sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
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fe3fda48a080297865db6440976cab95ed6e4d73e4d0d3fb5535730f61191575 | Text | 190 | 2 | # analysis-for-dMRI-in-PM-AD
Analysis scripts used in "Identification of diffusion, kurtosis, and propagator MRI markers of Alzheimer's Disease pathology in post-mortem human tissue" paper.
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33d1ca5c706a90029e23f48153825e88e827ba3b724f0361e0884a2401d72253 | Text | 191 | 1 | Repository associated with the paper "Explainable AI to Facilitate Understanding of Neural Network-Based Metabolite Profiling Using NMR Spectroscopy" published in Metabolites: add link here.
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5da094e51006114a5f64dc55be01d2fd781ab2d6fa23f6f09f7a6882f0d077bd | Text | 198 | 2 | # Chunk Neuron
The original code for the analysis of ""(Hirokane et al., "Representation of rhythmic chunking in striatum of mice executing complex continuous movement sequences. Cell Report. 2024)
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f834916db88a23aeb006c1f142c24d20d6e19e6199949418a2326d8b0d56f52a | Text | 198 | 1 | This code post processing the tubemap gt file into an matlab graph file and make density profile for each ROI of mouse brain according to Allen mouse Atlas https://mouse.brain-map.org/static/atlas
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6bd1e5365be658663ae6cf7edef6fde810de40ef49131fda971ddf34dce3f778 | Text | 201 | 5 | # Organoid epigenomics
Scripts to reproduce the analyses from the manuscript *Single-cell epigenomic reconstruction of developmental trajectories in human neural organoid systems from pluripotency*
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f0da9958272a61be091a355e09bed23752e3533480559a467f7c201a9ef4510e | Text | 207 | 1 | These scripts were used for the simulations in the paper Delamare et. al, Drift of neural ensembles driven by slow fluctuations of intrinsic excitability, eLife, 2023, https://doi.org/10.7554/eLife.88053.2
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fa49dee54e21c2936aeddea3def8be7186b5c992dc2d6dc9e65f9509f7b7e245 | Text | 207 | 7 | ## Deprecation notice
This fork is now deprecated.
PycoMeth is now maintened and developped by [Rene Snajder](https://github.com/snajder-r) at the following URL:
**https://github.com/snajder-r/pycoMeth**
|
28567384f54289c413c7a4b2ba17566bfc9948012bc8bbec01a69d228037b52f | Text | 221 | 2 | # Zebrafish-LFP
Matlab code for Local field potential analysis. For more information see Zebrafish models of candidate human epilepsy-associated genes provide evidence of hyperexcitability (DOI:10.1101/2024.02.07.579190)
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8f0c1def6f52863b5200010fad2455f33fe799a3032d7e34d1b581e0b366f14d | Text | 239 | 2 | # Custom-Data-Acquisition-Program-
Program used to acquire electrophysiological data. This requires labview main program to function.It works in conjunciton with multiclamp amplifier. This includes a .vi file and an executable .llb file.
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60fdb693f88c69d2b6166842166fe0eeb8b18874ddf53e3dd7642d953b6ec9cc | Text | 250 | 2 | transcriptome.fa - Reference transcriptome fasta file containing the sequence for known transcripts (Ensembl version 107), ERCC reference transcripts,
and new transcripts (no filter applied, everything bambu called a new transcript). |
351575abc8db508dbe8cb9abc25889418cc8c01d7e5e9daf0dc7567eb4424a88 | Text | 252 | 5 | # 3D_VGG_ADNI
This project is used to preprocess the ADNI dataset and implement classification based on the 3DVGG model.
The model files can be found at following URL:
https://drive.google.com/file/d/1QDFPQUN5FMzKDvH0In3thMQp5mXxZIUR/view?usp=sharing
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80b08222cacc5b15188a97dbf082c81e1c46e977230e171373398b1f58569345 | Text | 258 | 5 | # hera
hera is a tool for displaying heart rate data collected from brainamp converter, and correcting it for artifacts.
**DISCLAIMER: This tool was intended for internal usage only. It is made public for reproducibility reasons. No support is provided.**
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cb9c27a8d43374a48f65644ac8ab22c74212aa81cf05eec11dc0c583205ad203 | Text | 259 | 6 | # atlaskit
Tools for working with deterministic and probabilistic anatomic atlas labels.
[](https://zenodo.org/badge/latestdoi/33556742)
See the wiki for documentation (https://github.com/jmtyszka/atlaskit/wiki)
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fc27eb98631bb968d7608d5f674d28e09fd19d6f937af7f0025721bc36ca6771 | Text | 289 | 3 | # Website [qald.aksw.org](https://qald.aksw.org/)
The image is deployed from here to hub.docker.com and is deployed via docker-compose.yml to a server at Leipzig University (https://git.informatik.uni-leipzig.de/aksw/docker-deployment/-/tree/master/qald) where it is picked-up by traefik
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dff2b61ae5951f3baeaaf2af2453d302b0aa6ed4bc28253c8d3d6bc7486fed11 | Text | 305 | 5 | # brainampconverter
Tool to convert physiology data collected using Brainamp systems to format readable by matlab. Also cleans MRI artifacts from the Brainamp signals.
**DISCLAIMER: This tool was intended for internal usage only. It is made public for reproducibility reasons. No support is provided.**
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773ee3e3719ca3dedb217ead5f61e7c85c39067b622ce572174836337a8f89b0 | Text | 308 | 9 | # 2024_entopy_paper
matlab code for 2024 entropy paper
Notes:
get_logits folder has the code we used to generate the first 10k logits for each network from the MirFlickr 1M image collection
matlab data files containing the logits are also in that folder, there is no need to regenerate using this code.
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ef6fd62af999f10068eeca6236a22e636b11e525b6d2ffcf28b7cb6483e3ce23 | Text | 325 | 14 | # sbi-spectrome
simulation-based inference of spectral graph model
## Required packages
jupyter-lab
spectrome
sbi
scikit-learn
scipy
torch
## Instructions
1. Copy jupyter notebook to the notebooks folder of the spectrome installation
2. Load notebook (Examples_and_Figures_SBI of SGM_20220302.ipynb) in jup... |
3a6f6472d5582a5bcdb37e305020a022feb3e1122a17a1806830ad901d2f1ff3 | Text | 329 | 7 | All codes can be run from Pipeline.m by changing the relevant directories.
The source space data for Early auditroy cortex (EAC) and behavioral data can be downloaded from https://figshare.com/s/93ec964d59fd4efd76f5 under a CC-BY 4.0 license.
The folder "variables" contains matlab files needed to generate the main fi... |
71fc5f334492ddc3486b1fdbd1251a9873ee3dd25b5026bb9dc8c25303a1ac16 | Text | 330 | 10 | # C3NS IRG3-Collaboration
A repository for sharing the integration of an SNS neural circuitry model and a simplified biomechanical model for *Aplysia* feeding.
Participating Organizations:
Case Western Reserve University - Quinn Lab, Chiel Lab
Carnegie Mellon University - Webster-Wood Lab
University of Lincoln - Su... |
b6f8643adb9988e02e54364067252bdc880f37dc2568d45c84b18d5ca872d0a3 | Text | 331 | 7 | # Go_ZIKA_NHP_FetalBrain
Details for the analysis of RNA bulk sequencing data on Pigtail Macaque Fetal Brain regions infected with ZIKV
Codes for DE analysis 1.Analysis.r
Data available here: GSE226401 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE226401
or in data/ folder # Tisoncik-Go_ZIKA_NHP_BulkRNAseq_... |
0b08330b604121a6df7f3dd1982bb49112c9b3ccf3873d757379dfcd3dcd759b | Text | 341 | 3 | # from_MIA_to_metabolism
Repository for analysis of data related to the publication 'Pulmonary maternal immune activation does not cross the placenta but leads to fetal metabolic adaptation', Nature Communications 2024
Version 1 includes scripts for data (pre) processing, scripts for downstream analysis will be include... |
1e935581268f1bce10aa5083539bc76164619d4c0bb802497253265e6b41e5e4 | Text | 360 | 6 | # QDyeFinder
QDye Finder is a pipeline that is used to cluster fragments based on their colour alone
Further information is provided in the word document (UserGuide.docx).
Simply download the code and set the path in matlab and follow the user guides to run the codes.
This has been tested on MATLAB 2021b (v9.11). Down... |
83d30932f5e366ec1779b52c84bbfb408058d4368b035dd7ee7b74ebfa549f47 | Text | 376 | 12 | # NYU_EffiModel
This repository contains the source code accompanying the
paper "Efficient models of cortical activity via local dynamic
equilibria and coarse-grained interactions," to submitted to PNAS.
Meanwhile, if you have any questions, please contact one of
us.
Zhuo-Cheng Xiao <zx555@nyu.edu>
Kevin K. Lin <k... |
78d50ef1d6007931fe5133997ddae968ef9787008edb6dd246e8bec7076e795f | Text | 377 | 8 | # MEG_ProsodyEnhSyntax
Source code and data for the paper called: Speech prosody enhances the neural processing of syntax.
## Running the code
Within each folder (StimFeatures and BrainDecoding) there is a readme explaining the what can be run.
Look at these files for the dependency needed.
Remeber to set the ... |
7ae7275e278275adb52c098ce480bec3d85ef95c6fc62e41067b08e0ac0ea342 | Text | 389 | 14 | Code used in paper includes:
0) Bulk-tissue data pre-processing
1) Cell proportion calculation and evaluation
2) Cell-type expression calculation and evaluation
3) Marker gene identification
4）Reference construction
5) decon-eQTL mapping
6) Schizophrenia GWAS heribitability
7) Phenotype-associated gene (PAG) ... |
f829489d62d03131f3c7853d9514420865df92b6d28b2bca3fac8c375f29a33d | Text | 389 | 2 | # EEG-Visual-Multiclass-Classification
This work addresses the challenge of EEG multiclass classification into 40 classes for BCI applications, by using deep learning architectures. Multi-class classification approach offers BCI applications a significant advantage since it allows the supervision of more than one BCI i... |
3104da0b5c7b5a3f441ad64769fa148634484c30761066c9f3b8d6d72556d2e5 | Text | 404 | 11 | # image_seg_sorghum
This project use [detectron2](https://github.com/facebookresearch/detectron2) to segment different parts in AM fungi (within Sorghum). It has been tested on mutliple [dataset](tutorial/dataset.md).
# Getting start
The models were trained on HPC ([GACRC](https://gacrc.uga.edu)). Pleast refer to th... |
496fa9dd39b14c476bb5dd7ed4f172edc5b726f56e4d6b5e46913e50a9dee6af | Text | 406 | 2 | This code is designed for analyzing data formate from Wu et al., "Quantitative relationship between cerebrovascular network and neuronal cell types in mice." Cell reports (2022) PMID: 35732133 and Bennett et al., "Aging drives cerebrovascular network remodeling and functional changes in the mouse brain" Nature Communic... |
27c156149c69b1992e02387b1fe1a429fdf4037249100d76ef26bb161a1e4925 | Text | 417 | 6 | # BayesianNSI
Bayesian system identification for neural prediction.
The repository contains code for our manuscript:
Wu, N., Valera, I., Sinz, F., Ecker, A., Euler, T. and Qiu, Y., 2024. Probabilistic neural transfer function estimation with Bayesian system identification. PLOS Computational Biology, 20(7), p.e101235... |
622b108bcece2bdc6d539af62cb1905da108322437d77d1b513881ba21936f6b | Text | 431 | 3 | # Zebrafish-Neuron-Counter
FIJI Macro for quantifying tectal interneurons in tg(dlx6a-1.4kbdlx5a/dlx6a: GFP::vglut2:DsRed) zebrafish.
For more information refer to Mosaic and non-mosaic protocadherin 19 mutation leads to neuronal hyperexcitability in zebrafish (doi: 10.1016/j.nbd.2022.105738) and Zebrafish models of c... |
9796a0f12068ac5e1fff0a316df9d98c6c8457a2377e2690b02c90aec456c967 | Text | 441 | 12 | # C3NS IRG3-Collaboration
A repository for sharing the integration of an SNS neural circuitry model and a simplified biomechanical model for *Aplysia* feeding.
Participating Organizations:
Case Western Reserve University - Quinn Lab, Chiel Lab
Carnegie Mellon University - Webster-Wood Lab
University of Lincoln - Su... |
ff4fe3602e8425c4fdd70c5d6637455bdb42d6b622460f68ffbfd51657e983fd | Text | 441 | 4 | # calculate_kd
Matlab script to calculate degree rank order disruption index
The script is provided as is. The script was developed for the purpose of calculating degree rank order disruption index (kD) for a research project https://osf.io/e37td/. Actual file names in the script were replaced by dummies. It is very l... |
0491fea5c7e96ee3c2196a58f3bc2da029d7bbe7594d02689d4ece105533b1dd | Text | 447 | 5 | # The molecular mechanism of monovalent cation selectivity in the TRPM5 channel
This repository contains the molecular dynamics input files, and analysis scripts developed and associated with the publication Ives, Thomson and Zachariae, 2023.
> _Due to the size of the files, the simulation trajectories from this stud... |
06c9987a5fb0b402b7a0acb470543727053a2a0d7d46b741989a73844335e24e | Text | 447 | 7 | # pycilium
----------
Python package to read annotations and support data analysis in the paper:
["Nanometer-scale views of visual cortex reveal anatomical features of primary cilia poised to detect synaptic spillover"](https://www.biorxiv.org/content/10.1101/2023.10.31.564838v2)
## Level of Support
We are not current... |
ab9544ea40e56b8bf85b2d0cd6c6642c7b03725dabe70779e1f0a67841a97f95 | Text | 459 | 18 | # matspec
matlab code from spectro preprocessing
_siemens dicom spectro read into matlab
_simple spectra preprocessing for single spectra acquisition (and also MEGA press):
phase/frequency correction before summing
_ plot functions
_ lcmodel preparation of .CONTROL file
_ lcmodel results read to write csv output... |
649be377a232759c10ec6e0e06f66b524863b25cab9134352be3ac8b65a4df1f | Text | 461 | 6 | # NetActivity paper
Code for reproducing the results of NetActivity paper:
- scripts: Code for the analyses is placed in the scripts folder.
- docker_sources: Docker recipes of containers to reproduce the analyses.
- modules and workflows: Nextflow code for training the model. The same functionality has been implemente... |
b8690f61e1a60921fdbc75453c147546b7ae98482b5124e3719d22b267ccb71e | Text | 464 | 8 | # Ashwood-MIA-RNAseq-2023
Osman et al MIA placenta and fetal brain RNAseq analysis
Analysis of 3'Quant RNA Seq of placenta and fetal brain.
Raw Fastq QC, UMI collapsing, alignment, and gene counts was performed using the Master_QuantSeqAnalyisV2.sh script.
Reads were then read into R as a counts matrix, filtered, an... |
97307846395f185fd10a4b06c387b2d6c2069ed64a3febdce5d34e1f89fa544f | Text | 466 | 7 | # VidalPineiro_BrainAge
Scripts for Individual variations in ‘brain age’ relate to early-life factors more than to longitudinal brain change
Vidal-Pineiro et al. eLife 2021;10:e69995. DOI: https://doi.org/10.7554/eLife.69995
The repository includes the scripts used for preparing the abovementioned project.
Data not ... |
346a359efe61a393c1e9e858469c681c18ec3517fbbe4b413a7850b30d2b90fc | Text | 475 | 6 |
### This code is associated with the paper from Chang et al., "Distinct stages of synapse elimination are induced by burst firing of CA1 neurons and differentially require MEF2A/D". eLife, 2017. http://dx.doi.org/10.7554/eLife.26278
# Custom-Data-Acquisition-Program-
Program used to acquire electrophysiological dat... |
b779ded79b21428badc8ef4c7685d5f58077ee54e61ec38dfd59aee55b1d1b8b | Text | 482 | 7 | # Project Repository for "The mouse motor system contains multiple premotor areas and partially follows human organisational principles"
Welcome to the project repository for the materials and code accompanying _"The mouse motor system contains multiple premotor areas and partially follows human
organisational princip... |
e34dbafd7a73d4013f93ba3470548c152dcc3b734d5632a46eac2329aa78022f | Text | 490 | 5 | # Neighborhood-Structure-Guided-Brain-Functional-Networks-Estimation-for-MCI-Identification
All the data used in the experiments, as well as the models generated and the source code are available in this repository.
The data.xlsx and data.xlsx files are used to store the raw data required for the experiment. The raw ... |
c81bfddd2e0138497d33947c6a5bd8817cb4310e2a3e732a88032f09b4b1f135 | Text | 498 | 7 | # Supporting Material
This repository contains supporting material for the research performed at the Laboratory of Neurovascular Interactions (Université Laval, Quebec, Canada) directed by Dr. Ayman ElAli (https://elalilab.com/).
## Folder/File list
- **2024_Stroke_Pdgfd:** Contains the supporting files for the artic... |
0eb8dfb0b73ef566a0fc59c9158afc8df925d288dd1cf0892916314efe3bdc89 | Text | 506 | 12 | # Code supplement
This repository contains the code used to process and analyse the data presented in the "Supervised latent factor modeling isolates cell-type-specific transcriptomic modules that underlie Alzheimer’s disease progression" paper.
Create the conda python environment:
`conda env create -f environment.ya... |
3587e5e3724a6a93ffad2f64464a810a60646ec6c5fd70f4e59b36b541444f2b | Text | 508 | 10 | # OSproject
buildNeuronTable.m compiles data from all the FOV movies into one giant neuronTable in Matlab that include all data and metadata
OSpropAndTuning.m & plotWvfs.m computes and plots results from figures 1 & 2
For modelling lines on retina:
Run modelEllipseUI.mlapp in Matlab (was done on Matlab 2022a)
Will... |
253611a9dcd45d5db73a15b74e63fac56081ad7678226cf9595b3365cb5d5829 | Text | 509 | 7 | # Supporting Material
This repository contains supporting material for the research performed at the Laboratory of Neurovascular Interactions (Université Laval, Quebec, Canada) directed by Dr. Ayman ElAli (https://elalilab.com/).
## Folder/File list
- **2024_Stroke_Pdgfd:** Contains the supporting files for the artic... |
d41ff17d41fdb64c41304ee7ab35cd06ae797b3899b118e875ef1a226fead3fb | Text | 509 | 11 | # Microbiome Analysis
Here we will provide a selection of analytical approaches, tools, and utilities for the processing of microbiome data derived from either 16S rRNA amplicon sequencing or shotgun metagenomics.
View the wiki [here](https://github.com/mucosal-immunology-lab/microbiome-analysis/wiki)
## Rights
* C... |
9ede0d3e36005c3330ece6b32404fa9293360328adb8df73c58be3c0ed61d680 | Text | 548 | 13 | # Prepulse Inhibition Model
Code for the simulation of prepulse inhibition model. The main model code and the script for reproducing figures 1 and 5 can be found in the Jupyter notebook file 'PPIModel_PythonCode.ipynb'.
More details available in the paper: Bezerra, T. O.; Roque, A. C.; Salum, C. A Computational Mode... |
284ef7d145a52dfd5f22a04f21ab31d0bb94a32b8334323ffe2f3fd06e44880f | Text | 564 | 22 | # Programmable-MXene-Aerogel
Codes for "Machine Intelligence Accelerated Design of Conductive MXene Aerogels with Programmable Properties"
### Python environment & JupyterLab setup
```python
cd Programmable-MXene-Aerogel
conda env create -f environment.yml
conda activate matal-py10
jupyter lab
```
### Notebooks:... |
15149702ce4345e051ebf55721a20b73facd561b5406aa881d933bc6fe0a62af | Text | 590 | 25 | # glioblastoma-survival-classifier
Code used in deep learning models predicting survival of glioblastoma from MRIs
Inputs are:
* T1c MR sequence
* T2 MR sequence
There are three branches:
* T1c
* T2
* merged branch (predictions from T1c and T2 branches)
Link to publication: https://doi.org/10.1093/neuonc/noae017
... |
7ee5778b9680ca012ddf5c5b38ada82c88781c90010587ec62afd483ed35178d | Text | 601 | 4 | # Machine learning and dimension reduction techniques <br> for drug sensitivity prediction
Code collection for the manuscript ["A comprehensive benchmarking of machine learning algorithms and dimensionality reduction methods for drug sensitivity prediction" by Eckhart et al. (2024)](https://doi.org/10.1093/bib/bbae242)... |
1588a9ffd6085c223f89af71bb7130900df41508b4ec130e4ae57cb9fbe0d943 | Text | 610 | 15 | These datasets were used in Chang et al., 2024.
** Electrophysiology data (Chang et al, Figure 1-5)
-- cm_ephy_10msBin.mat (10 ms bin)
-- cm_ephy_100msBin.mat (100 ms bin)
** Behavior data (Chang et al, Figure 5a)
-- lickProb_rule_trans.mat (lick probability during rule transition)
** Data of inhibition ex... |
0a1108d427fedf141ef3bba6778e2da71a9d6ea42d34234d3021c3e4cd304506 | Text | 613 | 6 | # Hart_Kronauer2023
Processing code for calcium imaging data from "Sparse and stereotyped encoding implicates a core glomerulus for ant alarm behavior".
Raw data with .nwb files can be found at https://dandiarchive.org/dandiset/000467
To re-analyze data, first download the archived data at the above link. Next, run t... |
b02669cf2d13b301cd9c7406d60a5d00d7c8aaee5707eafc3d9cea4cb946e48c | Text | 615 | 14 | # BallisticMotorTask
This repository contains the source code behind Ballistic task. Movement And Neuroscience Uses this app for a multitude of different fine motoric experiments.
## System requirements
Script is build with MATLAB (v. R2012b, MathWorks inc.).
Computer screen (1920x1200 res, Dell U2415)
The accelerom... |
c36227610e438752e07416806581e9d643839c2ddd9b99e69b40361b10ba976d | Text | 615 | 9 | # ReproduceANNA16
This repository contains the codes for reproducing the development of ANNA16. ANNA16 is an end-to-end, web-based tool that predicts 16S rRNA gene copy number (GCN) from 16S rRNA sequence.
To use ANNA16, please visit https://colab.research.google.com/drive/1XwpTMCHSfTmzpHyKrmiD8aC8C_1nndUV#scrollTo=V_... |
ecd0568121e791727f97f5a5b9441a837f4e06dc30f17ce2b67a9747a8c07fdd | Text | 621 | 12 | This repository contains the code for the paper:
Linking genetic markers and crop model parameters using neural networks to enhance Genomic Prediction of integrative traits
Florian Larue , Lauriane Rouan , David Pot , Jean-François Rami , Delphine Luquet and Grégory Beurier *
Submitted to Frontier in Plant Science
... |
4db2719c30ba6224c4005fddd0568eb91c8e022d1f1c33dce74edb2fa488ad06 | Text | 630 | 24 | # Acoustic3DCNN: 3D Convolution Neural Network-based Identification of 3D acoustic image of benthic organisms in shallow marine sediments
This is the implenetation of 3DCNN model for classification of benthic organisms in 3D acoustic images.
## Requirements
- python 3.8
- tensorflow==2.5
- Keras 2.6.0
- Pillow 8... |
cf970b96545c979497f36b139809f25be3f777da727851cdccf35711b9aecdfb | Text | 640 | 9 | # Trad-204 Dataset
Computer vision single cell Tradescantia clone 4430 set of 204 images.
The Trad-204 can be used to study the Tradescantia cells colour and form anomalies. The dataset is a labeled set of 204 tiny images, collected by the authors. Trad-204 dataset consists colour images in 2 classes, blue or pink cel... |
a867f5c0385644e8152a8a1818ea2116da6802f6f88ea32fa2a9bf2a0632b8b9 | Text | 647 | 22 |
** Dataset for:
Ashida G, Wang T, Kretzberg J (2023/2024)
"Integrate-and-fire-type models of the lateral superior olive"
** How to use:
By running "plotFigX.m" in Matlab, corresponding plots will be generated.
These script files internally read the ".mat" data files.
** Author of the program:
Go Ashid... |
f958758bc28361313b5f43e17282966e0cf2495dc36baf28c21e8e82a0fcac92 | Text | 657 | 8 | # topological_filtering_networks
If you use this toolbox, you can cite one of the following articles:
[1]Dimitriadis SI et al., 2017.Data-Driven Topological Filtering Based on Orthogonal Minimal Spanning Trees: Application to Multigroup Magnetoencephalography Resting-State Connectivity.
Brain Connect. 2017 Dec;7(10):... |
68b7b6162aed2982daacee2d4b4fa2b9c4dc11de34bddd06df0a3d4a244200a0 | Text | 667 | 21 |
Course Data Analysis in Software Engineering usign R.
- Source: <https://github.com/danrodgar/DASE>.
- Website: <http://danrodgar.github.io/DASE/>.
## Build and preview
This project uses Quarto book rendering from `.qmd` chapters.
- Build: `quarto render .`
- Live preview: `quarto preview .`
- Output folder: `docs... |
f534d62caf968aa02126c5f74eb6e20a9c856e87cd460ad6a8039eb06698e53c | Text | 673 | 21 | # ThinSection
Sandstone Thin Sections Identification
## Minimum Requirements
This repository has the following minimum requirements-
- [MATLAB R2021b](https://uk.mathworks.com/products/matlab.html) or later
- [Deep Learning Toolbox](https://uk.mathworks.com/products/deep-learning.html)
- [Computer Vision Toolbox](h... |
664fd8c42d6e706563a6c5e37eaf3b713b220fb8b07a5fe577204aac2a6f1f30 | Text | 674 | 17 | # modularization
Implementation of a statistical test for functional modularizations of networks
Published in:
Häusler, Stefan. "Correlations reveal the hierarchical organization of networks with latent binary variables." bioRxiv (2023): 2023-07.
https://doi.org/10.1101/2023.07.27.550891
MATLAB (R2015a)
For informa... |
56955765e14a7a0d19c0a2251cedf2c47d1afc80ae2b1021b4e58b4aa0f248b8 | Text | 677 | 11 | # HON-Gluocse
Analysis codes for Viskaitis et al 2024 "Temporal features of blood glucose tracked by orexin neurons of behaving mice"
The workflow for 2-photon single-cell analysis :
- Cell Ca fluorescence extraction from hand drawn ROIs: "cell_f_extraction_2P_doublecheckplanes_24012022a.m"
- Align metadata with corr... |
2d0b2062f304d8f984283e69f83cd91094270eb10574008fd1edf6ae906e6199 | Text | 691 | 8 | Supplementary material: Mental flexibility depends on a largely distributed white matter network: causal evidence from connectome-based lesion-symptom mapping
Paper publish in Cortex, 2023
This repository contains supplementary material as well as custom material used for this study.
- Connectome-based Lesion-Sympto... |
59a7eb05300971592fd04e2bb3b647fbe644dc162f0e0c12749b4bc7d1e5fc1d | Text | 704 | 33 | - Allen Brain Atlas
AllenAtlasNorm.r
TemplateNorm..r
- Figure 2b, Figure 5a, Supplementay Figure S4
main_COPE_session1_TestandPlot.m
- Figure 3c
main_COPE_session34_TestandPlot.m
- Figure 3d & Supplementary Figure S11
visualizeAllTimeSeriesSession3vs4
- Figure 4b-c, Figure 5b-d, Table 3 & Supplementary Table TS3
m... |
4e9cf2e604498ef6c1a2fcb56e1571ff03bbb3f0da657c0b91d6d83f6bb3fc16 | Text | 711 | 9 | # AI-Segmentation-
Source Code for Intracranial 4D flow segmentation
When used for publications, the following papers have to be cited:
[1] H. Berhane, M. Scott, M. Elbaz, K. Jarvis, P. McCarthy, J. Carr, et al., ‘Fully automated 3D aortic segmentation of 4D flow MRI for hemodynamic analysis using deep learning’, Mag... |
6933596cc4baf85466bf80fa4c9d10140e6374cfe8756a3cd784167bcbadcccb | Text | 721 | 17 | # Code structure
- 'processSession_XXX' processes the 'basic.mat' file for each session.
- These processed files are then loaded to perform further analysis, plots and compute statistics using the relevant scripts (see each folder)
Note: some of the processSession functions may take over an hour to run. We encourage ... |
60ca24516e0b86390d87a3c7c94901ef4314a559338c55a9f950625488375972 | Text | 725 | 6 | # SMCAD dataset synthesis algorithm and graph data extraction algorithm
## Introduction
This repository contains code for generating and extracting graph data from the sheet metal part machining feature dataset (named the SMCAD dataset), which is mentioned in the paper "Adaptive recognition of machining features in she... |
872ae18dcc905b836f22e037848ae871d6868b310db39bfc4a8b123c70ca39fa | Text | 728 | 26 | [](https://zenodo.org/doi/10.5281/zenodo.11054876)
# Acoustic3DCNN: 3D Convolution Neural Network-based Identification of 3D acoustic image of benthic organisms in shallow marine sediments
This is the implenetation of 3DCNN model for classification of benthic organisms ... |
de669ab2d00772abef8067a8ac6fe4f3cef9af6cb4b0b61836c8dde9b251a037 | Text | 728 | 8 | # CWAS_2024_analysis
- `Data_preprocessing`: scripts for generating the annotation dataset used for CWAS analyses on autism spectrum disorder families.
- `CWAS_results`: CWAS burden test results for figure 3, 4 and supplementary figure 2
- Burden_test_dnv.variant_level.xlsx: burden test results (variant-level) for 14... |
770d7653c8072217ccee1d5b5b999bca0e6d3143cc4c468f6a8dfb19b22a3a6e | Text | 736 | 19 | # HENKES_SNN
[](https://doi.org/10.5281/zenodo.10948556)
Code of the publication "Spiking neural networks for nonlinear regression" published in
https://doi.org/10.1098/rsos.231606 by
Alexander Henkes from ETH Zürich, Jason K. Eshraghian from Universit... |
0e9b6639feeb591206f0674ea45f5a40f701da3c76782f3d2fcc77c795780199 | Text | 740 | 25 | # README #
### Dynamic clamp PCB board and code ###
* Dynamic clamp circuit adapted from Desai NS, Gray R, Johnston D. A Dynamic Clamp on Every Rig. eNeuro. 2017 Oct 23;4(5):ENEURO.0250-17.2017. doi: 10.1523/ENEURO.0250-17.2017. PMID: 29085905; PMCID: PMC5659377.
### Hardware ###
* microcontroller: teensy 3.6
... |
060ee42803f84da3311e954ce92023fefef3ca192c166ea5c91dcf40df89c304 | Text | 744 | 15 | # Overview
This repo contains a set of scripts used in analyses of genetics of gray and white matter structure and gene-by-environment interactions.
# GWAS analyses
GWAS analyses, follow-up clumping and GO scripts are located in the GWAS folder
# Genetic correlations
The LDSC folder contains the scripts used in genet... |
78509b20e39b51cd7384014a2b072eb5b346334af58877167497f4ebd9738dde | Text | 751 | 10 | # System requirements:
- MATLAB r2023b by Mathworks
The software has been tested on Windows 11 23H2, but the MATLAB code should also work on MacOs 14 Sonoma.
The data here presented has been obtained through the commercial software Advanced Design System 2023 Update 1.
# Installation guide
Here you can find a... |
a7464ff01cd0114949dc9c2641343154d1bb76c1e5310095eb3beff5e9504f30 | Text | 758 | 18 | # README #
* Experimental datasets, analysis scripts and example codes that generate the figures for "Probing Multiplexed Basal Dendritic Computations Using Two-photon 3D Holographic Uncaging".
### Folders ###
* //datasets: structured experimental datasets for analysis.
* //figure_generate: example matlab script t... |
4a500e82a9cc0e5a981f3eacbe5bdcd583c5e11e9f447920adcf6e0833c16f5a | Text | 768 | 6 | Code used in:
Rodrigo R. R. Duarte, Oliver Pain, Matthew L. Bendall, Miguel de Mulder Rougvie, Jez L. Marston, Sashika Selvackadunco, Claire Troakes, Szi Kay Leung, Rosie Bamford, Jonathan Mill, Paul F. O’Reilly, Deepak P. Srivastava, Douglas F. Nixon, and Timothy R. Powell. Integrating human endogenous retroviruses in... |
957f550ba64e4028b2ffbcf14171a31bff4e0dfbb70492af24c9eee6ba5a7183 | Text | 788 | 16 | # Prenatal_infection_child_brain_development
Hi everyone,
This repository contains the computer code for the manuscript: Examining longitudinal associations between prenatal exposure to infections and child brain morphology. Please find the full text article here: https://doi.org/10.1016/j.bbi.2024.05.014.
The scri... |
c69ab62ad0c563876fb0e1a604065e8ce0632ea1d5fe4d17d9c7d52ffe7c44b3 | Text | 788 | 23 | # Ancestral (Sequence Reconstruction), Molecular Evolution, and Structure
# Input
We use the `data/mammalian_REM2_codons.SA.fasta.SLAC.json` file as input, it is borrowed from the AOC-REM2 analysis.
This file is parsed using the `scripts/ancestralevolution.py` script. Resulting in `data/REM2_AA.fasta`, `data/REM2_D... |
6906716bb73e5a7db8e23b587e57ae67704ff711f9f538ccbac355a8d9c1fb37 | Text | 794 | 28 | # NLPpreprocessing
A comprehensive NLP preprocessing package for clinical notes sentence boundary detection, tokenization
## install
```sh
git clone https://github.com/uf-hobi-informatics-lab/NLPreprocessing
cd NLPreprocessing
pip install .
```
## use after install
```python
from nlpreprcessing.annotation2BIO import ... |
41cd61f4126ff865f0f3ae56bf949c5dd23340f5294391ee9db47d32006e4ddc | Text | 797 | 16 | This folder contains all the scripts used to conduct the preprocessing and analysis of the neuroimaging data in paper:
"Ultrasound system for precise neuromodulation of human deep brain circuits"
https://www.biorxiv.org/content/10.1101/2024.06.08.597305v1
Data is collected in multiple session types, each having a dif... |
a12abc13d85b8535e07925d26592d2effd1e72f770b771db6831b5ab8e775c0d | Text | 799 | 30 | # README #
Stochastic HH model solved with forward euler method.
different methods used for:
demo_script.py: quick demo script
stochastic_HH.py: Markov Chain C.C. Chow, J.A. White,Spontaneous action potentials due to channel fluctuations,Biophysical Journal,Volume 71, Issue 6,1996,Pages 3013-3021,ISSN 0006-3495,htt... |
8786a4250ce4ae36227ff9861b68569aae80b174107fafde91cf5e681ec2412c | Text | 801 | 19 | # FlyNet3.0: Drosophila melanogaster heart tube segmentation model
This repository contains the source code used to train the FlyNet3.0 model described in the paper [An Attention LSTM U-Net model for Drosophila melanogaster heart tube segmentation in optical coherence microscopy images]. The prediction files and loss ... |
17ab14a6063b6982208d4641fa28a7ab2a88ac8fbb110757e7c78f13a84c56ab | Text | 803 | 15 | # DrugGene
Environmental requirements: Pytorch3, cuda and related Python libraries.
data folder: Storing relevant datasets.
code folder: This folder contains source code resources.
result folder: Including various models.
pictures folder: Contains resource pictures and related data for manuscript.
Model file locat... |
6cb11b3fe76cf8a264efec544f546b3c768f805c19dc95aab377a874bc202e75 | Text | 803 | 28 | # PLIER
Pathway-Level Information Extractor (PLIER): a generative model for gene expression data
## Library dependencies
```
RColorBrewer
gplots
pheatmap
glmnet
rsvd
qvalue
```
## To install the R package from github repository
```
library(devtools)
install_github("wgmao/PLIER")
```
Check out the vignette [here](v... |
8b262534aeef944cdd4ff28125217cc6e64c04f11f19c7531207a50487adb165 | Text | 812 | 19 | SDCflows
--------
.. image:: https://circleci.com/gh/nipreps/sdcflows.svg?style=svg
:target: https://circleci.com/gh/nipreps/sdcflows
.. image:: https://img.shields.io/pypi/v/sdcflows.svg
:target: https://pypi.python.org/pypi/sdcflows/
:alt: Latest Version
SDCflows (susceptibility distortion correction work... |
e8284dd5a90866e64f35994b1280e4d87c6c7b94aa3daa4ee7387fa567a4760a | Text | 836 | 15 | # PiPaw
PiPaw is an automated home-cage system for assessing motor learning and movement kinematics in mice.
# Files
piPaw_amplitude.py - Main script required to run the PiPaw cage.
mice.cfg - This file maps each RFID to a mouse name, and stores a log of water received, rewarded and failed trials, day of testing an... |
bb5e03b8e0d6bde9d0795ab7abbe7b4fea9bfb48db943e3b1cdd4b093ac4ebaf | Text | 838 | 21 | [](https://zenodo.org/doi/10.5281/zenodo.10888356)
This is the repository with custom code used in [Pletenev, Bazarevich, Zagirova et al., 2024](https://doi.org/10.1093/nar/gkae271)
# Dependencies
Create conda environment from **env1.yml** to run the following scripts:
- ... |
6bec3e7e3994179542693c8ce7175c1ff0d9b4a8f60e8281d877bfd4111f88a3 | Text | 839 | 16 | reproducing_RNA_figures - Contains all references/annotations necessary for reproducing the stats, analysis, and figures for the RNA isoform analysis in the article.
reproducing_nextflow_pipeline - Contains all references/annotations necessary for reproducing the NextFlow pipeline.
proteomics - Fasta reference fi... |
7cb1ae195b7ed68429e5c877fbf7840d4b8b40b99a90fb00a2adf3aaa66cfb2c | Text | 843 | 19 |
**Demo:**
```matlab
load Demo.mat
[nonsimple,KT,D,T]=FastMarchingTopo(im,SVr,30,[1,1,1],true)
```
<img align='center' height='400' width='574' src="./docs/Demo.png"/>
- `Green circles`: Starting points `SVr`
- `Cyan squares`: Visited points `KT==1`
- `Red crosses`: non-simple points `nonsimple`
**References:**... |
53db2bd3431affa60a048149542aceaadbaa790e2bf1313eea9a063b8e0a9de4 | Text | 844 | 18 | ## Simultaneous cortical, subcortical, and brainstem mapping of sensory activation
This analysis code is shared alongside the manuscript found here: https://doi.org/10.1101/2024.04.11.589099
Relevant data files can be found on OpenNeuro: https://doi.org/10.18112/openneuro.ds005009.v1.0.0
## Code
### MRI pre-processin... |
5bff15a61cc5f621c6fabf8cef66fb74d232d84db632838709a29d1cee62bf66 | Text | 844 | 19 | # Clock-like signature attribution
See Methods in _Disentangling sources of clock-like mutations in germline and soma_, [`doi.org/10.1101/2023.09.07.556720`](https://doi.org/10.1101/2023.09.07.556720).
We assume that independent distributions govern the signature compositions of the age-dependent and age-independent ... |
ba6f08792d5df9ef9e1575be7a943a0351aa4919aab64283ae64c5920bcc1032 | Text | 845 | 12 | # DeepRetroMoCo
## Deep Retrospective Motion Correction :
It is a source code that corrected the motion of functional spinal cord data based on the unsupervised network. and also there are some scripts for evaluating the final result.
# Tutorial
Visit the DRM [tutorial](https://colab.research.google.com/drive/1p4OBh2m... |
576ad93eb166d71f76c5f6bec97e60699bae200fd05de0fa742186a5f6f1d856 | Text | 854 | 18 | # Hart_Kronauer2024
associated with manuscript "Pheromone representation in the ant antennal lobe changes with age."
Code for analysis of the behavioral response to alarm pheromone compounds in the clonal raider ant is stored in this repository:
These files were written by Lindsey Lopes.
alarm_behavior_plotting.py... |
2e635f67c9b8c03e09c2e486b95b8e37b1bc5c6bf26d6159aacfbfb31cf25157 | Text | 859 | 22 | # nat_comms_code_20240408
Matlab code used to analyze data and create figures for Meyer et al, 2024 nat comms
pipeline_2p and pipelie_1p are the main scripts for analysis of 2-photon and 1-photon (widefield) image series, respectively.
Required toolboxes/code packages:
Matlab data acquisition toolbox
Matlab sign... |
75f618c1892b64d58456fcc50e6ddf4e38b2fa83a1c194a76a8419761bbf43db | Text | 859 | 14 | # ECG-based_estimation_of_respiration-induced_autonomic_modulation_of_AV_nodal_conduction_during_AF
This repo contains supplementary material for our publication 'ECG-based estimation of respiration-induced autonomic modulation of AV nodal conduction during atrial fibrillation'
AV-node-model: A mathematical network mo... |
3db9188946e8ba17b943589ddd459f7321ca52244db14befab099a7b681d6a54 | Text | 879 | 22 | # Scripts for building the 3D ex vivo MRI atlas
## Scripts
1. "copy_inputs_flywheel" downdloads the scans from flywheel and does preprocessing. Perform n4 correction first. Then create manual raw-to-axisalign affine transformation. This script contains the function to apply the affine transform to n4 corrected scans... |
56cc4c36a815e4b934aa1725fdd6e567603ba29741e60ea07c67aaf7d1e94d20 | Text | 880 | 10 | # This section of the repository contains caffe model files that are usable with GNINA
## Breakdown of the different sub-directories
* acs2018 -- The models and atom maps used in [2018 Fall ACS National Meeting poster](http://bits.csb.pitt.edu/files/gnina2018_poster.pdf).
Included he... |
accd192d163de994eb40f174f92af211bbebf9c32d2e3dad46c3a60516910a17 | Text | 889 | 24 | # cppgd
CPP version of Gdata programme. Machine-learning-oriented data management and convertion for Gaussian output and Chargemol output
## Build guide
make cppgd
## Usage guide
Usage: cppgd -i<input format> [<input option>] <input path> -o<output format> <output path> [options]
You can also directl... |
91629843724a3e44f71d6908c959e4d1c03aa5eba2a981df1609caa9d7ae7f0b | Text | 898 | 14 | # ASDLanguagePredict
This is a data depository for the following publication:
Kuaikuai Duan, Lisa Eyler, Karen Pierce, Michael V. Lombardo, Michael Datko, Donald J. Hagler, Jr., Vani Taluja, Javad Zahiri, Kathleen Campbell, Cynthia Carter Barnes, Steven Arias, Srinivasa Nalabolu, Jaden Troxel, Peng Ji, Eric Courchesne... |
2758d9691a0b74d49751657466a84259f4bf94fc031586fcf3f813719e25e60f | Text | 912 | 36 |
<!-- README.md is generated from README.Rmd. Please edit that file -->
# GBA1 and GBAP1 manuscript
This repository contains the code used to generate the plots used in the GBA1 and GBAP1 manuscript.
## Code contents
Within this repository you will find:
<table>
<colgroup>
<col width="11%" />
<col width="88%" />
</... |
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