``true`` when the current room has at least one provider of
* category ``"filesystem"``.
*/
export function useHasFilesystemProviders(): boolean {
const { data } = useFilesystemProviders();
return (data?.length ?? 0) > 0;
}
|
effef851313f6875a3bc51ea3e2f2105002d8eeb740d6529c23bbd775372ee26 | TypeScript | 315 | 10 | export { ActivityBar } from "./ActivityBar";
export { BottomZone } from "./BottomZone";
export {
DockviewLayout,
ensureViewerPanel,
resetDockview,
} from "./DockviewLayout";
export type { BarPosition, PanelId } from "./registry";
export { PANELS } from "./registry";
export { SidebarZone } from "./SidebarZone";
|
e45769fe53f08bee4c70a39e26471c7fcd7765619e6beb6229a7c525c977f85e | TypeScript | 320 | 9 | /** Returns true when focus is on an input element where shortcuts should not fire. */
export function isInputFocused(target: EventTarget | null): boolean {
if (!(target instanceof HTMLElement)) return false;
return (
target.tagName === "INPUT" ||
target.tagName === "TEXTAREA" ||
target.isContentEditable
);
}
|
1f2b5d97b51a94ea9a6ecd79aafa137b8fefc5fbaf6e1a1a497262fae3cbf9d1 | TypeScript | 324 | 17 | // Generated by `bun init`
declare module "*.svg" {
/**
* A path to the SVG file
*/
const path: `${string}.svg`;
export = path;
}
declare module "*.module.css" {
/**
* A record of class names to their corresponding CSS module classes
*/
const classes: { readonly [key: string]: string };
export = classes... |
e30b9cff9670a3b507a356b48de8697c0cbfc0178f7275e5418c98e27b3a9a1b | TypeScript | 521 | 23 | import { defineConfig } from "@playwright/test";
export default defineConfig({
testDir: "./e2e",
timeout: 90_000,
expect: { timeout: 15_000 },
fullyParallel: true,
workers: 4,
retries: 0,
reporter: [["html", { open: "never" }]],
use: {
baseURL: process.env.ZNDRAW_URL || "http://localhost:8000",
screenshot:... |
b2d2660189bb0677b5304802bd99fe5967d32881e402b74e49278e342b3fc03b | TypeScript | 539 | 22 | /**
* Validate a room ID for creation/duplication.
* Returns an error message string, or null if valid.
*/
export function validateRoomId(
roomIdToCheck: string,
existingIds: string[],
): string | null {
if (!roomIdToCheck) {
return null; // Empty means auto-generate, which is valid
}
if (existingIds.include... |
9a0da87da997cf63079cb41028257a168693c6f87a4dc93eba7f9e2b6fe0add1 | TypeScript | 566 | 23 | import type { StateCreator } from "zustand";
import type { AppState } from "../../store";
export interface ExtensionFormSlice {
selectedExtensions: Record<string, string | null>;
setSelectedExtension: (category: string, extension: string | null) => void;
}
export const createExtensionFormSlice: StateCreator<
AppSt... |
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