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15870e1f6f05ef75f3c602dcf116439d5254f8d468e8d08d6f6ec8af471e6802 | Text | 7,822 | 135 | # alsf-scpca
Management and analysis tools for ALSF Single-cell Pediatric Cancer Atlas data.
- [Environment Setup](#environment-setup)
- [Nextflow](#nextflow)
- [Installing Nextflow](#installing-nextflow)
- [Nextflow Tower](#nextflow-tower)
- [Docker](#docker)
- [AWS](#aws)
- [Installing AWS Command ... |
34856b1a5ee471f0c03390636b71510175cf7df2917b653d4a854c21edd0c833 | Text | 7,863 | 140 | # DELiVR: A VR enabled, deep learning based cFos inference pipeline
<figcaption class="caption">Overview of the complete DELIVR protocol. This repository covers all the neccessary steps for inference.</figcaption>
## Table of contents
- ... |
2a23d7ffa3fb0746dd041823f2e86ca90a32e16cd7cff887eb7dbe99852266d2 | Text | 7,918 | 161 | Parsing-RepeatMasker-Outputs => parseRM
========================================================
Last update: 2017 Oct 18
Of interest if you are using the software RepeatMasker,
for transposable elements (TEs) annotation [see http://www.repeatmasker.org/].
This is a collection of perl scripts I wrote for me and my ... |
bbda5ebe9c1926f0c0cad7b741dd5bb33ee5e5f801f746906a4eccb09a99e0c5 | Text | 7,946 | 113 | # Kilosort4
[](https://kilosort.readthedocs.io/en/latest/?badge=latest)
[](https:... |
972012e898dd91dc9fb704ee0a4ab4db7a9c0c0669e018c08dc0c04638217e85 | Text | 7,962 | 118 | # Orbital-Graph-Convolutional-Neural-Network
OGCNN
This is the repository for our work on property prediction for crystals. In this work we have used ideas from the Orbital Field matrix and Crystal Graph Convolutional Neural Network to predict material properties with a higher accuracy.
Paper link:https://journals.aps.... |
7f82ff451aa8e956af5fb2feac3356f53f9dc14f2b66a193af5e92582de85613 | Text | 7,964 | 168 | ## SVision-pro
SVision-pro detects germline, de novo and somatic structural variants (SV), including simple SV (SSV) and complex SV (CSV).
Both long reads from HiFi or other technologies, and genome assemblies are acceptable.
SVision-pro implements genome-to-genome representation and comparative SV detection, genot... |
70423322662f7786f36b90fded7754692b01e6281d9831969e82d914d7ec120e | Text | 8,005 | 272 | # Predation without Direction Selectivity - Analysis Code
This repository contains the analysis code (Python and MATLAB) supporting the publication:
**Krizan et al., "Predation without direction selectivity", PNAS, 2024**
The code analyzes multi-modal neuroscience data investigating whether direction-selective neura... |
3327a67736e6e4b58bca74dee84d6e3ed0f58e14a8e12aa3bc5937e03702eb7a | Text | 8,221 | 39 | # Whole-brain turbulent-like dynamics and Hopf computational model
Code used in Martínez-Molina et al. 2024 "The evolution of whole-brain turbulent dynamics during recovery from traumatic brain injury" (Network Neuroscience).
Data was downloaded from the Open Neuro repository (https://openneuro.org/datasets/ds000220... |
44b0b90defc0b958d1890b190e67c0a6324c3ba98fe6bf28bfdb0ec35333e01b | Text | 8,351 | 151 | [](https://pypi.org/project/MiniSom/)
[](https://pepy.tech/project/MiniSom)
[![Python package](https... |
d217743c0d1fc7e75512d4e1fa646f3cada436221b9897aea523c049aace4138 | Text | 8,564 | 135 | # SeeElegans
For detailed information and insights about this software, please refer to our accompanying article "See Elegans: simple-to-use, accurate, and automatic 3D
detection of neural activity from densely packed neurons".
Requirements:
This software runs on MATLAB and requires the "Image Processing Toolbox"... |
4a775905a6654d8034bf7c53eb07934fded695af581c2e97fd711a9227574bca | Text | 8,598 | 155 |
# Signature reversion of three disease-associated gene signatures prioritizes cancer drug repurposing candidates
Background:
New therapeutic options are critical to increased cancer patient survival. Drug repurposing is promising, as approving a drug for a new indication requires less time and cost than for a new d... |
67ba0b9d79c737e77b58bf9a95606f6f26f91278252f26adce563d9cadbe56fa | Text | 8,601 | 233 | # Generating novel protein sequences using Gibbs sampling of masked language models
This repo was used to generate sequences from ESM-MSA in work described in work published in Nature Biotechnology: [Computational Scoring and Experimental Evaluation of Enzymes Generated by Neural Networks](https://doi.org/10.1038/s415... |
3317dd7d5dc0d6cde5e6565119d715510f156b68f85cbec7580e02d76442e73c | Text | 8,647 | 139 | # CELLECT
**CELL**-type **E**xpression-specific integration for **C**omplex **T**raits (**CELLECT**) is a computational toolkit for identifing likely etiologic cell-types underlying complex traits. CELLECT leverages existing genetic prioritization models to integrate single-cell transcriptomic and human genetic data ... |
b0b0af2cf1c059df6ee65de68f73bc136f6b8d8d6973136507f1a35f83db88bc | Text | 8,659 | 206 |
# bbbPythoN
**License:** [CC BY-NC-ND 4.0](https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode)
### Table of Contents
1. [Overview](#overview)
2. [Installation](#installation)
3. [Functionalities](#functionalities)
4. [Examples](#examples)
5. [Folders and Files](#foldersandfiles)
## Overview <a name="over... |
ef0d94b64050385b41db58d0484372abd119d54549d3331bda0d2ac8ffabad7d | Text | 8,764 | 200 | # txci-ATAC-seq
This pipeline is used for processing txci-ATAC-seq data, including removing Tn5 barcode (8bp) from Read 2 and appending it to the header, correcting barcodes, removing sequence adapters, and aligning, filtering, and deduplicating reads, and generating species-specific read count report for mixed species... |
69daee36815b72fd006bd6901f1505bf0d5742da68de6c78be50197e3732d1eb | Text | 8,817 | 197 | # GRUFFI
#### _Published in [Gruffi: an algorithm for computational removal of stressed cells from brain organoid transcriptomic datasets](https://www.embopress.org/doi/full/10.15252/embj.2022111118)_
The Gruffi... |
d01eec023eb13e44a4c441becd71ba4988b0b08c109d795871b0a9927719af4b | Text | 8,829 | 140 | # Chromosight
<img src="docs/logo/chromosight.gif" alt="animated logo" width="200"/>
[](https://badge.fury.io/py/chromosight) [](http://bioconda.github.io/re... |
69ba04b16fd79f8b6eaa73adf351e83e08ad4f9d4a8d9f27a889c148a0f08bcb | Text | 9,021 | 157 | <img src="https://assets.cloud.pennylane.ai/pennylane_website/spotlights/Spotlight_PLSurvey_2024-03-05.png"
width="200px"
align="left" />
Share your voice in the 2026 Unitary Foundation Survey to guide where open-source quantum software goes next (closes October 29, 2026). [Take the survey →](https://bit.ly/... |
a2ece66f0fc7101e998468c1ebee9db4c8284c544a305c023cb3c1fad48f7ee7 | Text | 9,041 | 191 |
<div align="center">
<h1 align="center">RC-MVSNet: Unsupervised Multi-View Stereo with Neural Rendering</h1>
<p align="center">
<a href="https://boese0601.github.io">Di Chang</a><sup>1</sup>,
<a href=https://aljazbozic.github.io/ target=_blank rel=noopener>Aljaž Božič</a><sup>1</sup>,
<a href="https://... |
ba05ced3260cf9ab45c07a3a8cb1dcf542e8d39dcab206e1de04d2b3d2ba5924 | Text | 9,064 | 133 | # Tractify Pipeline
### About
Tractify is an efficient and reproducible tractography pipeline built with [Nipype](https://nipype.readthedocs.io/en/latest/). This allows anyone to get started with tractogra... |
2f7ff7732764a2022c9b5a720b3d92ab0bfbaa52863fd360dfed975d4a8cd3bf | Text | 9,082 | 222 | ## EquiPNAS: improved protein-nucleic acid binding site prediction using protein-language-model-informed equivariant deep graph neural networks
by Rahmatullah Roche, Bernard Moussad, Md Hossain Shuvo, Sumit Tarafder, and Debswapna Bhattacharya
published in [Nucleic Acids Research](https://doi.org/10.1093/nar/gkae039)... |
f9dbc39ea3b9ae45fe6a097236b428d520b199c779e5015f97c116b7fdbb7204 | Text | 9,118 | 154 | # Continuous-Time Deconvolutional Regression (CDR)
In many real world time series, events trigger "ripples" in a dependent variable that unfold slowly and overlap in time (temporal diffusion).
Recovering the underlying dynamics of temporally diffuse effects is challenging when events and/or responses occur at irregula... |
20598a07e5f81f1d85edaedba49b07b59d666c4ee31cc1df5e52fbf4079485a1 | Text | 9,210 | 156 | # web-h5j-loader
[](https://zenodo.org/doi/10.5281/zenodo.6772505)
## Summary
This module provides JavaScript functions to load data from files in [H5J format](https://github.com/JaneliaSciComp/workstation/blob/master/docs/H5JFileFormat.md). A H5J file is an [HDF5 conta... |
fb2cb47f031616e1d2f8574c0c417d6596d3583f9f16e2ed2bb99603e0bdc7d3 | Text | 9,223 | 128 | # DeeperGATGNN
Github repository for our paper - **"Scalable Deeper Graph Neural Networks for High-performance Materials Property Prediction"** [PDF](https://www.cell.com/patterns/pdfExtended/S2666-3899(22)00076-9). Now published in Patterns:
Omee, Sadman Sadeed, Steph-Yves Louis, Nihang Fu, Lai Wei, Sourin Dey, Rongzh... |
ae1e48cba3058fc960e209724c68d9168fe5150f5e8297a9a3853e70d971b1da | Text | 9,295 | 160 | [](https://github.com/debbiemarkslab/EVcouplings/actions) [](https://badge.fury.io/py/evcouplings)
# EVcouplings
Predict protein struc... |
8aa2a07d8e36369b9bcae3b9694d80b785230cd33e6314708f6f9026d74e7572 | Text | 9,327 | 148 | <h1>
<picture>
<source media="(prefers-color-scheme: dark)" srcset="docs/images/nf-core-hadge_logo_dark.png">
<img alt="nf-core/hadge" src="docs/images/nf-core-hadge_logo_light.png">
</picture>
</h1>
[. It adds stratification by ancestry/sex, genotype-by-sex interactions, dynamic Miami Plots, a real API, and many other improvements.**
---
For a list of available instances of PheWeb, navigate [here](http://pheweb.sph.umi... |
0e14498d00aab8868248e1c4cfbbf375c4c4e0a5fe364f4dba791f0842a97d90 | Text | 9,391 | 156 | # StellarPath: patient classifier <img src="https://raw.githubusercontent.com/LucaGiudice/supplementary-files/main/sp/Logo.png" width=350 align="right" />
## Brief description
StellarPath is a deep learning patient classifier which leverages state-of-the-art bioinformatics techniques to select biologically meaningful... |
0f6b774942f96f5bc6c49e7fa027bc0f9d46f86b1a683f852d674dbfcabd0316 | Text | 9,706 | 177 | # a GP-GCN framework for genomics
This is a python package for genomics study with a GP-GCN (Gapped Pattern Graph Convolutional Networks) framework.
# Getting started
## Prerequisite
+ cython
+ numpy
+ Biopython
+ editdistance
+ pytorch ... |
19e0814e60da853300519e978a1f7cbe6cbf811f4a1a728538d942fff6ffc9b7 | Text | 9,706 | 95 | Single-cell Interpretation via Multi-kernel LeaRning (**SIMLR**)
================================================================
| Branch | Status |
| --- | --- |
| master | [](https://github.com/Bat... |
5b4c45fb43fef30e70a868b2c6f557d0f4a3ad94234d9b7884cac9c5228e51c1 | Text | 9,789 | 158 | # Dev-ResNet
## Introduction
A novel network for automating the detection of developmental events, specifically applied here to embryonic stages of the aquatic snail, *Lymnaea stagnalis*. We supply training, evaluation an... |
6410b9f521927a92d37c1487abd9d323b2822926f7fa359ad7df7049ba158e04 | Text | 9,839 | 135 | # scSplit
### Genotype-free demultiplexing of pooled single-cell RNA-seq, using a hidden state model for identifying genetically distinct samples within a mixed population.
#### It has been tested on up to 8 real mixed samples.
### To cite the package:
Xu, J., Falconer, C., Nguyen, Q. et al. Genotype-free demultiple... |
df02ceadd1fc26ea4070da7c3e6a3fbc390c77869e1271a73c11234aad99beb3 | Text | 9,945 | 130 | # COVIDx-US: An open-access benchmark dataset of ultrasound imaging data for AI-driven COVID-19 analytics
The COVID-19 pandemic continues to have a devastating effect on the health and well-being of the global population. Apart from the global health crises, the pandemic has also caused significant economic and financ... |
172b63a43db1e6faebe697fb838a44e3c97aef92b4ca6816d03d10960ee949bf | Text | 9,986 | 197 | ## BASALT - Binning Across a Series of AssembLies Toolkit
BASALT is a versatile toolkit that recovers, compares and optimizes MAGs across a series of assemblies assembled from short-read, long-read or hybrid strategies. Firstly, BASALT uses high-throughput assembly methods to automatically assemble/co-assemble multipl... |
1a71e1a4d8f977f9fe1c1870a875cd4e7d5a3dcbab5992ed09309fa12f795f07 | Text | 10,033 | 161 | <picture align="center">
<source media="(prefers-color-scheme: dark)" srcset="https://pandas.pydata.org/static/img/pandas_white.svg">
<img alt="Pandas Logo" src="https://pandas.pydata.org/static/img/pandas.svg">
</picture>
-----------------
# pandas: A Powerful Python Data Analysis Toolkit
| | |
| --- | --- |
| ... |
ba623aae449ad9db881f81b157c1b98868646e00158042c0b8127ba11a4ef1f7 | Text | 10,078 | 228 | # Real-Time Brain-to-Brain Synchrony Estimation Algorithm
**Implementation of a Real-Time Brain-to-Brain Synchrony Estimation Algorithm for Neuroeducation Applications**
*Mendoza-Armenta et al., Sensors (2024), 24(6): 1776* :contentReference[oaicite:0]{index=0}
---
## Overview
This repository hosts a Python-base... |
42a71d7fcea23c1bf705b732b77dc57161ff9d2f2a6ae34a347bbcba4f00c06e | Text | 10,131 | 151 | # EPG-X
An Extended Phase Graph (EPG) approach for modelling of MRI sequences for systems with Magnetization Transfer or Exchange
The EPG algorithm is extended to coupled exchanging systems that are:
1. governed by the Bloch-McConnell equations (BM) or
2. described by the 'binary spin bath' model for pulsed magnetiza... |
e94c579077f78bfbfc808e80e44503873499afee964840edb191289ef1b2c4cd | Text | 10,169 | 159 | # Artificial Cerebellum on an FPGA
![langage][langage-shield] ![target][target-shield] ![environment][environment-shield] ![license][license-shield]
## Overview
This repository is a real-time adaptive controller using a realistic cerebellar spiking neural network model on an FPGA. It is published in [Y. Shinji, ... |
9449498b0ad195675eda5dcb0dafe1e924157e6e6885f0cffd42d53b63eb8456 | Text | 10,206 | 176 | # Predicting Which Patients with Cancer Patients will see a Psychiatrist or Counsellor from their Initial Oncology Consultation Document Using Natural Language Processing
By John-Jose Nunez, on behalf of the co-authors
## Overview
For the manuscript "Predicting Which Cancer Patients Will See a Psychiatrist or Counse... |
8d59008732430057fa63774113785c0b30ce5aac84d49fbc98d127f8856aa9ef | Text | 10,249 | 124 |
## Disclaimer
This material was prepared as an account of work sponsored by an agency of the United States Government. Neither the United States Government nor the United States Department of Energy, nor Battelle, nor any of their employees, nor any jurisdiction or organization that has cooperated in the development... |
4bbe490560b1e9469ad12ad69628e4055f92b8802c5fa4938b58402b2cc62951 | Text | 10,282 | 224 |
[![Version][version-shield]][version-url]
[![Python versions][python-shield]][python-url]
[![Platforms][platform-shield]][python-url]
# CHANGE-seq: Circularization for High-throughput Analysis Nuclease Genome-wide Effects by Sequencing
This is a repository for CHANGE-seq analytical software, which takes sample-spe... |
1b0536646ad198b825c21f9e1d50a23f69b1a7e9756f556cb50b791b1eda8b30 | Text | 10,297 | 179 | # Prospective de novo drug design with deep interactome learning
[](https://www.python.org)
[](https://pytorch.org)
[ are: pre-release versions, **not necessarily ISO compliant**, intended for Res... |
588afa8b0618f459515453bfcc1cba5293cc3a56ce8d3c2cc8605d6ea9d690d7 | Text | 10,989 | 115 | [](https://zenodo.org/doi/10.5281/zenodo.10145352)
# Cortical spike synchrony as a measure of Gestalt structure
This repository contains the code used for the publication Cortical spike synchrony as a measure of Gestalt structure: link.
It includes all scripts used to crea... |
c43c7491bf9a31d43b685e2d728139f4acb09a7016c38e565d31c98f3653ee41 | Text | 10,992 | 102 | Repository for the software that implements the AGRN model described in
# Neural network model of cell differentiation on Waddingtonian landscapes
Mátyás Paczkó<sup>1,2,* </sup>, Dániel Vörös<sup>1,2,* </sup>, Péter Szabó<sup>1</sup>, Gáspár Jékely<sup>3</sup>, Eörs Szathmáry<sup>1,4,5</sup>, András Szilágyi<sup>1</s... |
eca3d1fff0ce8e02515d645512d29c05af08a4edeff2d8ad3e79e19e605f1b23 | Text | 11,067 | 197 | <div align="center">
<img src="docs/images/logo.png" alt="PyCaret" width="200"/>
# PyCaret — open-source self-hosted ML platform
### The engine, the control plane, and the UI — all in one box.
[](https://github.com/pycaret/pyc... |
dde8e04873cbdb379a8c02fe145363f882a88ab065b606a8bf15c95eda73376c | Text | 11,091 | 200 | # Tetris-inspired Detector with Neural Network for Radiation Mapping
In recent years, radiation mapping has attracted widespread research attention and increased public concerns on environmental monitoring. In terms of both materials and their configurations, radiation detectors have been developed to locate the direc... |
8318b921474d3de5d815e0ffa32f8d7b4bb70e252022939a90403aa50d0b148a | Text | 11,096 | 104 | [](https://zenodo.org/doi/10.5281/zenodo.10556584)
Repository for the software that implements the AGRN model described in
# A neural network-based model framework for cell-fate decisions and development
Mátyás Paczkó<sup>1,2,* </sup>, Dániel Vörös<sup>1,2,* </sup>, Péte... |
5c63b18d017b2200be7474166621177a311f461a9a5cf15813b865bacb4f2b9b | Text | 11,348 | 188 | <picture align="center">
<source media="(prefers-color-scheme: dark)" srcset="https://pandas.pydata.org/static/img/pandas_white.svg">
<img alt="Pandas Logo" src="https://pandas.pydata.org/static/img/pandas.svg">
</picture>
-----------------
# pandas: A Powerful Python Data Analysis Toolkit
| | |
| --- | --- |
| ... |
5b7f4b0bc9832db96ec13118a016d3719e286b23a421cdc9a5793e5b445422b2 | Text | 11,441 | 157 | # Functions to work with fibration symmetries.
Author: **Ian Leifer, Levich Institute and Physics Department, City College of New York, New York, NY 10031**
Advisor: **Hernan Makse, Levich Institute and Physics Department, City College of New York, New York, NY 10031**
Contact ianleifer93@gmail.com with any question... |
926c2bcb8ff6ea9af2fdb50aa4bbf175bb03cb9a48b73f5c9aab083caeba4b0a | Text | 11,463 | 254 | 
<p align="center">
<a href="https://hspark1212.github.io/MOFTransformer/">
<img alt="Docs" src="https://img.shields.io/badge/Docs-v2.2.0-brightgreen.svg?style=plastic">
</a>
<a href="https://pypi.org/project/mo... |
3ef619f4b377e46d7ec0e17c58342193d3ccd154e598cac8efa7a5c70fe1e609 | Text | 11,972 | 116 | # Sample code for: Control of working memory maintenance by theta-gamma phase amplitude coupling of human hippocampal neurons
[](https://opensource.org/licenses/BSD-3-Clause)
[... |
aa27202f2a34e0f1275a2351f4bed4fdc1963c2c26304c46b297548232878983 | Text | 12,099 | 116 | # Sample code for: Control of working memory by phase–amplitude coupling of human hippocampal neurons
[](https://opensource.org/licenses/BSD-3-Clause)
[](https://github.com/rut... |
19dff72ff03cb656930fb345758803eaffd73cddcab33cdfd30257c71edd4ed8 | Text | 12,112 | 471 | Pianno: a probabilistic framework automating semantic annotation for spatial transcriptomics
------
`pianno` is a Python package that automatically annotates the biological identity of spots in spatial transcriptomics based on marker genes.
[TOC]
# System Requirements
## Hardware Requirements
`pianno` package re... |
921f88e3ef672bf6ee5863c4c11549071940887d20bee4af7eafe328dde506d4 | Text | 12,200 | 231 | # DrugCell: a visible neural network model for drug response prediction
DrugCell is an interpretable neural network-based model that predicts
cell response to a wide range of drugs. Unlike fully-connected neural networks,
connectivity of neurons in the DrugCell mirrors a
biological hierarchy (e.g. Gene Ontology), so... |
b4af905c74cb0ed2fb279d5be1446b698c567f89c33d770eaa6f15259915d571 | Text | 12,357 | 222 | # cDNA_Cupcake
Last Updated: 08.23.2022
**MAJOR UPDATE (08/23/2022)!!!** With many of the core Cupcake functions now moving into official [isoseq](https://isoseq.how) software, including support for bulk and single-cell Iso-Seq data... |
9404cee144b9c441100025b03d90656bf0d4e68a455086c1887c24eab0a6829a | Text | 12,433 | 120 | Dataset release for "Cataract-1K: Cataract Surgery Dataset for Scene Segmentation, Phase Recognition, and Irregularity Detection"
=================================================================================================================================
The [Cataract-1K](https://arxiv.org/pdf/2312.06295.pdf) dat... |
cb4c7d2e7514c17752822bc7e17acfc8ebceb8a024aafc4c1017ff3293102d93 | Text | 12,561 | 301 | .. image:: https://raw.githubusercontent.com/pyxu-org/pyxu/master/doc/_static/wide-logo.png
:target: https://pyxu-org.github.io/
:alt: Pyxu logo
Pyxu: Modular and Scalable Computational Imaging
================================================
.. image:: https://img.shields.io/badge/Documentation-View-blue
:t... |
fa88532b9d4edc4a618f6a8bfa287fd27e6541003f1eaf4d5fcc196b332adb42 | Text | 12,576 | 217 | [](https://travis-ci.org/jdidion/atropos)
[](https://pypi.python.org/pypi/atropos)
[](https://zenodo.org/badge/latestdoi/61393086)
> **⚠️ Archived — use [fast... |
7cbac417bbc26f09ca3fcc3d990a20addb0774e67a15c80a1830d1ef26b4b8f0 | Text | 13,240 | 264 | # FEICP
FEICP (Finding Exon-Intron circular RNAs from paired-end RNA-seq) is for EIciRNAs (Exon-Intron circular RNAs) detection from paired-end RNA-seq.
The whole FEICP pipeline has three main parts:
- **1. Detecting circular RNAs from RNA-seq using BWA and CIRI2**;
- **2. Getting those BSJs (back splicing read... |
eb2ca5cf2a397217eb65803f44f375dd24b4fc99e6ff381e7270fae617dacce2 | Text | 13,348 | 222 | How many times you hoped to easily plot variants in your VCF files in order to operate a fast visual analysis on them?!
It happened to me soo many times...and this is exactly why we created this R package for you! :wink:
Let's take a brief look at how it works
# Install plotVCF
Installing `plotVCF` is as simple as:
`... |
a5d0ea23bce6bcd91dc68ea6ee2e6931b24d7cdfd8d1157e47424c521884df7c | Text | 13,562 | 181 | # Predicting Chemical Reaction Yields
> Predicting the yield of a chemical reaction from a reaction SMILES using Transformers
Artificial intelligence is driving one of the most important revolutions in organic chemistry. Multiple platforms, including tools for reaction prediction and synthesis planning based on machi... |
cf45489a491840ec720abe78331f3cf0c18f756bc5dfe3bf9c45b26d4442ecae | Text | 13,608 | 271 | # Multimodal AD Detection
Code accompanying **"Automated Detection of Alzheimer's Disease: A
Multi-modal Approach With 3D MRI and Amyloid PET"**, published in
[Scientific Reports (2024)](https://www.nature.com/articles/s41598-024-56001-9)
([doi:10.1038/s41598-024-56001-9](https://doi.org/10.1038/s41598-024-56001-9)).
... |
d5f7c37956c5554587fb6395ddc91f015e011cc61ecbba3507a2f3dca990b044 | Text | 14,279 | 270 | # PlateletSubpop-ML-ScTranscriptomics
[](https://doi.org/10.3390/ijms25115941)
[](https://opensource.org/licenses/MIT)
[](https://www.r-p... |
cc150577b96e19594fd9b7ad88c455e37e1fb916e28b3d64ee826fb3bf30a91a | Text | 15,616 | 346 | # Isaac Gym Benchmark Environments
[Website](https://developer.nvidia.com/isaac-gym) | [Technical Paper](https://arxiv.org/abs/2108.10470) | [Videos](https://sites.google.com/view/isaacgym-nvidia)
### About this repository
This repository contains example RL environments for the NVIDIA Isaac Gym high performance en... |
01671a35dce1bc0d101bfe8f48ec067b595e456b701bfa3f60e9286bc1ca4c05 | Text | 15,626 | 205 | # Progres - Protein Graph Embedding Search
[](https://github.com/greener-group/progres/actions)
This repository contains the method from the paper:
- Greener JG and Jamali K. Fast protein structure searching using structure graph embeddi... |
8e277de5982c8c9d0f83d6db387b754703b008238c00983d2af5a1bb43c38899 | Text | 15,752 | 342 | Pytorch modules and utilities for modeling biological sequence data.
Here we will demonstrate the application of several tools we hope will help with modeling biological sequences.
## Installation
```
$ pip install sequence-models
$ pip install git+https://github.com/microsoft/protein-sequence-models.git # ... |
92a08384a58f6bbb1db16ce5cf4434b22bb3e2907086e8c43ec91a58c4501b62 | Text | 15,879 | 409 | TreeShrink is an algorithm for detecting abnormally long branches in one or more phylogenetic trees.
- **Inputs**:
- One or more phylogenetic trees with branch lengths. If more than one, the trees should be on overlapping sets of species (though missing data are allowed).
- Optional: a number `k` ≤ the tota... |
243964232c4709e6e0192a46427dd33fb1ce397adda8ddcaa2548b35efeaffad | Text | 15,898 | 238 | # Microscopy Image Registration
Code to register czi microscopy images or OME.TIF with **python 3**.
This code is optimised at a memory level to be able to reassemble and register (translation + rotation) high resolution images in **ome.tif**. This code can also save the final image in a compressed tiled pyramidal OME... |
cf312e439f3d2edcbe0228fd391282e01cbfc71aa1177a1ae275147b96b94e99 | Text | 16,068 | 232 | # MM2SF
This repository gathers the MM2SF code along with some instructions and README files.
MM2SF is a simple code to create an optimum collection of Atom Centered Symmetry Functions (ACSFs) **[1-2]** for a chemical system. The code uses a Gaussian Mixture Model (GMM) to decompose the characteristic chemical space o... |
e66a897d2567d50b530bb5e639a584c74b05e6acecf130384754290e07719710 | Text | 17,186 | 443 | # NeSVoR: **Ne**ural **S**lice-to-**Vo**lume **R**econstruction
<p align="left">
<a href="https://github.com/daviddmc/NeSVoR/releases" alt="releases">
<img src="https://img.shields.io/github/v/release/daviddmc/NeSVoR?display_name=tag" />
</a>
<a href="https://hub.docker.com/r/junshenxu/nesvor/tags" alt="dock... |
298aec37dbc245ee3426671165033737e21962df023dddc67c97173036a1f760 | Text | 17,502 | 219 | # Connectivity Matrices
Run `cifti_conn_wrapper.py` to generate correlation matrices from BOLD dense or parcellated time series data.
## Prerequisites
### Installation
Clone this repository and save it somewhere on the Linux system that you want to use it from.
### Dependencies
- [Python v3.5.2](https://www.python... |
412a7e3569dba17af660b8e278623f57d37ee049ba1027a7176ab07e951ee3e6 | Text | 17,590 | 163 | # disc-pg-gan
This software can be used to train a discriminator to detect selection in real population genetic data, assess the strength of this ability, and make predictions on the possibility of selection in new data.
Python 3.6 (or later) is required, along with the following libraries (these exact versions a... |
f9e93b6ae307bfabf4789e2f47bb7631c5960e80f739a9270a00bd5bae5e0afd | Text | 17,832 | 286 | # Application for Big Computational Data (ABCD) Specification (v1.1)
#### MIT Copyright (c) 2020 brainlife.io The University of Texas at Austin and Indiana University
### Authors
- Soichi Hayashi (hayashis@iu.edu)
### Contributors
- Franco Pestilli (pestilli@utexas.edu)
### Funding Acknowledgement
brainlife.io is p... |
fc91d76be322661914b7c1f93f6e349bddfce14d6861b0e0ea3844abf4a658c6 | Text | 17,875 | 592 |
`pymatch`
=====
Matching techniques for observational studies. Inspired by and adapted from Jasjeet Singh Sekhon's [Matching](https://cran.r-project.org/web/packages/Matching/Matching.pdf) package in R. I wrote an adaptation in Python that is better suited for my work at Mozilla which incorporates:
* Integration wit... |
e39c79eacf4175469016a90db17c7cdab86fcbb9d65fd7a4bd141cca476b4325 | Text | 17,977 | 210 | # GenoFLU classification for H5N1 HPAI 2.3.4.4b viruses in North American flyways
[](https://github.com/USDA-VS/GenoFLU)
[]()
[](https://anacon... |
73366f9cde9c5bd434e8919ac6862a984a7d941b818f64ce6d646321528b3449 | Text | 18,309 | 409 | # genome_updater [](https://app.travis-ci.com/pirovc/genome_updater) [](https://codecov.io/gh/pirovc/genome_updater) [ for [direct volume rendering](https://en.wikipedia.org/wiki/Volume_rendering#Direct_volume_rendering) in a web browser using the [Three.js](https://threejs.org/) wrapper for [WebGL 2](https://www.khronos.org/webgl). Its basic... |
a0831f499bd3e938c543cc7b2809536c0ef1e79cf42c198787d8729efaff368d | Text | 19,199 | 277 | Utils
=====
Utils scripts:
TE-analysis_Coverage.pl
provides a way to visualize which parts of the TEs are in the set (coverage graph on consensus);
it requires the output of the TEanalysis_pipeline.pl
TE-analysis_get_big_tables.pl
Util script to merge results of several runs
will o... |
494df07b172823f178777e26c6c99f8c34763d3b4d423ec8f9c2189e17961972 | Text | 19,672 | 535 | # Distributed Color Depth MIP Search
[](https://zenodo.org/badge/latestdoi/98349943)
[](https://github.com/JaneliaSciComp/colormipsearch/actions/workflows/maven.yml)... |
36e95a1214d19d22c108881d2a8d2fec481bcf305e2aaa5ca362b2be62c357e9 | Text | 20,541 | 402 | # DASDC
## *Domain Adversarial Sweep Detection and Classification*
## _Note：The following contents will be added later:_
_<1>*we will continue to add trained models as potential options to save the user's time*_.
## Configuration required for operation
Applicable platform: Linux
Resource requirement: Since mod... |
93f147ccd20078e8eeb7e7dbf1683934eb18eb2cf70c03b51eb40454681cb609 | Text | 20,788 | 336 | # BASALT: Binning Across a Series of Assemblies Toolkit
[](LICENSE)
[](https://github.com/PKU-EMBL/BASALT/releases/tag/V1.2.2)
[](https://github.com/bids-standard/bids-matlab/actions/workflows/run_tests_matlab.yml)
[![tests_octave](https://github.com/bids-standard/bids-matl... |
1b83a4c9097333c45fcdd4404761861e920d9fad26435f726995ad007a547802 | Text | 21,202 | 352 | <div align="center">
# GCPNet
<a href="https://pytorch.org/get-started/locally/"><img alt="PyTorch" src="https://img.shields.io/badge/PyTorch-ee4c2c?logo=pytorch&logoColor=white"></a>
<a href="https://pytorchlightning.ai/"><img alt="Lightning" src="https://img.shields.io/badge/-Lightning-792ee5?logo=pytorchlightning&... |
71c480809e13f1d476b0aedc664a5ff77c7f2d075fd856f49ae3c7fa69d50d07 | Text | 21,579 | 482 | # Recreation and Enhancement of MSDeepAMR: A Deep Learning Approach for Antimicrobial Resistance Prediction from MALDI-TOF Mass Spectrometry Data
[](https://www.python.org/)
[](https:/... |
029a201e7bcb31ee359c94c8aef1de45e0a5d8400e97b941be1247e564b97f0c | Text | 21,791 | 270 | <!-- markdown-link-check-disable -->
<!-- .. only:: html -->
[](https://github.com/bids-standard/bids-matlab/actions/workflows/run_tests_matlab.yml)
[](https://zenodo.org/doi/10.5281/zenodo.6772512)
## Summary
This module implements a [React component](https://reactjs.org) for [direct volume rendering](https://en.wikipedia.org/wiki/Volume_rendering#Direct_volume_rendering) in a web browser using the ... |
7b2bf0f35384fe4521e98b5b173231668f9a17e5aa1c26c585814c34e7804c74 | Text | 23,004 | 291 | # rippl-AI
__rippl-AI__ is an open toolbox of Artifical Intelligence (AI) resources for detection of hippocampal neurophysiological signals, in particular sharp-wave ripples (SWR). This toolbox offers multiple successful plug-and-play machine learning (ML) models from 5 different architectures (1D-CNN, 2D-CNN, LSTM, S... |
2af7f520174f39d8e46d67572bf9fcc4c0e90eac4da6c7134f55ead5f4fd4574 | Text | 23,846 | 158 | # Autoturbo-DNA: Turbo-Autoencoders for the DNA data storage channel
**Autoturbo-DNA** is a comprehensive autoencoder framework designed for the specific challenges of DNA data storage. It leverages the principles of Turbo Autoencoders (Jiang et. al., 2019) while integrating critical components for DNA data storage ap... |
e367857bb990a98a58ae63f0c044a045ee59a107cc6b2c358509507a9b962063 | Text | 24,874 | 583 | wordfreq is a Python library for looking up the frequencies of words in many
languages, based on many sources of data.
Author: Rob Speer
## Installation
wordfreq requires Python 3 and depends on a few other Python modules
(msgpack, langcodes, and regex). You can install it and its dependencies
in the usual way, eit... |
4110912ee1574d54111665fcbf711fca0adb057131ee4283d9ecf9b11cdc9cec | Text | 26,866 | 366 | # CLfinder-OrthNet
## Synopsis
A pipeline to detect co-linearity in gene orders among multiple closely-related genomes (CLfinder) and build networks of orthologs, or OrthNets, connecting ortholog nodes with co-linearity information (co-linear, transposed, or unable to determine) among them as edge properties (ONfinder)... |
766c4ef7a596ed9dc0ef7b31bac7d6aef274990e8992ee246558297037985870 | Text | 27,998 | 254 | # MVPA-Light
Matlab toolbox for classification and regression of multi-dimensional data
> [Treder, M. S. (2020). MVPA-Light: A Classification and Regression Toolbox for Multi-Dimensional Data. Frontiers in Neuroscience, 14, 289. https://doi.org/10.3389/FNINS.2020.00289](https://www.frontiersin.org/articles/10.3389/fni... |
1fc7dcdc12d4443064255082ac44e2748c18354d19bff6e2d2287ecf520b3a62 | Text | 28,984 | 557 | <!-- !test program bash -eo pipefail -->
# vg
[](https://gitter.im/vgteam/vg?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge) [](https... |
a436cf8401586663e4ff99b1e59228c544a1d100dfd5e50fb061095afce2964d | Text | 31,073 | 539 | # Backend for Real-time Asynchronous Neural Decoding (BRAND)
## Overview
BRAND is built using a graph architecture with small, individual nodes that can be flexibly interconnected. Each node is a separate process, so as to allow for parallelization and re-prioritization of each node. Interprocess communication and dat... |
783e3b2a5da02f06dc752e8bce0031895b49e3529eb5f56ff9df6fef6d40ad50 | Text | 35,867 | 765 | ------------------------------------------------------------------------------
* libmpMuelMat: Open Library for Polarimetric Mueller Matrix Image Processing
* version: 1.0
* project: HORAO - Inselspital, Bern, CH -- 2022
* developer: Dr. Stefano Moriconi (stefano.nicola.moriconi@gmail.com)
---------------------------... |
65e80263c5de6a946252fb8dc07bcb0d9e61a7af4fcbbd5cde40c033d011eb33 | Text | 50,855 | 636 | <h1 align="center">rl_games</h1>
<p align="center"><b>High-performance reinforcement learning for GPU-vectorized simulation.</b><br>
PPO and SAC in PyTorch, thousands of environments per GPU, multi-GPU training, asymmetric actor-critic, ONNX export.<br>
Trains directly on <a href="https://github.com/isaac-sim/IsaacLab... |
da4763c9a13e90324eac2ab5322e9b204b44b691e218979104537f85863ec419 | TypeScript | 49 | 3 | export const redirects = {
//'/': '/About',
} |
c9b6cc93fee22e06c13c8d60f29981b8e795f319bda3e713955ed5e0df7f0fca | TypeScript | 51 | 3 |
export class SaveCancelledError extends Error {}
|
865397f11ba6264a8b39db75b9b19913ede97ff4b48b2817a40c756ec9507d63 | TypeScript | 68 | 4 | export enum SortOrderDirection {
Asc = "asc",
Dec = "dec",
} |
cc9c01ab82cd866d596b11028637a284c3cca4b115d2aa5a02c31d2c59977fc1 | TypeScript | 71 | 2 | /// <reference types="svelte" />
/// <reference types="vite/client" />
|
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