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9a8f69fd0ed65afacf16a48751420e1a34f6d4eaa6b8529c2c78c4846782b190 | Text | 2,920 | 82 | # DELAY: DEpicting LAgged causalitY across single-cell trajectories for accurate gene-regulatory inference
---
# Quick Setup
1. Create a new conda environment (recommended):
```
conda create -y -n DELAY python=3
conda activate DELAY
```
2. Install PyTorch for CPU or GPU (recommended): https://... |
e52fd38b98c1b49d302ae334bfddc6581f917250ab82a1f40b8bc706cea5bcb8 | Text | 2,920 | 23 | # tFUS-mVEPBCI-Analysis
v1.0.0 DOI: 10.5281/zenodo.10968398
These codes were used for the analysis of EEG BCI data as part of the study: J. Kosnoff, K. Yu, C. Liu, and B. He, “Transcranial Focused Ultrasound to V5 Enhances Human Visual Motion Brain-Computer Interface by Modulating Feature-Based Attention.” bioRxiv, p... |
0c394e3e672fe951b891a232d0c950eac057ccafe354e891916880842679be56 | Text | 2,922 | 73 | # Neuralpredictors
[](https://github.com/sinzlab/neuralpredictors/actions/workflows/test.yml)
[](https://codecov.io/gh/sinzlab/neuralpredictors)... |
557a2024f5f0f4bfddd8dd0e78286d85dad8455cf921287ed5304ac1290d6c5b | Text | 2,933 | 95 | # Latent ODEs for Irregularly-Sampled Time Series
Code for the paper:
> Yulia Rubanova, Ricky Chen, David Duvenaud. "Latent ODEs for Irregularly-Sampled Time Series" (2019)
[[arxiv]](https://arxiv.org/abs/1907.03907)
<p align="center">
<img align="middle" src="./assets/viz.gif" width="800" />
</p>
## Prerequisites
... |
f57e8fc228ebb13c406ce16b34eb4ccba83bc18b397e8adf05d023036fe7e1bb | Text | 2,946 | 42 | # Mapping medically relevant RNA isoform diversity in the aged human frontal cortex with deep long-read RNA-seq
## Link to Article: https://doi.org/10.1038/s41587-024-02245-9
### This repository contains all code and documentation used for the analysis contained in the article above.
## Repository structure:
`artic... |
d9605207bf62404bc81ce2f9ca5395bf69bb6b362428f234361f4cbb9e79711a | Text | 2,948 | 56 | [](https://pycro-manager.readthedocs.io/en/latest/?badge=latest)
[](https://github.com/micro-manager/pycromanager/raw/master/LICENSE)
[) to perform clustering.
## MATLAB Implementation
### Requirements
A MATLAB version of the algortihm is provided.
We have tested this on MATLAB versions 2020 and above and no additional libraries are required
... |
06b7a20d6b388eca52df5da6be9ded66353778938f128019e42c2e1125a25b7f | Text | 2,982 | 82 | # The PHOIBLE Database as CLDF StructureDataset
This dataset provides the data of PHOIBLE, which is curated at
[phoible/dev](https://github.com/phoible/dev)
as [CLDF StructureDataset](cldf/). This CLDF data is
browsable online at https://phoible.org
The semantics of the CSV files in the [cldf directory](cldf/) are a... |
f7dfc134e1d4c421e4826697c59d3570c3c21f0dbf8ef92f65aed6daa67f7663 | Text | 2,985 | 85 | # Manuscript Code Repository
**Manuscript title**: From Neglecting to Including Cultivar-Specific Per Se Temperature Responses: Extending the Concept of Thermal Time in Field Crops
Plant Phenomics 2024;6:Article 0185.
(https://doi.org/10.34133/plantphenomics.0185)
## Published Custom Software
Relevant custom soft... |
a44763fd79e99726bd903db7ee493c650ff484eee7ee0ea88e39441c9af94312 | Text | 2,989 | 52 | # hBayesDM <img src="https://github.com/CCS-Lab/hBayesDM/raw/master/logo.png" align="right" width="200px">
[](https://www.repostatus.org/#active)
[](http://pymaid.readthedocs.io/en/latest/?badge=latest) [](https://github.com/navis-org/pymaid/actions/workflows/run-tests.yml) [
#### Environments
MIGA requires anaconda with python 3.7 or later, cudatoolkit=11.1 and below packages
```
torch ... |
a19cf963a1b5f822dbed3f13540205e74126a1375324aca2298a99b46e0ea47a | Text | 3,013 | 52 | # BakingTray
<a href="https://www.youtube.com/watch?v=3-nLt7j6tMM">
<img src="./BakingTrayScreenshot.png">
</a>
### What is it?
BakingTray is a complete software platform for 2-photon serial tomography STPT.
It plugs into [ScanImage](https://www.mbfbioscience.com/products/scanimage/) and runs within [MATLAB](http:/... |
4ddc83a1f4a9442e6a1fe83ba13b8d385a665f392d7b24cbc431d18cb4b4026c | Text | 3,018 | 72 | # Microneurography-Toolbox
OVERVIEW
The program is a comprehensive MATLAB-based toolkit developed for the analysis of microneurographic signals. It provides a user-friendly interface for processing and interpreting data related to peripheral nerve activity.
_____________________________________
FEATURES
User-Friend... |
d7bbcfa1752dce9d63e92716f396b9836ef4817ef52230fddebab757b84f6cae | Text | 3,027 | 49 | # MousiPLIER
MousiPLIER (a portmanteau of Mouse and [MultiPLIER](https://www.cell.com/cell-systems/pdfExtended/S2405-4712(19)30119-X)) consists of two parts. The first part is a pipeline to learn MultiPLIER latent variables from 190,111 recount3 mouse RNAseq samples. The second part uses the latent variables to analyz... |
a5670a90b9da565c5a973db510f7db2b38001b6f8674141b5e752387c478e3a8 | Text | 3,031 | 78 | # Simulations to identify the relationship structure among multiple datasets using Independent Vector Analysis
This package contains the code for reproducing the simulations of our paper:
Isabell Lehmann, Tanuj Hasija, Ben Gabrielson, M. A. B. S. Akhonda, Vince D. Calhoun, Tülay Adali,
**Identifying the Relationship ... |
1a27240610c8e906638acb7174dbfa03245bdb7fd0d228ad770a650507571507 | Text | 3,041 | 82 | # MRtrix
[](https://github.com/MRtrix3/mrtrix3/actions)
[](https://twitter.com/MRtrix3)
*MRtrix3* can be installed / run through multiple avenues:
- [Direct download]... |
c520e547940f09ed38dbbb0d47f6b034bf5262b6527b2c676e69dc1dc1201652 | Text | 3,047 | 105 | NOTE: ``vmdpy`` is officially distributed with, and maintained in, [``sktime``](https://github.com/sktime/sktime/), since August 2023.
Please ask questions or open issues or PR on the [``sktime`` repository](https://github.com/sktime/sktime/).
# vmdpy: Variational mode decomposition in Python
Function for deco... |
7fe5f4c8168737ff85d4babb1dfaaa2337ec34e2f417a13f4862cbcffaafdf59 | Text | 3,059 | 26 | # KineticAssembly_AD
Python code for numerical simulations of self-assemly with optimization by automatic differentiation
## Installation ##
The easiest way to install the simulator is to clone this repo and then build an environment containing all dependencies using the provided `base_requirements.txt` file. In orde... |
e8907cee2f739e457f88419195b989dc6e8c192569754aa14e1c466cb56f6209 | Text | 3,061 | 38 | # CCGtools
This is a collection of Python and Cython tools for processing CCG. It contains a pretrained parser, efficient loading of trees, A* search, latex style files, visualization, extraction of semantic dependencies, evaluation scripts etc. It is not very polished but you may find it useful. Probably the most int... |
2b86e001b4597aae622a28b56aa801a47b9430d5d26c910939cb2403158b0e52 | Text | 3,069 | 85 | # ptrnets
[](https://img.shields.io/github/v/release/sacadena/ptrnets)
[](https://github.com/sacadena/ptrnets/actions/workflows/main.yml?quer... |
853d4d0f7de27f7d5c8c9e30904e762a5e11b46f548e1df9104f500b965493d3 | Text | 3,069 | 63 | # ISTART-socdoors: Social Doors Task Data and Analyses
This repository contains code related to our in prep project related to neural responses to social and monetary rewards. All hypotheses and analysis plans were pre-registered on AsPredicted in fall semester 2019 (https://aspredicted.org/blind.php?x=JNH_EGK) and dat... |
a4b5ab25d0d0b18918de9e9834f067aeb674e85f29b42da87a0f08b96c6793d7 | Text | 3,069 | 58 |
Code is divided into MEG analysis and Behavioral Analysis.
#### Behavioral Analysis
This was done using Julia version 1.5.2
Model fitting was done with an em procedure. EM code (contained in folder em) was written by Nathaniel Daw. Functions that interface with this code to fit models are in the file model_fitting... |
99fee6bd55f32e1749665d3df9b48b0e8fa8a113d51431ad0b9e6e2a7205e067 | Text | 3,129 | 106 | # BERNN-MSMS
Batch-effect-aware representation learning and classification with an
estimator-style `fit(...); predict(...)` interface.
## Install
```bash
pip install bernn
```
## Basic usage
```python
from bernn import TrainAEClassifierHoldout
from bernn.config.training_config import TrainingConfig
config = Train... |
d6ba11bb963b4acab1616c7eace8962554bb133d16ae296245cb4125f32e2690 | Text | 3,154 | 45 | # Histological-Hyperspectral-Glioblastoma-Dataset
This project is intended to provide a basic example of how to load and perform some basic preprocessing for hyperspectral data in ENVI format using Python and MATLAB. The data used in this project corresponds to the Histological Hyperspectral Glioblastoma Dataset ([Hist... |
7e0fae61efdd2023603555d5af6d826dba2ca59cd5f17a62cede81092e7c0fc1 | Text | 3,164 | 60 |
# ARACHNE
## version 3.0
## Update 04/03/2021. Added the installation version of the Arachne (Arachne_web.exe) for Windows. This version allows you to compute both on a local computer and on a remote cluster.
ARACHNE is a newly designed simulation environment in which neural and neuroglial network organisation, ... |
37a1f9a36d24e142d152f533c5983da7333e38fca2abb13cd0aae01eaacdfec7 | Text | 3,198 | 41 | [](https://www.python.org/)
[](https://pepy.tech/project/spatialid)
[](https://spatialid.readthedocs.io/e... |
2858c2f1bd9860666bdb3e117acc9c5a727f413a5032765782d3dd6d573c1ca9 | Text | 3,201 | 58 | # Bayesian Network Regression model for microbiome networks as covariates on biological phenotypes as response <picture> <source media="(prefers-color-scheme: dark)" srcset="docs/src/logo-dark_text.png"><img alt="bayesiannetworkregression logo" src="docs/src/logo_text.png" align=right></picture>
[ machine learning models and module. This module has the same requirements as nn4dms, with a few additional dependencies. Use [conda](https:/... |
43051e6670a89f052974e6ef81d4db60fbb3b852887d787a5601a98ec83cd3d5 | Text | 3,213 | 63 | # SENPAI
A modular framework for multi-scale tissue imaging and neuronal segmentation
%%%%%%%%%%%%
Manuscript: "A modular framework for multi-scale tissue imaging and neuronal segmentation", Cauzzo et al., Nature Communications, 2024
%%%%%%%%%%%%
!!!! System Requirements and Dependencies:
This code is written in th... |
405a9251dd034e505708d916e599699b52f75f566965c9b5040c3c9bcdb5707f | Text | 3,230 | 67 | # BTR: Bioinformatics Tool Recommendation System
Implementation of the Bioinformatics Tool Recommendation system for the paper in review.
Programing language: Python
Operating system: Any
License: MIT License
## Installation and Setup
### Prerequisites:
* Python 3.7+
### Download repository and install requireme... |
7471ea9730a9d8761d59443515820594fadbc0c48a5423821f1ea9490fc173f6 | Text | 3,231 | 35 | # Metabotropic signaling within somatostatin interneurons controls transient thalamocortical inputs during development
[](https://doi.org/10.5281/zenodo.11074523)
## Authors
Deepanjali Dwivedi, Dimitri Dumontier, Mia Sherer, Sherry Lin, Andrea MC Mirow... |
bad9cbd2d9c4af959a001e63f52c50fac0889ec02398edd5b397c23b05547fd5 | Text | 3,242 | 48 | [](https://github.com/choderalab/openmmtools/actions?query=branch%3Amain)
[](https://anaconda.org/omnia/openmmtools)
[ distribution on a given chromosomal region [Bianco2018];
- predict_bs: probabilistic prediction of bs in t... |
7d572880005b6a01827ebffdb602e6f13cda69f0d7d93bc3411160caa991c032 | Text | 3,295 | 2 | # High-fat diet impact on the gut microbiota, serotonergic systems within the dorsal raphe nuclei, and anxiety-like behavior
Anxiety and obesity are two conditions that affects the population in a consistent manner. In experimental rats’ model of long-term induced-obesity by HFD intake, anxiety-like behavioral response... |
cac19398e3c0fd263c1965f698cde37efb26cc61c271e4594fed5089c3c1fcc6 | Text | 3,306 | 34 | # Color-Advertising Strategies of Invasive Plants through the Bee Eye: A Study Case in the French Pyrenees
Martin Dessart, João Marcelo Robazzi Bignelli Valente Aguiar, Eric Tabacchi, Sylvie Guillerme and Martin Giurfa
# Correspondence
Email: sylvie.guillerme@univ-tlse2.fr ... |
e2bc1fac07881ff50887d034a6ba3c7579ca032a9bae268012ac39a748ec98dd | Text | 3,322 | 71 | ========
Overview
========
.. image:: https://readthedocs.org/projects/omicscope/badge/?style=flat
:target: https://omicscope.readthedocs.io/
:alt: Documentation Status
.. image:: https://github.com/guireiso/omicscope/actions/workflows/github-actions.yml/badge.svg
:alt: GitHub Actions Build Status
:... |
b327402368e4dff9e135b077b8c562dd59c7972e13680f6330f4d22edb85b23f | Text | 3,358 | 64 | Shield: [![CC BY-NC-SA 4.0][cc-by-nc-sa-shield]][cc-by-nc-sa]
This work is licensed under a [Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License][cc-by-nc-sa].
[![CC BY-NC-SA 4.0][cc-by-nc-sa-image]][cc-by-nc-sa]
[cc-by-nc-sa]: http://creativecommons.org/licenses/by-nc-sa/4.0/
[cc-by-nc-s... |
a6ed817929f77380b4270ac01b086e65e309d5b1c9dab14bc0f460376e4d843e | Text | 3,369 | 143 | <h2 align="left">BTSTN (version 1.0)</h2>
<p align="left">
<a href="https://www.python.org/"><img alt="Python version" src="https://img.shields.io/badge/Python-v3.7--3.11-blue?logo=python&logoColor=white"></a>
<a href="https://pytorch.org/"><img alt="powered by Pytorch" src="https://img.shields.io/badge/PyTorc... |
e1fbc1c565dccbfdaa769e194fed9bc3def32123bb348386e84a4ba1ac48b9b6 | Text | 3,414 | 54 | # Imaging+ <img src="docs/source/files/imagingplus-logo.png" width="200" title="imagingplus logo" alt="a python -x- calcium spike" align="right" vspace = "50">
imaging+ is a Python package and tool-suite for essential processing and analysis of 2photon imaging data.
Especially, there is a fully implemented pipeline f... |
c713d272c2c0dd0c8eaf5fd7ec70061a2a228dfb9ac5bca9fbfbbc590363595a | Text | 3,417 | 83 | # patternsfromattacks
## Description
This repository contains the necessary python files to use the **Adversarial Classifier**.
It is a decoder that takes advantage of gradient based adversarial attacks in order to
probe the decision hyperplane. Models built on Pytorch and attacks built on Foolbox are
used. (**mode... |
104b1d42d73ee7664d1fbad404de0521b2854a8062c064489e1c7e999a315d23 | Text | 3,437 | 56 | # csLFM-master
Codes for csLFM PSF conversion and 3D reconstruction
Version: 1.0
Lisence: GNU General Public License v2.0
# Overview
We develop a confocal scanning light-field microscopy (csLFM), which synchronously employs scanning light-sheet illumination and a camera rolling shutter to selectively collect in-... |
eeb845679a17b0bf027c6c55c410a955377d1098669a98ec1a73a36d22d2613b | Text | 3,456 | 73 | # ants_tbss
[](https://travis-ci.org/trislett/ants_tbss)
TBSS (FSL) implementation with ANTs and T1w registration to template. [ants_tbss](bin/ants_tbss) creates the TBSS skeleton using ANTS without FA to FA registrations.
There are essentiall... |
0abc5794c1168a9885d4e043373ee5573276dfb520edbfe543bbe46df4fe949a | Text | 3,459 | 55 | # Calibration of Neural Networks
## Introduction
This repository contains all scripts needed to train neural networks (ResNet, DenseNet, DAN etc) and to calibrate the probabilities. These networks are trained on 4 different datasets and the model weights and output logits are available for use in this repository.
## S... |
059ba2c7a829bb0882326b8bc5dff0a87b185b222e3ca16e2a01e082bbd70e44 | Text | 3,483 | 59 | # Synergistic information supports modality integration and flexible learning in neural networks solving multiple tasks
by Alexandra M. Proca, Fernando E. Rosas, Andrea I. Luppi, Daniel Bor, Matthew Crosby*, Pedro A.M. Mediano*<br/>
(* – joint senior authorship)
Code and data for https://doi.org/10.48550/arXiv.2210.... |
aa05596d367b8008efdc48a1d4ab7688937b609b41b5bede4fe59d94eb70969f | Text | 3,513 | 71 | <!--- [](https://travis-ci.org/choderalab/perses/branches) --->
[](https://github.com/choderalab/perses/actions?query=branch%3Amaster)
[ approach with the aim of reducing the scanner bias of models trained on
single-scanner data. If you use this code please cite our paper:
>Meyer, M.I., de la Rosa, E., Pedrosa de Barros, N., Paolella, R., V... |
3467b60143bf7cd13f1a9e199e59b5b280b8ed8df8cddc038c371e7558e99a26 | Text | 3,627 | 71 | **This repository has moved to: https://gitlab.tugraz.at/ibi/mrirecon/papers/nlinv-net**
# NLINV-Net
This repository contains scripts to train and apply NLINV-Net on cardiac real-time data.
Reconstructions of the manuscript can be reproduced by running
```
$ ./01_reproduce_figures.sh
```
This script downloads the ex... |
fd104f6a81003b3a6c35770d72b369664889c55976faae1328275337ae419638 | Text | 3,638 | 71 | ## Analysis of Orthologous Collections (AOC) on REM2, REM2: a member of the RGK (Rem, Rem2, Rad, and Gem/Kir) family of small GTPases.
This repository contains all code, data, and results for the evolutionary analysis of mammalian REM2.
### Clone repository
`git clone https://github.com/aglucaci/AOC-REM2.git`
`cd AOC... |
d961ad4093b23ea4d91f5775b82b4c4e3ecf0cc349b02211a39a047d06d53e70 | Text | 3,662 | 40 | # DI-Inference
## Description
Python translation of the Matlab implementation of the Directional Information (DI) inference method to estimate single-trial directional interactions between discrete time series in sequential time windows. Original code in Matlab is available at https://github.com/AdTau/DI-Inference. I... |
1a82b57e45cc649106e50bcf9d1ad85b3eb9085bff4b89edc9cf94cd7c770ee6 | Text | 3,674 | 37 | # ECG-signal-analysis
Код для обработки ЭКГ сигнала и анализа аномальных данных.
## Описание
Этот проект включает код для обработки данных ЭКГ сигнала, выявления ключевых точек (P, Q, R, S, T), а также для анализа аномальных данных с использованием алгоритма Isolation Forest.
## Данные для анализа
Identified labels... |
9b9773957b0d37c82a90971255e11a7ad9e26c4ad6d97206b6ded327a833bd7e | Text | 3,678 | 45 | # ProcessDE
### Processing RNA-seq data for gene expression analysis
Starting from either isoform-level counts quantified with [_Salmon_](https://combine-lab.github.io/salmon/) (recommended), BAM files quantified with [_samtools_](http://www.htslib.org/doc/samtools-idxstats.html), or [_vast-tools_](https://github.com/... |
4e5a56c9f486dd34f9d312671fd01f13dd1b2b510491ee40f20e74acaa362630 | Text | 3,688 | 68 | # single_molecule_matlab_scripts #
Single molecule scripts of the Brunger lab.
Note:some of the scripts require these MATLAB Add-Ons: Statistics and Machine Learning Toolbox, Image Processing Toolbox, Signal Processing Toolbox
## /fusion_detector ##
matlab script to detect fusion events in time trace files
... |
13894856603d863b705d7d11f539b04007e40edf33043a97b1d30eae29ef6698 | Text | 3,699 | 61 | # Matcycle
This is a repository of functions that detect EEG oscillation bursts based on the shape and periodicity of the signal. It is a MATLAB implementation of the cycle-by-cycle analysis outlined by [Cole & Voytek, 2019](https://journals.physiology.org/doi/full/10.1152/jn.00273.2019) originally created in [pytho... |
a9d02ded90a51d305462e6e031549636d27d61fc92bec8dae9b07b435c1ada84 | Text | 3,739 | 61 | # PlantCommunityModellingCH
The files contained in this folder represent a minimal working example of the core DNN fitting and prediction as conducted in the paper "Deep learning from citizen-science data to model plant communities" by Brun et al. They can be used to fit the DNN architecutre with different cost functi... |
59690392e261bad3f27711527ddd6de3c2007073867404019e6b52134f66f731 | Text | 3,753 | 63 | # scRNA-seq Analysis Pipeline
Scripts for statistics and plotting figures in the single-cell RNA-seq study of brain tissues and gut bulk RNA-seq, covering differential expression analysis, cell-type marker visualization, GO enrichment, Ro/e tissue distribution analysis, and volcano plots.
## Repository Contents
- /f... |
557e7da2cf99cb9f7bbdc7ee040fae604d17c9f625824276c238508d595f5dbd | Text | 3,758 | 80 | # Adversarial learning for MRI reconstruction and classification of cognitively impaired individuals
This work is published in _IEEE Access_ (https://doi.org/10.1109/ACCESS.2024.3408840).
# Introduction
This is the repo for the model proposed in the paper. Briefly, the model performs medical image (scans) reconstruc... |
7ed81e0423d3f6abf84318d8fe17646c0d456fa3b293849a2b212b950f36d6fa | Text | 3,764 | 89 | # Independent Vector Analysis
This package contains the Python versions of Independent Vector Analysis (IVA-G [1] and IVA-L-SOS [2]), converted from the [MLSP-Lab MATLAB Codes](http://mlsp.umbc.edu/resources.html).
- **Website:** http://mlsp.umbc.edu/jointBSS_introduction.html
- **Source-code:** https://github.com... |
2583796f94fb583f0fcc7a64955137f3361aee464ca77493f2881e336ac0d79e | Text | 3,803 | 41 | # `ECG-Image-Kit`
***A toolkit for synthesis, analysis, and digitization of electrocardiogram images***
The ECG (Electrocardiogram) is a widely used and accurate diagnostic tool for cardiovascular diseases. Traditionally recorded in printed formats, the digitization of ECGs holds immense potential for training machine... |
011a64fc7e6f97fc4ae94582c7b4433b9b50ec3a9cd505bbc073fa909b095905 | Text | 3,831 | 58 | # Linear-unmixing-Qdye
# Overview
When imaging samples with two or more fluorescent dyes, we need to obtain images at different excitation/emission ranges.
However, it is still difficult to obtain fluorescence signals for just one type of dye when samples are labeled with multiple types of dyes with overlapping e... |
ca46f146fe4aff2a462f6c61fce9d3d58d79a24567ce5b75e6c243ab555076b5 | Text | 3,857 | 38 | # Mammalian Methylation Consortium Github Page
This page contains all the annotation and tools generated by Mammalian Methylation Consortium to analyze generated data using Mammal40k and Mammal320 arrays:
Here are the summary of the content:
1- Genome coordinates for different species
2- R code for alignment and ... |
8f3f199079edc7f0fb5a3c6357b5e596eb88da2d5f524805ee659209fe0105ee | Text | 3,891 | 78 |
# Trajectory Reconstruction Tradeoff
Charting cellular trajectories over gene expression is key to understanding dynamic cellular processes and their underlying mechanisms.
While advance... |
dc96f1fdb1f0bf1701da13cb1cb3fac1559d22974b1b20b5d1b99b34d16e524c | Text | 3,894 | 132 | Network Portrait Divergence
===================
Python code for computing **network portrait divergences**, a simple, general-purpose
tool for comparing networks.
<p align="center">
<img src="portraits_figure.png" alt="Networks and their portraits" width="75%"/>
</p>
Please see the paper for more details:
**An in... |
384f16ff4933c9ca7eb6d9dd4c770b2b70d96aa68111dab3ddcb2f21fe32f87e | Text | 3,897 | 51 | # ProcessDE
### Processing RNA-seq data for gene expression analysis
Starting from either isoform-level counts quantified with [_Salmon_](https://combine-lab.github.io/salmon/) (recommended), BAM files quantified with [_samtools_](http://www.htslib.org/doc/samtools-idxstats.html), or [_vast-tools_](https://github.com/... |
fadfc0d31988ffe72420b8675df822214e3e8a9f6dc39c6b84ec981fcf4dc42b | Text | 3,903 | 75 | # Multi-Time Attention Networks (mTANs)
This repository contains the PyTorch implementation for the paper [Multi-Time Attention Networks for Irregularly Sampled Time Series](https://openreview.net/forum?id=4c0J6lwQ4_) by [Satya Narayan Shukla](https://satyanshukla.github.io/) and [Benjamin M. Marlin](https://people.cs.... |
8dc360a972c2c7e0a2a42bea0e58ff15187db36e1cf4f13d1e7c7b81e72ff35d | Text | 3,927 | 51 | # Code for the analysis of light sensitivity in the prefrontal cortex
Code used in the "Prefrontal cortex neurons encode ambient light intensity differentially across regions and layers" paper.
Please contact the leading author, Mr. Elyashiv Zangen (elyashiv.zangen@mail.huji.ac.il), if you have any questions about the ... |
6540c3a64a270e0736d1831329f813102e91ad149ecbc2d08db95ecb3e3e5b37 | Text | 3,983 | 87 | <img src="docs/source/_static/uniPort.jpg" width="40%" height="40%">
[](https://opensource.org/licenses/MIT)
[](https://badge.fury.io/py/POT)
[ <doi:10.5281/zenodo.7838056>.
## MrBayes
Folder containing... |
0de14f211153d36ff14cebd4684f2983746f7d20930d620ca88d31880556fb01 | Text | 4,055 | 70 | samtools
========
[](https://cirrus-ci.com/github/samtools/samtools)
[](https://github.com/samtools/samtools/actions/workflows/windows... |
1148a8b828af0cb7fce8347ecf47e2903c2dd0549cc868312970a9753d2c8fed | Text | 4,063 | 103 | # Decorrelation using Optimal Transport
## Overview
This repository contains code for implementing a decorrelation classifier using Convex Neural Optimal Transport Solvers (Cnots). The decorrelation classifier is a mathematical framework for reducing the correlation between a classifier's predictions and a protected ... |
2570d72d1a4242cbaaff713ee5d278e47c8069643b853cb6e60ba41e53292750 | Text | 4,069 | 103 | # BASNet (New Version May 2nd, 2021)
'[Boundary-Aware Segmentation Network for
Mobile and Web Applications](https://arxiv.org/pdf/2101.04704.pdf)', Xuebin Qin, Deng-Ping Fan, Chenyang Huang, Cyril Diagne, Zichen Zhang,
Adria Cabeza Sant’Anna, Albert Suarez, Martin Jagersand, and Ling Shao.
## Salient Object Detectio... |
1636e757462840d5a692867d9c3316a44a5b99c38452a01099c3b2d850727a4c | Text | 4,077 | 99 | # keras-yolo3
[](LICENSE)
## Introduction
A Keras implementation of YOLOv3 (Tensorflow backend) inspired by [allanzelener/YAD2K](https://github.com/allanzelener/YAD2K).
---
## Quick Start
1. Download YOLOv3 weights from [YOLO website](http://... |
d1c1be283be049efba3f470bbee3b030590734d433aeb6d082b927a3f0fc12af | Text | 4,096 | 50 | # ChromaticAberrationCorrection
Codes to measure and then correct chromatic aberration.
These codes are written for use in MATLAB. NB You will need the Statistics and Machine Learning tooldbox for the regress function. But with some searching I believe you can find some others who have written the same function.
Other... |
706400c59c82fe2d283588940a90e28a6330cf8be9a8fbf2124817bb5e6fd86b | Text | 4,108 | 84 | # EDM: E(3) Equivariant Diffusion Model for Molecule Generation in 3D.
<img src="equivariant_diffusion/overview.png" width="400">
Official code release for the paper Equivariant Diffusion for Molecule Generation in 3D.
**If** you want to set-up a rdkit environment, it may be easiest to install conda and run:
``conda... |
a24ec7c24da09af08191afbccc09b8b9361f883ebba409210e62cd8328c04057 | Text | 4,161 | 63 | # FridgeSnap
An image-classification Android application developed to generate recipes from user-taken images of food items.
# About the Project
FridgeSnap has been developed to assist with the reduction of global food waste. FridgeSnap uses image classification and machine learning technologies to generate recipes f... |
39614a4df21de69307e249ef985d9d60dd6f3d854e18fe458e99cff9858fd3be | Text | 4,189 | 109 | # DeepMapper
**No-filtering, attribute-back analysis of high-dimensional omics.** DeepMapper keeps
every feature (no highly-variable-gene selection, no dimension reduction), reads the
full matrix with a configurable backbone over several feature arrangements, and
attributes each result back to named features. That sur... |
d224f4bd6784e2f1ac9199ad062f6c1eee0daa98a10f8e6b0f7a1fe7799e748f | Text | 4,222 | 39 | # Thalamocortical Neural Network Analysis
## Introduction
This repository contains the computational tools and scripts used in our recent study on the hierarchical organization of the thalamocortical network during sensory processing. The study focuses on how functional connections within and across brain areas influe... |
dbc5e129dec6e011a823c87a2fd040043e9f910a7b88a7a08e477f197a686e71 | Text | 4,222 | 49 | # Diffusion MRI SWIN UNETR
In this repository, we use SWIN transformers to perform generalized diffusion MRI denoising and super-resolution. Our model is robust to:
- wide array of scanners (ge, siemens, etc.)
- different acquisition parameters (TE, TR, b-value, b-vector, etc.)
- diverse patient populations (adult pat... |
107bb4b40343db3410237624234e949bc134e8bd9c5344edb96ef5d0004010c3 | Text | 4,229 | 100 | # nnSegNeXt: A 3D Convolutional Network for Brain Tissue Segmentation based on Quality Evaluation
---
## Installation
#### 1. System requirements
We run nnSegnext on a system running Ubuntu 18.04, with Python 3.9, PyTorch 1.10.1, and CUDA 10.7. For a full list of software packages and version numbers, see the Conda en... |
6115d552a223dc5859aa4c7c6f50a2d9b1dfcc5b43349fd8bad66d898b028601 | Text | 4,231 | 177 | # MEnet <img src="./img/MEnet.png" width="20%" align="right" />
MEnet is a neural-net based deconvolution method for methylation data. MEnet can be used only for humans so far.
## Installation
### Without Docker
1. Install pytorch. [https://pytorch.org/get-started/locally/](https://pytorch.org/get-started/locally/)... |
4c355abbaf6d6c3959d50958f88cd01bd00cf079557fe5c4d4e0cc1a150b5b38 | Text | 4,249 | 82 | # AnnoSpat automatically annotates cell types and quantifies inter-cellular arrangements from spatial proteomics
Aanchal Mongia, Diane Sauders, Alvin C. Powers, Ali Naji, Gregory W. Schwartz and Robert B. Faryabi
## Introduction
`Annospat` is a tool for annotating and inferring patterns in single cells from spatial
pr... |
ba983278fcfb25c278191deb21b8b5cf294d7ae1710d2ab4e6854244e34b7f24 | Text | 4,269 | 44 | # StabilitySelection
This is package for performing stability selection in MATLAB, using a variety of feature selection/ranking algorithms that come packaged with MATLAB's machine learning toolbox. This comes with a variety of live code tutorials that show how to: 1) run stabSel, 2) properly set up cross-validation and... |
066f7fcea26d3650faa57fed9db77cb4df338c800bce3f8db8eb1cfe1ee1dc91 | Text | 4,298 | 117 | # DiPGNN
**[Link to Paper](https://www.science.org/doi/10.1126/sciadv.adk2799)**
This repository hosts the TensorFlow implementation of the research paper titled "Predicting the Pathways of String-like Motions in Metallic Glasses via Path-Featurizing Graph Neural Networks," published in Science Advances, 10: eadk279... |
52ebe1b03a039c804e7dbd8d78b37962ad29348da4b9364ba8f3fbcaf346464b | Text | 4,313 | 109 | # sc2marker
sc2marker is a toolkit for identification of cell specific markers for clusters of cells in a single cell RNA sequencing data set. In particular, sc2marker focus on markers that have valid antibodies to be used for either imaging or flow analyis.
## Install
You can install sc2marker with the following co... |
f7df251ae4d06e39bc31766315e1eca3a9f611c98d0b6dff37ba256117c813cb | Text | 4,315 | 138 |
# ggcor
The goal of `ggcor` is to provide a set of functions that can be used to
visualize a correlation matrix quickly.
## Installation
Now `ggcor` is not on cran, You can install the development version of
ggcor from [GitHub](https://github.com/) with:
``` r
# install.packages("devtools")
devtools::install_githu... |
1f0bdb24405305de17229643ead1e732f5224d1cd698aaecb6b42f9d489c8994 | Text | 4,373 | 91 | # Covariance Data Frames for Predictive M/EEG Pipelines
<!--  -->
Coffeine is designed for building biomedical prediction models from M/EEG signals. The lib... |
b60162e48d7bea504c661fb132a0d0382f1771340384bb1794236f10c7a47cc8 | Text | 4,377 | 110 | # tfdone
TensorFlow implementation of DONE ([It's DONE: Direct ONE-shot learning with Hebbian weight imprinting](https://arxiv.org/abs/2204.13361)). DONE is the simplest one-shot learning method that can add new classes to a pretrained DNN without optimization or the backbone-DNN modification.
 to model and understand the echolocation process in bats, focusing on the challenges posed by acoustic data interpretation without phase information. Leveraging insights from the field of optical NeRFs, our model, termed So... |
031844c0f34dd85a5ba4ec29a5c56ac322151b2b14649078ca15b64400f4f4bb | Text | 4,457 | 114 | # DeepMapper
[](https://doi.org/10.5281/zenodo.20967454)
**No-filtering, attribute-back analysis of high-dimensional omics.** DeepMapper keeps
every feature (no highly-variable-gene selection, no dimension reduction), reads the
full matrix with a configurable backbone ove... |
44ff5bcce34ae13a4083927ca55ad7e2b867c4d8904be6189d5bbd88345d6b4a | Text | 4,463 | 145 | QupKake - Predict micro-pKa of organic molecules
==============================
[//]: # (Badges)
[](https://github.com/shualdon/qupkake/actions?query=workflow%3ACI)
[
This repository accompanies the manuscript "Shared functional specialization in transformer-based language models and the human brai... |
cf21a7f336183d38cfeb9d238cbb254446e9c15e0bf07f99622eee036ff3a424 | Text | 4,530 | 118 | # README
*scana* is an abbreviation for "(s)ingle (c)hannel (ana)lysis" and
is intended to help with the data analysis of single channel measurements.
# Installation
The *scana* software is a tool written in Python and can
therefore be run on various platforms. The starting point
is an installed Python3 interpreter, ... |
73a6b68e0de6fd99c7d953becd4dc5389215980c1d62f497683235f40fd809f2 | Text | 4,538 | 52 | # ProcessVast
Scripts and files to perform routine analyses of alternative splicing, based on [_vast-tools_](https://github.com/vastgroup/vast-tools) output
## Summary
This is a tool to make sense of _vast-tools_ output by providing several standard analyses, including similarily of single samples, numbers of changin... |
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