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38905c1735e174588775608bf175253d3e9102d3c692dfe15f9820571eb95fbc | Text | 4,387 | 96 | # 1000MonkeyGenome
This repository contains scripts related to manuscript "Adaptive Functions of Structural Variants in Human Brain Development"
# Table of contents
- Content
- Contact
## Content
- **DerivedAlleleFreq_bootstrap.R:** A R script to do the 1,000 bootstrap of derived allele frequencies classfied by diff... |
b6aefb3970024de56c18ce79a0d8421f3b42e3a3fd309ac7c2d6fe739c12f759 | Text | 4,390 | 77 | # FastMRI Prostate
[[`Paper`](https://www.nature.com/articles/s41597-024-03252-w)] [[`Dataset`](https://fastmri.med.nyu.edu/)] [[`Github`](https://github.com/cai2r/fastMRI_prostate)] [[`BibTeX`](#cite)]
### Updates
02-07-2024: Updated [files](https://github.com/cai2r/fastMRI_prostate/pull/11) for slice-, volume-, exa... |
a3af23032d2729f69ebd8762ee7fc27b87ac04eb4ac775be873cdd983b77a0e7 | Text | 4,391 | 58 | # Hirsch-et-al.-2023-test-of-the-diet-hypothesis-for-brain-expansion
This repository contains r code related to Hirsch et al 2023 test of the diet hypothesis for brain expansion
Original movement data are hosted on [Movebank](https://www.movebank.org/) (Processed data: Movebank ID 1120749252; Unprocessed data: Moveban... |
7e041bf82070581115868987eff42b3694a3267728e8dbdef0d96e1dfb585815 | Text | 4,420 | 40 | # State-transition dynamics of resting state fMRI data
When you use the code provided here, please cite the following paper:
[State-transition dynamics of resting-state functional magnetic resonance imaging data: Model comparison and test-to-retest analysis](https://arxiv.org/abs/2308.11910)
This repository provides ... |
fb9a2d4ae82f4e889641beaf92b0ae6a47574bf488a99ea9f9973c36b06a7675 | Text | 4,547 | 64 | [](https://github.com/DecodeGenetics/graphtyper/actions/workflows/ci_linux.yaml?query=branch%3Amaster) [ downscaled on 1:10 for the usage in the [F1TENTH Gym](https://github.com/f1tenth/f1tenth_gym) and [F1TENTH Simulator](https://github.com/f1tenth/f1tenth_simulator).
# Paper Reference
The collected research papers in th... |
81732a224133c5c7824f9151bb4ccfda4b1370c39e91bac1ab5fa581cee4072a | Text | 4,658 | 79 | # DeepDecon accurately estimates cancer cell fractions in bulk RNA-seq data
### Overview
Here, we present `DeepDecon`, a deep neural network model leveraging single-cell gene expression information to accurately predict the fraction of cancer cells in bulk tissues. `DeepDecon` was trained b... |
47c640a3a078dcd580ddebc7e0f222c9f3db77ef80cd662b43fd38047ea45c12 | Text | 4,676 | 116 | # 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 direct... |
2f638d354a387d246ec46a46fb033ec42e520898880aa90a967c67b4c7e6944f | Text | 4,695 | 50 | # Neuroscience meets behavior: a systematic literature review on Magnetic Resonance Imaging of the brain combined with real-world digital phenotyping
Authors: Ana María Triana, Jari Saramäki, Enrico Glerean, and Nicholas Mark Edward Alexander Hayward.
This repository contains the code used to produce this systematic l... |
e22f30382dc61599f0ec3bc3e4d86abb98be001d3afc9361da53f504879aae9f | Text | 4,706 | 57 | This is the repo for performing inference using the baseline graph-pmhc model introduced in https://www.biorxiv.org/content/10.1101/2023.01.19.524779v1
# Inference Instructions
First clone the repo and enter a terminal in the repo folder
Next, create your virtual environment:
```
mamba env create -f environment... |
fb3625a6befa50f129ae321c7faef95d332b7057c24e765bc788e93eb2c37857 | Text | 4,712 | 70 | This README file was generated on 31.01.2024 by Ralph Gradisch, PhD
Last updated: 31.01.2024
--------------------
GENERAL INFORMATION
--------------------
// Title of manuscript: De novo variants in GABRA4 are associated with a neurological phenotype including developmental delay, behavioral abnormalities and epileps... |
0c4965f26aebbc473e4b5614287b2aae436c5a702a5828ec12dc140f8ded25b4 | Text | 4,738 | 97 | # DISCERN: Diagnosis In Susceptibility Contrast Enhancing Regions for Neuroncology
The app uses a pretrained CNN classifier scheme for voxel-wise classification of enhancing brain tumours into P-CNS-lymphoma, glioblastoma or brain metastasis, from dynamic susceptibility contrast (DSC) MRI data.
, a transformer ... |
530cbffea936e9a1a9a8aaf3be979ccffd3a50406a8544b8f57295c7e45c494c | Text | 4,747 | 41 | # Grid Codes versus Multi-Scale, Multi-Field Codes for Space
## 1. General Information
This repository contains the code used for the investigations of multi-scale, multi-field (MSMF) place codes and their comparison against grid codes which is presented in Dietrich et al. [[1]](#4-references). This MSMF code was rec... |
0465bffd28316900c127f618127381caac0535f8f41cf2ace28d3996550f307a | Text | 4,748 | 91 | # SBMLToolkit
[](https://julialang.zulipchat.com/#narrow/stream/279055-sciml-bridged)
[](https://do... |
363735d8c42a657f611eb8d14a4940768ed62d3ed45d42ed54789dc2e39b59dd | Text | 4,759 | 150 |
<!-- README.md is generated from README.Rmd. Please edit that file -->
# STew <img width="28%" align = "right" src="https://github.com/fanzhanglab/STew/blob/main/STewlogo.png">
[](https://github.com/fanzhanglab/STew/ac... |
9fc5f3a02c1f7717dc3977269a971a874807e76d555073cd7bc356ad0b56b9f1 | Text | 4,772 | 91 | 
An unsupervised method for identifying cell behaviour in heterogeneous cell trajectory data
cellPLATO workflow:
1. takes tracking and segmentation data as input
2. measures morphology and migration at each timepoint ... |
0439d55e2f407ea7addf01ad4df46fb020537c0408507337cc7f7b43cfa2f1af | Text | 4,780 | 123 | [](https://github.com/drugilsberg/paccmann/actions/workflows/build.yml)
# DISCLAIMER:
This code gives the `tensorflow` implementation of PaccMann as of our paper in [Molecular Pharmaceutics](https://pubs.acs.org/doi/10.1021/... |
cd30b4cfe724a513ea096a6c0e2d315bee94bcbc6c1d7e6ce293af84cc97cd8a | Text | 4,832 | 101 | # AccuSleep
## Updates
**11/09/2022** - A [video walkthrough](https://www.youtube.com/watch?v=O81qdHlzTbc) is now available.
**06/12/2021** - Support for scoring more than three brain states is now available with [AccuSleep X](https://github.com/zekebarger/AccuSleep_X).
**08/11/2020** - Mac compatibility. Acc... |
1e5dcefb2da9f129ebec67e69a296ef83d03523bab1722ac3e2efebfbd4f959c | Text | 4,861 | 94 | 
[](https://discord.gg/tDUPdRj4BM)
[
assemblyfire -v consensus configs/np_10seeds.yaml # find "consensus" assemblies (across repetitions)
assemblyfire -v conn-mat c... |
1a9f2abfb7f25c1e96b049079d87bc2b112953c256f4b742e8e67f52019b97d4 | Text | 4,883 | 34 | # pumpprobe
This repository contains code for the high-level analysis of the functional connectivity data in Randi et al. (submitted). It contains several scripts to generate figures, that rely on the 3 main classes Funatlas, Fconn, and ExponentialConvolution, as well as the Python modules [wormdatamodel](github.com/l... |
1fee8d391e8ef54d8a3bd01bfc1ff3d98a3dab4ff823d36a145e8427fae5f182 | Text | 4,883 | 97 | # Mol2vec
[Mol2vec](http://pubs.acs.org/doi/10.1021/acs.jcim.7b00616) - an unsupervised machine learning approach to learn vector representations of molecular substructures
[](http://mol2vec.readthedocs.org/en/latest/)
## Requireme... |
60f1ebfd97034c876802c33f231101a32e482f0f2811d07ace4ce524dbeed007 | Text | 4,900 | 113 | # MRI-Linac_SuperResolution
## Integrating deep learning into an MRI-linac
Authors: **James Grover**
Contained here is the code and documentation required to integrate super-resolution into Gadgetron.
## Build
### Prerequisites:
#### Gadgetron, Docker, CUDA.
[Gadgetron](https://github.com/gadgetron/gadgetron) is di... |
7c49287292fd680b3fcda6726dff3ba3a0aa327fe84a90e3599c7cc6f4dc35e5 | Text | 4,953 | 81 | # Detecting subtle transcriptomic perturbations in single-cell CRISPRi screening using a sparse supervised autoencoder neural network (SSAE)
This is the code from :
Detecting subtle transcriptomic perturbations induced by lncRNAs Knock-Down in single-cell CRISPRi screening using a new sparse supervised autoencoder n... |
1b376c058f8c4b292e75fa5255f8b469d1a27b4e49e6e7996655783caeb90969 | Text | 5,002 | 95 | # DISCERN: Diagnosis In Susceptibility Contrast Enhancing Regions for Neuroncology
This is the code repository of the brain tumour classification pipeline described in the work [*An accessible deep learning tool for voxel-wise classification of brain malignancies from perfusion MRI*](https://doi.org/10.1016/j.xcrm.202... |
1e35ac07db6cbbd871de70ceb9684436d6bcecd33869837718e6a5df2974617c | Text | 5,067 | 88 |
# Deep Transition Repository #
:tiger2: This repository provides an implementation of the gap-crossing scenario for the CPG-RL framework in the following paper:
- Viability Leads to the Emergence of Gait Transitions in Learning Agile Quadrupedal Locomotion on Challenging Terrains
Milad Shafiee, Guillaume Bellega... |
ee745c9c3f57dc6d3132169ed6b150b5b426ba4aa73d88f23ab30b6976650d95 | Text | 5,134 | 74 | # Welcome to Circle-Map official repository!
[](https://pypi.python.org/pypi/Circle-Map)
[](https://anaconda.org/bioconda/circle-map)
[ of AccuSleep is now available! Please consider switching to
this version. It offers several improvements over the original and will be more actively maintained.
**11/09/2022** - A [video walkthrough](https://www... |
e772fb9f47a61ab7e2388e6f42333218111747687255cc7c551011aadcbab6fd | Text | 5,194 | 123 | # "Spatiotemporal single cell analyses reveal a transient population of retinal progenitor cells in the ciliary margin of developing human retina"
This repository contains the analysis code needed to reproduce the results in the above paper.
## Data
The raw and processed data can be downloaded from GEO under the
fol... |
9e17cbd87640e7ae7dcaa1a6ae02af5518671eb25f4fc11727553053c5a9406e | Text | 5,225 | 81 | # Neurite Exchange Imaging (NEXI) model estimator for gray matter diffusion MRI
[](https://pypi.org/project/nexi)
[](#)
[](#)
[](https://github.com/ehb54/ultrascan3/actions/workflows/codeql-analysis.yml)
This is the home of the UltraScan GUI software source code.
More information is available [here](https://ultrascan.aucsolutions.com)
The UltraScan... |
f4191e43eda3d1cce7642464c714a9808cac37f58af3a307d42ea5c8a1890744 | Text | 5,380 | 89 | ## DeepBet - U-Net Brain extraction tool for nonhuman primates
Date: April 12th, 2021
----
## Description
This repo includes the brain extraction tool (DeepBet v1.0) for skull-stripping the nonhuman primate images. We also include brain masks of 136 macaque monkeys (20 sites) from [PRIME-DE](http://fcon_1000.projects... |
f25ffdf8b1bd3c476d955e6a96904625a5fc2416b6a0ea91c7048d622a407a2b | Text | 5,390 | 73 | # Midlands PM2.5 population exposure and health risk profiles
Code and derived data for *Population exposure and health risk profiles for fine particulate matter in Midlands Province, Zimbabwe* (Nyoni, Moyo, Chinwadzimba, Sibanda and Tigere; manuscript under review).
The analysis combines modelled daily and annual PM... |
d0786ec151f5587ce9757cd65da8ca47017c0c772084edec67bd3d3da9df7120 | Text | 5,410 | 173 | # Modeling Human Sentence Processing with Left-Corner Recurrent Neural Network Grammars
This repository provides the code for the paper [Modeling Human Sentence Processing with Left-Corner Recurrent Neural Network Grammars](https://aclanthology.org/2021.emnlp-main.235/).
> [Modeling Human Sentence Processing with Lef... |
8ff4002329ddc9c4287f0666d4c39aaad07674c9e51f007d2d86a2353b38f08b | Text | 5,473 | 113 | # Progeni
## Overview
This is the repository for the paper "A probabilistic knowledge graph for target identification."
Progeni is a novel machine learning-based framework for target identification.
Progeni integrates literature evidence with heterogeneous biological networks to construct a probabilistic knowledge ... |
a3ff7f315d84278afbdc906f9dbbb50a0e8339418c98522de3314a19849cff93 | Text | 5,476 | 194 | [](https://travis-ci.com/atarashansky/self-assembling-manifold)
# self-assembling-manifold -- SAM version 1.0.1
The Self-Assembling-Manifold (SAM) algorithm.
## Requirements
- `numpy`
- `scipy`
- `pandas`
- `scikit-lear... |
aa5cba58e3ea093670e15be26422ff9b039e07dad3070b035e338c0f05d915e7 | Text | 5,513 | 85 | <!-- Your title -->
# Welcome to the easy Lucas-Kanade PIV GitHub Page! 👋
This is a SUPER EASY TO USE version of a previously used and published method to do optical flow analysis in cells.
I got a version from **_Ivan Rey-Suarez_** and **_Arpita Upadhyaya_**, "Nanotopography modulates cytoskeletal organization and... |
f7bc43f0e5b896965c72de8f08ef6a914be5ea164982c270eea3807915a774b9 | Text | 5,560 | 130 | # graphite
A repository for implementing graph network models based on atomic structures.
## Implemented or replicated works
- ALIGNN
- [*Atomistic Line Graph Neural Network for improved materials property predictions*][ALIGNN paper]
- **ALIGNN-d** (our work, see [demo](notebooks/alignn/demo.ipynb))
- [*Eff... |
842f6f667276fc0c9ea6730a97e633a855fb4c1d9ad252ea145b27ce11578d03 | Text | 5,587 | 94 | <p align="center">
<img src="docs/_static/spycon_logo.png" />
</p>
# spycon: A toolbox for benchmarking neuronal connectivity inference
## Introduction
Numerous methods have been proposed that attempt to infer neuronal connectivity from parallel recorded spike trains.
Here we provide the `spycon` framework, that ... |
2d44332b943c7dbe4b03324bb46a33817caf576f73c0791bd5dc66761ce22b3d | Text | 5,598 | 111 | # Codes for Decoing Attended Spatial Location during Complex Scene Analysis with fNIRS
[](https://github.com/NoPenguinsLand/fNIRSCodes_Manuscript)
[   [![CI x64](https://github.com/macs3-project/MACS/actions/workfl... |
2f478839fad7625b353611004627f31442899e155c31fea6880ff128d379616a | Text | 5,625 | 88 | # Segmentation of breast and fibroglandular tissue in MRI: a publicly available dataset and deep learning model
This repository contains the source code and trained models for the research study titled "Segmentation of breast and fibroglandular tissue in MRI: a publicly available dataset and deep learning model".
Br... |
24e198fa037c5370442a701235ac79f8f625c06aa90e336e97850f8591332561 | Text | 5,626 | 82 | # non-B-gfa
gfa programs for Non-B site at NCI/FNLCR
gfa is a Suite of programs developed at NCI-Frederick/Frederick National Lab to find sequences associated with non-B DNA forming motifs
DNA exists in many possible conformations that include the A-DNA, B-DNA, and Z-DNA forms; of these, B-DNA is the most common form... |
2364182419176f1a08a2be7076500921dfb82c3355033f6f5978f96e1210e717 | Text | 5,756 | 115 | # UCell: Robust and scalable single-cell gene signature scoring
[](https://bioconductor.org/checkResults/release/bioc-LATEST/UCell)
[](https://bioconductor.org/packa... |
09096b30e1db6edf0b103436b2c0a06aafe6da65c339c4baac450b24d71c4472 | Text | 5,768 | 126 | # twixtools
[](https://github.com/pehses/twixtools/actions/workflows/test_action.yml)
### Purpose
twixtools provide reading and limited writing capability of Siemens MRI raw data files (.dat).
### Installation
Naviga... |
363a29e990157cebd1043c2d689cddcaf91394e8253205d2a736c1006a44f8e0 | Text | 5,781 | 36 | # Code supplement to the CNV asymmetry study
[](https://lbesson.mit-license.org/)
[]([https://doi.org/10.1101/2023.04.17.537199](https://doi.org/10.1101/2023.04.17.537199))
This repo... |
90f312a747bfa6df58d70c50e9153affccb8ab0205e25eac33469c4e5fe2d1b4 | Text | 5,955 | 104 | # suMRak
<b> A Simple Utility MRi Analysis Kit </b>
 
------------------------------------------------------------------------
suMRak is a MATLAB application created with the aim of simplif... |
4dd8f4f0800ddb50276668fe6c0525372acffa3df7f80106dcf7b56c3b00cecb | Text | 5,982 | 170 | # esmologs
Local homology search powered by the ESM-2 protein language model, Foldseek, HMMER, and hhsuite.
See also the paper associated with this code:
Johnson, Sean R., et al. “Sensitive Remote Homology Search by Local Alignment of Small Positional Embeddings from Protein Language Models.” eLife, vol. 12, Feb. 202... |
7fc2d67beb072dc27807e589a553183a9487eaa993780df3151b31f28b310379 | Text | 6,003 | 155 | [](https://pypi.python.org/pypi/cellex/)
# CELLEX
CELLEX (CELL-type EXpression-specificity) is a tool for computing cell-type Expression Specificity (ES) profiles. It employs a "wisdom of the crowd"-approach by integrating multiple ES metrics, thus co... |
0232c3e85490b18a68a358e8f4a8cf476863a1dbb5cadef09feed22c9cec7dbb | Text | 6,005 | 45 | # cameraCalibrationCMOS
Why calibrate your camera? If you want to compare the intensities of images recorded on different instruments or images recorded with different acquisition settings (e.g. different em-gain), you need to convert the pixel values from analog-to-digital (ADU) units to photoelectrons:
<p align="ce... |
ec28797ff34ed8fe2057774a11a95e10a406538213d1dce965ffdb392043306b | Text | 6,071 | 70 | Rtsne example
=============
This repository contains a short example showing how to calculate and plot a 2-dimensional t-SNE projection from a 13-dimensional mass cytometry data set, using the Rtsne package in R.
### t-SNE and Barnes-Hut-SNE
The t-SNE algorithm (t-SNE stands for *t-Distributed Stochastic Neighbor E... |
a37d690b090088675192309af45b9a5c2251dc74a2e5936f4db56462ceb48e3b | Text | 6,078 | 91 | ### MBID-db: Database for fusion of biomedical imaging studies
### Basic commands and miscellaneous information
* Script `run.py` will start Flask API and create DB. In order to create all tables, is necessary to run this command. `python run.py`
* Script `flask db migrate` will check changes in the db, and command `f... |
83db9affd15d807753ecbc2ca365ca09b80313da91375c7fe7077d04497fe27b | Text | 6,111 | 117 |
# Deep Transition Repository #
This repository provides an implementation (Simulation code) of the CPG-RL framework in the following paper:
<td style="padding:20px;width:75%;vertical-align:middle">
<b> Viability Leads to the Emergence of Gait Transitions in Learning Agile Quadrupedal Locomotion on Challengi... |
4cf9f23c7ee8459c08e4ad13f2afbd7ba52609c7c85c08e6b99a3eef01a00427 | Text | 6,115 | 132 | # Accurate and interpretable drug-drug interaction prediction enabled by knowledge subgraph learning
## Contents
- [Overview](#overview)
- [Repo Contents](#repo-contents)
- [System Requirements](#system-requirements)
- [Installation Guide](#installation-guide)
- [Examples](#Examples)
- [Results](#results)
- [License... |
7133a7e8a32a8aedde2755fdaf6bfbb17d6094114cdf5db6053e5cf8b0024565 | Text | 6,155 | 99 | # myProMS Server
Mass spectrometry(MS)-based proteomics data management and analysis software.
**myProMS** is a web server developed to allow MS specialists and their collaborators to efficiently manage, process and interprete MS-based proteomics data.
Go to **myProMS** [home page](http://myproms-demo.curie.fr) for mor... |
780e89ae00c334e9da49a45b2b343621419987b75d9d9f64f40aaf1921336fe6 | Text | 6,164 | 94 | <p align="center">
<img height="160" src="docs/_static/logo.png" />
</p>
##
[](https://github.com/lucascamillomd/pyaging/actions/workflows/ci.yml)
[: e0302169, 2024](https://doi.org/10.1371/journal.pone.0302169)
<a href="mailto:nadezhda.koriakina@it.uu.se">Nadezhda Koriakina</a>:envelope:, <a href="mailto:natasa.slado... |
c44883d5c947e5dba86e7ebac8259cd84e89996097718875822c30a411a52b7d | Text | 6,257 | 61 | # IMAXT StarDist Cellpose
## Training data
This repository includes StarDist [1,2] and Cellpose [3] nuclei segmentation models trained using all publicly available and IMAXT data. It also includes notebooks for running the inference using these models. For the instalation of StarDist and Cellpose please refer to the ... |
9da81026fdc064988aa4bba4b9a6569db366426ebff7a495216c763ea09d7842 | Text | 6,259 | 92 | <!-- PROJECT LOGO -->
<br />
<div align="center">
<h3 align="center">Blur Training</h3>
<p align="center">
This GitHub repository contains the training code for data augmentation using blurry images, as detailed in the research paper "Improved modeling of human vision by incorporating robustness to blur in co... |
be283273b373f6091c957b1ed1a7d951c0dd6ab4b1501b05ad55d25b95330f02 | Text | 6,278 | 113 | ## About
This package allows you to load event files produced by Med Associates software, and eases working with the resulting data. Also includes a growing library of analysis routines.
## Install
We recommend you use anaconda virtual environments. Two main ways to install. The first, create the virtual environment, ... |
ac4a007470ee0be85f249fe52e8e0c705e5a9d93b1df0dd89cfdc1d37da6657a | Text | 6,294 | 77 | # [CVPR 2023] Official Implementation of VideoMAE V2
[](https://paperswithcode.com/sota/spatio-temporal-a... |
36c8bcb416fc5187e2d757d0b8a8e3d75dc8e21de6fe0274d8eec42b7f1ac610 | Text | 6,306 | 114 | ## Enhanced short fiber bundle segmentation
This repository contains the code used in: "Short fiber bundle filtering and test-retest reproducibility of the superficial white matter". Which enables the segmentation of well-defined Superficial White Matter (SWM) fiber bundles.
Four fiber bu... |
cc285fa6aca1d65332edcebe82b081f605c68fd9b301e27c205cd85962958468 | Text | 6,319 | 91 | # Brain Metastasis Detection
Deep learning-based Metastasis Detection to Enhance Reproducibility and Reduce Workload in Brain Metastasis Screening with MRI: A Multi-center Simulation Study
**Summary statement**
- Deep learning-based detection of brain metastasis has the potential to result in a more reproducible and s... |
3c82316b5655058cf969d780e5338b2d0207407d60254c7fc652f3dc95122258 | Text | 6,378 | 81 | # Delayed Speech Synthesis
Repository accompanying the study **Online speech synthesis using a chronically implanted brain-computer interface in an individual with ALS** by Angrick et al. [1] containing scripts to train and run the speech synthesizer.
This Brain-Computer Interface (BCI) enabled an individual living w... |
301655510ce1a6a2d1db4d7a9ec459c18ad2bd63ba6e2fe64964900f741d7b96 | Text | 6,411 | 129 | # Neural Speech Decoding
By Xupeng Chen, Ran Wang, Amirhossein Khalilian-Gourtani, Leyao Yu, Patricia Dugan, Daniel Friedman, Werner Doyle, Orrin Devinsky, Yao Wang, Adeen Flinker
[](https://zenodo.org/doi/10.5281/zenodo.10685177)
## DEMO
Check our [Demo Page](https://x... |
e7ab229212c45d9a7d63d8713a98fc3e139561a4e5486ea5e5f471c2cf738427 | Text | 6,432 | 74 | # Audiovisual Moments in Time: A Large-Scale Annotated Dataset of Audiovisual Actions
This repository contains code corresponding to https://arxiv.org/abs/2308.09685. Feature embeddings can be found at https://zenodo.org/record/8253350.
Feature extractor code (used to produce the embeddings) and example code to show ... |
d419e1c64faa656543bf01c10e85c43929f40c92af4280840462df73674feea9 | Text | 6,554 | 177 | # Multichannel time series lossless compression in Python
[](https://travis-ci.org/int-brain-lab/mtscomp)
[](https://codecov.io/gh/int-brain-lab/mts... |
a8262a2b56d6c5a729a425d0c0728888bdc48e315aaa562c0491334affe56553 | Text | 6,608 | 139 |
# <div align="center" style="text-align: center; font-size: 32px;"> <b><a href=https://github.com/chan-labsite/SC-Track>SC-Track: a robust cell tracking algorithm for generating accurate single cell linages from diverse cell segmentations</a></b></div>
<div align="center"> <img src="docs/icon/license.svg" width = 22... |
85d80f6d94f41a0696c81dc05651f5fcdd3bbfe5ccc09c7fef9c9defcefa9feb | Text | 6,622 | 71 | # Dvoretskova-et-al
This repository includes the necessary code to reproduce the analysis presented in the paper titled 'Spatial enhancer activation determines inhibitory neuron identity.'
## Data and Code Associated with the Study
**Title:** Spatial Enhancer Activation Determines Inhibitory Neuron Identity
**DOI:*... |
0243bb723fa81cccf5c37e661f7a437daa989720cf498c513af5451353a02e90 | Text | 6,628 | 85 | # GNOVA-2.0
GNOVA (GeNetic cOVariance Analyzer), a principled framework to estimate annotation-stratified genetic covariance using GWAS summary statistics. **The major different between GNOVA-2.0 and the previous version of GNOVA is that GNOVA-2.0 provides the estimation of SE for genetic correlation.**
## Requiremen... |
a96732666e80b4401cf9b3f41c301622ea4343334d54fc756f5180845c75728b | Text | 6,737 | 193 | <div align="center">
# NEATmap documentation
</div>
_**NEATmap: a high-efficiency deep learning approach for whole mouse brain neuronal activity trace mapping**_
<p align="center">
<img src="doc\Html\NEATmap_demo.PNG"
height="300">
</p>
The explanation is as follows:
## Content
* [**1. Abstract & Availability*... |
0fbdfc713bd876324f7cd2befcea7f306f74a5bf44a1cf8c71834534aeef4833 | Text | 6,783 | 85 | # TrackerSeq
TrackerSeq is a single-cell RNA sequencing compatible method (e.g. 10X genomics, plate-based sequencing, etc.) that labels cells with a unique lineage barcode. This repository contains a maintained TrackerSeq preprocessnig pipeline and preliminary analysis scripts including multi-core processing that can ... |
eb6d02e90e980125f665be41013d76a60165d87fc5c0c85fdcf4f7a88e2bddd4 | Text | 6,818 | 107 | # Osprey
Osprey is software for phasing or imputing copy number variants using SNP genotypes.
## History
Osprey is derived from methods developed for imputation of VNTRs in a collaboration between Bob Handsaker
in the lab of Steve McCarroll (http://mccarrolllab.org) and Ronen Mukamel and Po-Ru Loh in the Loh lab
(ht... |
84b8422bd60470c70e07c5b1a2157921aa23c8c8029f04132a91ac5c64de6597 | Text | 6,875 | 150 | # SuperBigFLICA
SuperBigFLICA is a semi-supervised framework for multimodal neuroimaging data fusion. It learns shared latent components and modality-specific spatial maps while predicting a clinical or behavioral target.
The current pipeline learns fresh dictionaries, uses fixed equal loss weights, and selects a mod... |
b7d69603b1594b3d07200eaf79cbb1221d7dc532e33ae0d43764b4811ea1ded3 | Text | 6,950 | 125 | # MothDrinks
This repository contains data for the paper submission titled "Feeding rate in *Manduca sexta* is unaffected by proboscis
submersion depth"
Code can be found in the repository at [https://github.com/Tomas-Pierce-at-UNC/MothDrinks](https://github.com/Tomas-Pierce-at-UNC/MothDrinks).
## Goals
* measure ra... |
b848957cb07a68fc66451992004c040fe10cbdc1e1d47ef3d6674e0d802d67f1 | Text | 6,963 | 128 | # MothDrinks
This repository contains code and data for the paper submission titled "Feeding rate in *Manduca sexta* is unaffected by proboscis
submersion depth"
## Goals
* measure rate of nectar ingestion from video data
* measure proboscis submergence depth from video data
* evaluate whether nectar ingestion rate an... |
9f93ced73b4f43fd905494efb1ee6d2c3cb21d315ebba164956e416ca339d707 | Text | 7,047 | 139 | ---
<div align="center">
# Predicting Mortality after Transcatheter Aortic Valve Replacement using Preprocedural CT
[](https://www.nature.com/articles/s41598-024-63022-x)
</div>
The repository provides `PyTorch Lightning` code fo... |
a381e4e0188dd96166e252a86e67f9768d76aa8aa994ded506b1721310c82e38 | Text | 7,107 | 119 | 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:
Thi software run on MATLAB and requires Image Processing Toolbox
It has been tested on... |
499cec239fb99e8038f4e4a6cc251e79cecdc2c22dab9024be3f16233fa7c8f9 | Text | 7,133 | 133 | <h1 align="center">Roost</h1>
<h4 align="center">Representation Learning from Stoichiometry</h4>
<h4 align="center">
[](https://github.com/comprhys/roost/graph... |
84aa725e3ea075f622169bbfe501131ada2dda3dba91312b16fe8d0b65593a33 | Text | 7,160 | 184 | # cptools2 — Python package
A lightweight command-line package to generate and manage CellProfiler analysis jobs for HPC clusters. cptools2 builds image lists, splits work into jobs, creates space-optimized plate batches, generates submission scripts, and can join and optionally transfer result CSVs after analysis.
-... |
76d77f07ffa85e04a39938ff6152f81a8b34dbe557039329c8638fbf003d63ba | Text | 7,215 | 128 | # The Actigraphy Project
[](https://zenodo.org/badge/latestdoi/267943462)
# Contents
- [Overview](#overview)
- [What's New](#whats-new)
- [Repo Contents](#repo-contents)
- [System Requirements](#system-requirements)
- [Installation Guide](#installation-guide)
- [Reading ... |
7fdd9fe99dba881f3398328af1da0ae3712ddda521155766608dad0f4614cb73 | Text | 7,255 | 126 | # moseq2-lda
## A framework for LDA analysis of moseq data
This package gathers some common methods and formalizes a framework for rapid execution of LDA analysis with moseq data.
## Installation
Code relies on `moseq2-viz`. Please be sure to install this dependency prior to installing this library.
Specific version ... |
db9978ceb24ffcb996f59e87b161cf809c68d3293cb41c4bd695404b349554a1 | Text | 7,316 | 34 | # Spatiotemporal immune atlas of the first clinical-grade, gene-edited pig-to-human kidney xenotransplant
This repository contains analytics files and code used in the generation of the manuscript: *Spatiotemporal immune atlas of the first clinical-grade, gene-edited pig-to-human kidney xenotransplant*
##### Fi... |
a489c2b505c29ee0b2a63e0abfad91219f647a199246479ef9363ed4d5c611dc | Text | 7,345 | 186 | # Welcome to DenRAM
## Repo Content
- `requirements`: directory containing the requirements files for macOS and
Linux
- `reproduction`:
- directory containing the expected results (`expected_results_fig4d.csv`)
and figures (`expected_fig4d_D1andD2.jpg`) of the execution of `code/reproduce_fig4d_D1andD2_training... |
718d37a53a84615961dcdf519602cfaf1467b192bb691f8e880fbadf9e92de0d | Text | 7,354 | 95 | # Benchmarking Neural Network Robustness to Common Corruptions and Perturbations
This repository contains the datasets and some code for the paper [Benchmarking Neural Network Robustness to Common Corruptions and Perturbations](https://arxiv.org/abs/1903.12261) (ICLR 2019) by Dan Hendrycks and Thomas Dietterich.
Requ... |
b8763b60042207994fac22b9c14ab555de42107d4cf3113dca6fce0a4abdb327 | Text | 7,412 | 139 | mantel
======
Python implementation of the Mantel test (Mantel, 1967), which is a significance test of the correlation between two distance matrices.
Installation
------------
The `mantel` package is available on PyPI and can be installed using `pip`:
```shell
$ pip install mantel
```
Once installed, the package ... |
dd3ba53fe73b62abe838859cbcd23c11bc9d06cb4bcf525552d20e346991b7b5 | Text | 7,422 | 163 | # deltaVinaXGB
This is a machine-learning based protein-ligand scoring function.
### Setup
Create environment
```
make Makefile create_environment
conda activate DXGB
make Makefile requirements
```
Install xgboost, rdkit and obabel, these packages can be easily installed using anaconda
```
conda install -c conda-forge ... |
89224b7eff906a01abe7f8193fa22473379f0c4bfc8aff2c4c96afea2d011b43 | Text | 7,474 | 142 | # UrsoNet for Monocular Spacecraft 6D Pose estimation
Tensorflow/Keras implementation of UrsoNet, the network used on the [European Space Agency's Pose Estimation Challenge](https://kelvins.esa.int/satellite-pose-estimation-challenge/) that achieved 3th place.
<p align="center">
<img src="./media/demo.gif" width="50%... |
4c6aa03d7face1d9e3fd9c315dc182b6445d038a129d569edd2fda51d82733da | Text | 7,503 | 104 | <p align="center"><img width="70%" src="figures/logo.png" /></p>
<div align="center">
[](https://github.com/MrGiovanni/ModelsGenesis/starga... |
5ce9b84f5f8fcf2068c16f79d911b7a11c5dd43a3ebe93901904e230ba2efdcd | Text | 7,692 | 75 | <h1 align="center"><img width="300px" src="docs/logo_pb-metagenomics-tools.svg"/></h1>
<h1 align="center">pb-metagenomics-tools</h1>
<h3 align="center">Tools for performing metagenomic analyses using HiFi sequencing data.</h3>
Welcome! Here you can find a variety of tools and pipelines for HiFi metagenomics.
The cu... |
f8ca0d8e96288b8bf1b037220044ece880789b0b2fd79c35457cfc9c2be7a7fc | Text | 7,713 | 183 | # **SIMS**: Scalable, Interpretable Modeling for Single-Cell RNA-Seq Data Classification
SIMS is a pipeline for building interpretable and accurate classifiers for identifying any target on single-cell rna-seq data. The SIMS model is based on [Tabnet](https://arxiv.org/abs/1908.07442), a Deep Learning model specifical... |
33dba6d2f71ed9a11841d634de46a3cc8ab81a3dd2da2496f88989b1deda768a | Text | 7,728 | 150 | # RL Toolkit
[](https://github.com/markub3327/rl-toolkit/releases)
[](https://github.com/markub3327/rl-toolkit/is... |
99a2bec023788e5d3dc6d195b3e28452192ecbd21b6a94fd830a3ef26e321395 | Text | 7,729 | 194 | # LEMBAS - Large-scale knowledge-EMBedded Artificial Signaling-networks
- LEMBAS enables genome-scale simulation of intracellular signaling.
- Abstract:
Mammalian cells adapt their functional state in response to external signals in form of ligands that bind
receptors on the cell-surface. Mechanistically, this i... |
706b97ad32f68e33709b869751e3227f53a7325a98f8a7202e36fac0fee0318a | Text | 7,731 | 117 | <h1 align="center">
<picture>
<source media="(prefers-color-scheme: dark)" srcset="https://raw.githubusercontent.com/PTB-MR/mrpro/refs/heads/main/docs/source/_static/logo_white.svg">
<source media="(prefers-color-scheme: light)" srcset="https://raw.githubusercontent.com/PTB-MR/mrpro/refs/heads/main/docs/source/_st... |
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