Tag: github

Supercharge Your RStudio Workflow with ChatGPT and gptstudio Table of Contents: Introduction Benefits of Using Large Language Models in Rstudio 2.1 Increased Efficiency 2.2 Enhanced Capabilities Available Models for Rstudio 3.1 OpenAI’s GPT-4 3.2 Hugging Face Models 3.3 Anthropics’ Claude 3.4 Google’s PaLM Models Setting up Rstudio and Packages Installation…

Introduction Short-read metagenomic sequencing is the technique most widely used to explore the natural habitat of millions of bacteria. In comparison with 16S rRNA sequencing, shotgun metagenomic sequencing (MGS) provides sequence information of the whole genomes, which can be used to identify different genes present in an individual bacterium and…

DOI: 10.18129/B9.bioc.genomation     Summary, annotation and visualization of genomic data Bioconductor version: Release (3.6) A package for summary and annotation of genomic intervals. Users can visualize and quantify genomic intervals over pre-defined functional regions, such as promoters, exons, introns, etc. The genomic intervals represent regions with a defined chromosome…

PROJECT TITLE: AN IMPROVED DEEP LEARNING METHOD TO PREDICT THE ABILITY OF SGRNA OFF-TARGET PROPENSITY Download all the required/available files from gdrive (3.5MB): drive.google.com/drive/folders/1rDPcagh_iWWV1W9OWdIn8BeVnKdsxWSl?usp=sharing Project Objectives: (a) To review prediction of deep learning method for sgRNA off-target propensity. (b) To model the prediction of sgRNA off-target propensity using CnnCrispr. (c)…

Unlocking PyTorch’s Power: Introducing TorchInductor 2.0 Introduction Principles of Torch Inductor Torch Inductor as PyTorch Native Python First Approach Focus on General Design Technologies Used in Torch Inductor Defined-by-Run Loop Level AR Support for Dynamic Shapes and Strides with Senpai Leveraging the Triton Language Understanding Mine by Run Loop Level…

Provided by: genometools_1.6.5+ds-2_amd64 NAME gt-encseq-encode – Encode sequence files (FASTA/FASTQ, GenBank, EMBL) efficiently. SYNOPSIS gt encseq encode sequence_file [sequence_file [sequence_file …]] DESCRIPTION -showstats [yes|no] show compression results (default: no) -ssp [yes|no] output sequence separator positions to file (default: yes) -des [yes|no] output sequence descriptions to file (default: yes) -sds [yes|no]…

[This article was first published on coding-the-past, and kindly contributed to R-bloggers]. (You can report issue about the content on this page here) Want to share your content on R-bloggers? click here if you have a blog, or here if you don’t. 1. What is a violin plot? A violin…

Cho, C. et al. Haploinsufficiency of protamine-1 or-2 causes infertility in mice. Nat. Genet. 28, 82–86 (2001). Article  CAS  PubMed  Google Scholar  Oliva, R. Protamines and male infertility. Hum. Reprod. Update 12, 417–435 (2006). Article  CAS  PubMed  Google Scholar  Balhorn, R. The protamine family of sperm nuclear proteins. Genome Biol….

DOI: 10.18129/B9.bioc.BioNERO     This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see BioNERO. Biological Network Reconstruction Omnibus Bioconductor version: 3.15 BioNERO aims to integrate all aspects of biological network inference in a single package, including data preprocessing, exploratory analyses, network inference, and analyses…

Podcast: Explain Podcast Erschienen: 09.02.2024Dauer: 01:10:43 Getting the most out of Machines Chapters: 04:30 PhiX 14:30 low complexity 19:30 UMIs 32:10 FastQC 43:00 MultiQC 56:40 PycoQC PhiX concentrations for loading a validation run: knowledge.illumina.com/instrumentation/general/instrumentation-general-reference_material-list/000001536 Dnatech on why UMIs are used: dnatech.genomecenter.ucdavis.edu/faqs/what-are-umis-and-why-are-they-used-in-high-throughput-sequencing/ BMH learning on UMIs: www.youtube.com/watch?v=sRPMsnhIBK0 FastQC for QC of…

Hi, so I have this very basic and unrealistic example: a = torch.linspace(-1,1,100).reshape(-1,1) b = a c = torch.nn.Sequential( nn.Linear(1,10), nn.ReLU(), nn.Linear(10,1) ) opt = torch.optim.Adam(c.parameters(), lr=1e-3) for i in range(10): opt.zero_grad() b_hat = c(a) loss = F.mse_loss(b_hat,b) loss.backward() opt.step() So sure, it’s not a realistic training, however it should…

JThurston (Josh Thurston) January 19, 2024, 8:05pm 1 Hi all! I’m currently working through a Qiime2 pipeline analysing Illumina miseq paired-end amplicon data. I’ve successfully analysed bacterial (16s) amplicons from importing, filtering through to taxonomic assignment. However, I also have amplicon data for a functional gene (nifH; nitrogenase for N2…

Bacteria Strain Cori.ST1911 was isolated from fresh stool of 20-week-old C57/BL6J mice fed a HFD at the Animal Center of the West China Hospital of Sichuan University. Briefly, faecal particles were ground with a glass grinding rod and suspended in sterile phosphate-buffered saline (PBS). After gradient dilution, the suspension was…

Hamblin MT, Di Rienzo A. Detection of the signature of natural selection in humans: evidence from the Duffy blood group locus. Am J Hum Genet. 2000;66:1669–79. Article  CAS  PubMed  PubMed Central  Google Scholar  Hamblin MT, Thompson EE, Di Rienzo A. Complex signatures of natural selection at the Duffy blood group…

gnomad api 0 I have installed the source code for gnomad api from broadinstitute.github.io/gnomad_methods/#gnomad. I would like to run the utils.constraint in that package and then use compute_pli to calculate pLi score for the set of genes I have just like how it shows for individual genes in the online…

Overview OAuth 2.0 is a popular open standard authorization framework that enables you to verify that incoming requests are authorized to use your API. There are three main pieces to using OAuth 2.0 with Huma: Issue an access token to a client application Document the auth scheme and required permissions…

[](https://travis-ci.org/QuackenbushLab/yarn) # YARN: Robust Multi-Tissue RNA-Seq Preprocessing and Normalization The goal of yarn is to expedite large RNA-seq analyses using a combination of previously developed tools. Yarn is meant to make it easier for the user to perform accurate comparison of conditions by leveraging many Bioconductor tools and…

You might be familiar with Spring Boot, a Java framework often utilized for building Restful APIs. While the open-api-generator is a robust tool providing various features, including generating resource models, controller interfaces, executing validation logic, and even creating model and API tests, it’s important to note that the Node.js version…

Join us for a 3-part workshop series meant to introduce you to R and RStudio. We will walk through the basics of how to handle data in R and how you can create data visualizations! Please note: There is one meetup link per workshop, please register for each workshop separately….

DOI: 10.18129/B9.bioc.dcanr     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see dcanr. Differential co-expression/association network analysis Bioconductor version: 3.12 Methods and an evaluation framework for the inference of differential co-expression/association networks. Author: Dharmesh D. Bhuva [aut, cre] Maintainer: Dharmesh D. Bhuva <bhuva.d…

It’s also a great way to adjust parameters like temperature, maximum output length, and top-k value, as well as get sample implementation code. You can request different formats of output, such as json, markdown, bullet lists, etc. We won’t get into prompt engineering or tuning these parameters here, but it’s…

Submission Notes: You need to solve this task using XGBoost ML Algorithm, You need to upload a Jupyter Notebook, Follow the remaining steps below. Question #1: (15 Points) Kaggle hosts a data set which contains the price at which houses were sold for King County, which includes Seattle – city…

Let’s shape the future – University of Antwerp The University of Antwerp is a dynamic, forward-thinking, European university. We offer an innovative academic education to more than 20000 students, conduct pioneering scientific research and play an important service-providing role in society. We are one of the largest, most international and most innovative…

Parallel Computing With R & Rstudio: Complete Tutorial GuidePublished 12/2023MP4 | Video: h264, 1920×1080 | Audio: AAC, 44.1 KHzLanguage: English | Size: 1.30 GB | Duration: 1h 30m R Programming, RStudio, Parallel Computing, Multicore, Data Science, Speed Optimization What you’ll learn Understand core parallel computing concepts. Explore essential R packages…

Job Description Who we are Genomines is a young biotechnology company based in Paris and Saclay, specialized in sustainable extraction of Nickel from plants. The mission of Genomines is to usher in a new era of sustainable mining by using genetically enhanced plants to extract metals from soil (agromining). Through…

Abstract Microbial communities usually harbor a mix of bacteria, archaea, plasmids, viruses, and microeukaryotes. Within these communities, viruses, plasmids, and microeukaryotes coexist in relatively low abundance, yet they engage in intricate interactions with bacteria. Moreover, viruses and plasmids, as mobile genetic elements, play important roles in horizontal gene transfer and…

To say 2023 was a year taken up mostly by AI would be a massive understatement. Following the release of ChatGPT at the very end of 2022, generative AI blew up in 2023.  According to Reuters, ChatGPT had grown to 100 million active users by January 2023, which was just…

Photo by Maël BALLAND on Unsplash A few months back I had a requirement of checking the APIs for the product I’m working on for breaking changes (Backward Compatibility Check) during CI/CD. As part of that research, I created an action called openapi-validations, which is essentially a wrapper on top…

Tool:Dot_plot_like_in_BLAST, a standalone tool for making dot plots similar to what online BLAST makes 0 The online BLAST (blast.ncbi.nlm.nih.gov) makes dot plots which look like this: Unfortunately, the standalone BLAST lacks the capability of making dot plots. I have made a tool, named Dot_plot_like_in_BLAST, specifically for this purpose. Basically, it…

The Biostar Herald publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed. You too can submit links here. This edition of the Herald was brought to you by contribution from Mensur Dlakic, Istvan Albert, and was edited…

by Aaron Shi, Zachary DeVito This is part 2 of the Understanding GPU Memory blog series. Our first post Understanding GPU Memory 1: Visualizing All Allocations over Time shows how to use the memory snapshot tool. In this part, we will use the Memory Snapshot to visualize a GPU memory…

Hey there, fellow code wranglers and AI enthusiasts! I’m Cami, your friendly neighborhood tech explorer, and I’m about to take you on a wild ride through my latest adventure: contributing to PyTorch without being an expert in it. Yes, you read that right! My Unexpected Journey into PyTorch So, I…

On Tue, Dec 19, 2023 at 1:54 PM John Cremona <john.c…@gmail.com> wrote: > > I am finding it impossible to get simple PRs to get past the automatic testing workflow system, which are repeatedly failing for reasons which have noting to do with any code I have changed. > > Two…

* gnu/packages/bioinformatics.scm (r-sccustomize): Update to (git-version 2.0.1 revision commit). Change-Id: I4e4b499a658eaed0396263d1d9fd277a541a13d9 — gnu/packages/bioinformatics.scm | 87 ++++++++++++++++—————– 1 file changed, 43 insertions(+), 44 deletions(-) Toggle diff (108 lines) diff –git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 2546454acd..3e7b99ee61 100644 — a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10245,55 +10245,54 @@ (define-public r-presto (license license:gpl3)))) (define-public r-sccustomize – (let…

Job Title: Sr. Software Engineer in Test (Bioinformatics or Data Sciences) Location: Mississauga, CAD Impact Healthcare Roche Sequencing is not only changing science, but we are changing lives. Our software teams are laying the groundwork for the future by developing powerful bioinformatics algorithms, data analysis tools, and software/systems infrastructures so…

Job Title: Sr. Software Engineer in Test (Bioinformatics or Data Sciences) Remote Description: Responsibilities: •         Implement and maintain an end-to-end automation test framework for running UI integration tests and quality dashboards using various tools: Java, JavaScript/TypeScript, Cypress, Selenium WebDriver, Cucumber, TestNG, Junit •         Design and develop requirements based test cases •         Implement automated…

Alston JM, Sambucci O. Grapes in the world economy. In: Cantu D, Walker MA, editors. The grape genome. Springer International Publishing; 2019. p. 1–24. Google Scholar  Rahemi A, Dodson Peterson JC, Lund KT. Grape rootstocks and related species. Cham: Springer International Publishing; 2022. Walker MA, Heinitz C, Riaz S, Uretsky…

In the vast landscape of API development, effective documentation is the linchpin that ensures seamless collaboration between developers and their creations. Swagger, now known as the OpenAPI Specification, stands out as a robust tool that streamlines API documentation and fosters enhanced teamwork. This blog post will unravel the essence of…

Description Convenor: Alexia Cardona (CDH RSE Methods Fellow) Please note this workshop has limited spaces and an application process in place. Application forms should be completed by noon, Friday 16 February 2024. Successful applicants will be notified by the end-of-day Wednesday 21 February 2024. Version control helps you to write…

Can sangeranalyseR be changed to read SCF files? 0 Hello! I am working with sanger sequences where half of them are in the ab1/abi format, the other half is scf. I am using sangeranalyseR, an R package (github.com/roblanf/sangeranalyseR), to do quality-trimming and alignment of my ab1 files, and all seemed…

In a previous post, I was able to deploy a R Studio container into Snowpark Container Service. This allows me to run R code directly in Snowflake, but I still need to connect to Snowflake to grab data. So when I attempted to use the dbConnect syntax from the original…

Swagger is a suite of tools for API developers from SmartBear Software and a former specification upon which the OpenAPI Specification is based. Generate Swagger documentation and publish the swagger specification in Organization’s Central Swagger Portal As per objective the implementation in broken in two sub objectives. Generating Swagger Specification…

Study objectives and endpoints The main objective consisted in identifying predictive biomarkers of efficacy by exploring correlation between baseline potential biomarkers and radiological and metabolic responses to afatinib. Secondary objectives were to identify potential pharmacodynamic biomarkers, to evaluate the efficacy and safety of afatinib and to assess the metabolic and…

How AlphaFold2 fits within Nuclera – guided protein design Widely hailed as a breakthrough in biological research and a leap in the development of vaccines and synthetic materials, AlphaFold2 is an AI model developed by DeepMind for predicting the 3D structure of a protein based on its 1D amino acid…

The Kaggle Master Abhinand Balachandran has launched “Tamil-Llama,” an Indic LLM engineered specifically to elevate the Tamil language domain. This AI model is built on top of Meta’s Llama 2. Check out the GitHub Repository here. Tamil-Llama is meticulously crafted, integrating additional Tamil tokens and harnessing the LoRA methodology for…

Traditionally, educators create unit tests to automatically score students’ programming tasks. However, the precondition for running unit tests is that the project codes must be runnable or compiled without errors. Therefore, if students cannot keep the project fully runnable, they will only receive a zero mark. This is undesirable, especially…

Lung cancer ICB cohort Advanced non-small cell lung carcinoma patients who were treated with anti-PD-1/PD-L1 monotherapy at Samsung Medical Center, Seoul, Republic of Korea were enrolled for this study. The present study has been reviewed and approved by the Institutional Review Board (IRB) of the Samsung Medical Center (IRB no….

Provided by: libbio-coordinate-perl_1.7.1-4_all NAME Bio::Coordinate – Modules for working with biological coordinates VERSION version 1.007001 SYNOPSIS # create Bio::Coordinate::Pairs or other Bio::Coordinate::MapperIs somehow $pair1; $pair2; # add them into a Collection $collection = Bio::Coordinate::Collection->new; $collection->add_mapper($pair1); $collection->add_mapper($pair2); # create a position and map it $pos = Bio::Location::Simple->new (-start => 5, -end…

So I’m trying to iterate through a list of files within a specific path in my repository. Currently using matrix as a for loop but when it iterates through the path, it uses the wildcard ‘*’ when running az import command. Below is my code. name: API Azure Deployment on:…

Photo by Sandy Millar on Unsplash Welcome to an exhilarating journey into the realm of Generative AI, a frontier where intricate technology is translated into user-friendly, practical tools. Whether you’re a newcomer to the AI world or often find yourself tangled in a web of technical jargon, this adventure is…

Job Description The Earth and Biological Sciences Directorate (EBSD) leads novel and necessary research in three core areas: Atmospheric and Climate sciences, Biological Sciences, and Environmental Molecular Sciences. The contributions of EBSD staff are many as we continue to elevate the impact of PNNL’s science mission: to understand, predict, and…

Deep learning has the potential to enhance molecular docking by improving scoring functions. Current sampling protocols often need prior information to generate accurate ligand binding poses, limiting scoring function accuracy. Two new protocols, GLOW and IVES, developed by researchers from Stanford University, address this challenge, demonstrating enhanced pose sampling efficacy….

Here are 10 free data sources that data scientists can leverage for their projects and analyses Data is the fuel that powers the engine of data science, and having access to diverse and reliable datasets is essential for meaningful analysis and insights. In 2024, several free data sources will continue…

Name Last modified Size Parent Directory   – golang-github-go-openapi-swag-dev_0.0~git20160704.0.1d0bd11-1_all.deb 2017-04-30 03:24 13K golang-github-go-openapi-swag-dev_0.15.0-1_all.deb 2019-10-29 18:46 18K golang-github-go-openapi-swag-dev_0.19.15-1_all.deb 2021-10-19 20:32 26K golang-github-go-openapi-swag-dev_0.21.1-1_all.deb 2022-05-12 00:24 27K golang-github-go-openapi-swag-dev_0.22.4-1_all.deb 2023-10-26 21:32 28K golang-github-go-openapi-swag_0.0~git20160704.0.1d0bd11-1.debian.tar.xz 2017-04-30 02:00 1.6K golang-github-go-openapi-swag_0.0~git20160704.0.1d0bd11-1.dsc 2017-04-30 02:00 2.3K golang-github-go-openapi-swag_0.0~git20160704.0.1d0bd11.orig.tar.xz 2017-04-30 02:00 20K golang-github-go-openapi-swag_0.15.0-1.debian.tar.xz 2019-10-29 18:45 2.7K golang-github-go-openapi-swag_0.15.0-1.dsc 2019-10-29 18:45 2.3K golang-github-go-openapi-swag_0.15.0.orig.tar.gz 2019-10-29…

Provided by: libbio-eutilities-perl_1.77-2_all NAME Bio::EUtilities – BioPerl low-level API for retrieving and storing data from NCBI eUtils VERSION version 1.77 SYNOPSIS See Bio::DB::EUtilities for example usage with NCBI. DESCRIPTION This distribution encompasses a low-level API for interacting with (and storing) information from) NCBI’s eUtils interface. See Bio::DB::EUtilities for the query…

DOI: 10.18129/B9.bioc.chimeraviz     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see chimeraviz. Visualization tools for gene fusions Bioconductor version: 3.12 chimeraviz manages data from fusion gene finders and provides useful visualization tools. Author: Stian Lågstad [aut, cre], Sen Zhao [ctb], Andreas M….

Job Summary: The Meyer lab at Cedars-Sinai is seeking one research bioinformatician to work on projects related to proteome informatics, mass spectrometry, metabolomics, multi-omic data integration, single cell transcriptomics, single cell genomics, single cell proteomics, computational drug discovery and/or cheminformatics. We are open to hiring at multiple levels of education,…

Streamline Machine Learning Operations with SQL and BigQuery Table of Contents: Introduction Background Purpose of the Series Overview of the Workflow 4.1 Data Preparation 4.2 Model Training 4.3 Model Evaluation 4.4 Model Deployment 4.5 Model Monitoring 4.6 Generating Predictions 4.7 Orchestrating the Workflow Previous Videos in the Series 5.1 O1:…

Problem You want to modify the legend of a graph made with ggplot2. Solution Start with an example graph with the default options: library(ggplot2) bp <- ggplot(data=PlantGrowth, aes(x=group, y=weight, fill=group)) + geom_boxplot() bp Removing the legend Use guides(fill=FALSE), replacing fill with the desired aesthetic. You can also remove all the…

Wang, A. L. & Wang, C. C. Viruses of the protozoa. Annu. Rev. Microbiol. 45, 251–263 (1991). Article  CAS  PubMed  Google Scholar  Banik, G., Stark, D., Rashid, H. & Ellis, J. Recent advances in molecular biology of parasitic viruses. Infect. Disord. – Drug Targets 14, 155–167 (2015). Article  Google Scholar …

DOI: 10.18129/B9.bioc.clusterProfiler     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see clusterProfiler. statistical analysis and visualization of functional profiles for genes and gene clusters Bioconductor version: 3.12 This package implements methods to analyze and visualize functional profiles (GO and KEGG) of gene…

Comment: Reduce single cell experiment size to use as reference for annotation with Singl by elgomez • 0 Thank you, James! I ended up running seurat FindVariableFeatures with nfeatures = 10000 and then subsetting the object to just those varia… Comment: Help with model.matrix and creating the right contrast matrix…

denth December 15, 2023, 8:21am 1 Any ideas how implement possibility to ask ChatGPT (Plus) to read and create notes in Google Keep, and trigger time/place notes? redfive December 15, 2023, 11:56pm 2 A version of the openapi schema for Keep is here: openapi-directory/APIs/googleapis.com/keep/v1/openapi.yaml at main · APIs-guru/openapi-directory · GitHub…

Currently I’m using transfer learning with Detection Transformers from Meta Research (github here). I have images with data from multiple sensors of a car. I projected all the sensors to a reference sensor (RGB camera), so the data is well aligned. After that, I stacked them up in a 15-channel…

Machine learning is only possible when there’s enough of data available. Data collection is one of the most vital components of the machine learning lifecycle, but it’s also the one that’s often overlooked. Web scraping—programmatically collecting data from web pages—is often the primary technique used to collect information from the…

A Bioinformatics Engineer is required to join a small but rapidly expanding company – by joining early in the journey you will gain exposure to the various facets of start-up life and have a unique chance to contribute to the technology and influence company culture. As the company expands this…

Show Your Support: This site is primarily supported by advertisements. Ads are what have allowed this site to be maintained on a daily basis for the past 19+ years. We do our best to ensure only clean, relevant ads are shown, when any nasty ads are detected, we work to…

Unfolding the Benefits of AlphaFold for Scientific Discovery Who Stands to Benefit from AlphaFold? Picture a vast sea of scientists, their brows furrowed in concentration, diving deep into the mysteries of proteins and their complex folds. It is these brave explorers who stand to reap the plentiful rewards of AlphaFold…

extracting instruments for mendelian randomization analysis 0 Cross-posted on bioinfo SE: bioinformatics.stackexchange.com/questions/21952/extracting-instruments-for-mendelian-randomization-analysis I am looking at extracting genetic variants associated with physical activity (to be used as exposure) from gwas id ebi-a-GCST006097. The gwas has nsnp = 11808007 library(TwoSampleMR) library(ieugwasr) gwasinfo (“ebi-a-GCST006097”) However, when I extract this, I end up…

I get the following error in the console when I I press Enable Github Copilot in Tools > Copilot:Error in .rs.ensureDirectory(targetDirectory) :failed to create directory at path ‘C:/Users/user/AppData/Local/Microsoft/Windows/INetCache/RStudio/copilot/dist’In addition: Warning message:In dir.create(path, recursive = TRUE) :cannot create dir ‘C:\Users\user’, reason ‘Permission denied’. In addition I get a popup error.r error…

Hello, I have a problem with my shiny app. When I run the code, some results are inconsistent with what I get from R studio for the results from a specific package called “glmmTMB”. The code is working just fine on Rstudio but when I use the shiny app, I…

Miguel_C (Miguel) December 15, 2023, 12:30am 1 I’m building an image captioner using Huggingface models with Pytorch and I’m getting different results for the first iteration (and for the following iterations obviously) when the effective batch size is the same (mini batch of 4 with 16 gradient accumulation steps vs…

by Aaron Shi, Zachary DeVito During your time with PyTorch on GPUs, you may be familiar with this common error message: torch.cuda.OutOfMemoryError: CUDA out of memory. Tried to allocate 512.00 MiB. GPU 0 has a total capacity of 79.32 GiB of which 401.56 MiB is free. In this series, we…

Article Summary Box Recognizing various data types like numeric, integer, and logical in RStudio is essential for accurate data manipulation and import. Effective environment setup, including package installation and global option configuration, is pivotal for streamlined data import processes. Utilizing data.table’s fread function for handling large datasets enhances import efficiency,…

Installation: Tax4Fun2 package are not found and github repository is not maintained anymore 5 Hi everyone! I have tried to find the R package Tax4Fun2 from the paper (pubmed.ncbi.nlm.nih.gov/33902725/) . This R package lets analizes the microbiome in an easy way to predict functional profiles from metagenomic 16S rRNA data….

Animals All experimental procedures were performed in compliance with animal protocols approved by the Institutional Animal Care and Use Committee at Boston Children’s Hospital (Protocol no. 20-05-4165 R). Mice were provided with food and water ad libitum, housed on a 12-hour light/dark schedule (7 a.m.–7 p.m. light period) with no more than five mice…

Mouse breeding and husbandry All experimental procedures related to the use of mice were approved by the Institutional Animal Care and Use Committee of the AIBS, in accordance with NIH guidelines. Mice were housed in a room with temperature (21–22 °C) and humidity (40–51%) control within the vivarium of the AIBS…

Nucleus preparation from frozen brain tissue for Chromium single-cell multiome ATAC and gene expression analysis M1 tissue was obtained from three human donors (male, aged 42, 29 and 58 years), three macaque donors (male, aged 6 (Macaca mulatta), 6 (M. mulatta) and 14 (Macaca fascicularis) years), three marmoset (Callithrix jacchus)…

Unable to install bioconda and bowtie 0 ➜ ~ conda install -c “bioconda/label/cf201901” bowtie Collecting package metadata (current_repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Collecting package metadata (repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. PackagesNotFoundError: The following packages…

SAM-guided Graph Cut for 3D Instance Segmentation(arXiv) Author : Haoyu Guo, He Zhu, Sida Peng, Yuang Wang, Yujun Shen, Ruizhen Hu, Xiaowei Zhou Abstract : This paper addresses the challenge of 3D instance segmentation by simultaneously leveraging 3D geometric and multi-view image information. Many previous works have applied deep learning…

docs.stackable.tech/home/stable/demos/jupyterhub-pyspark-hdfs-anomaly-detection-taxi-data So, this is an article in an ongoing series where I investigate the deployment tools of Stackable.tech This firm supplies supported versions of many open source data engineering tools to easily build data platforms on Kubernetes (k8s) clusters. These can be on your own premises, in a data centre,…

Issue 75428 Summary clang crash when build IPEX code. Labels clang Assignees Reporter xuhancn The error msg: “`cmd Stack dump: 0. Program arguments: /usr/bin/clang++ -DAT_PARALLEL_OPENMP=1 -DUSE_C10D_GLOO -DUSE_DISTRIBUTED -DUSE_RPC -DUSE_TENSORPIPE -Dintel_ext_pt_cpu_EXPORTS -I/home/xu/conda_spaces/ipex_cpu/frameworks.ai.pytorch.ipex-cpu -I/home/xu/conda_spaces/ipex_cpu/frameworks.ai.pytorch.ipex-cpu/csrc/include -I/home/xu/conda_spaces/ipex_cpu/frameworks.ai.pytorch.ipex-cpu/csrc/cpu -I/home/xu/conda_spaces/ipex_cpu/frameworks.ai.pytorch.ipex-cpu/csrc/cpu/aten -I/home/xu/conda_spaces/ipex_cpu/frameworks.ai.pytorch.ipex-cpu/csrc/cpu/utils -I/home/xu/conda_spaces/ipex_cpu/frameworks.ai.pytorch.ipex-cpu/csrc/cpu/jit -I/home/xu/conda_spaces/ipex_cpu/frameworks.ai.pytorch.ipex-cpu/csrc/jit -I/home/xu/conda_spaces/ipex_cpu/frameworks.ai.pytorch.ipex-cpu/csrc/utils -I/home/xu/conda_spaces/ipex_cpu/frameworks.ai.pytorch.ipex-cpu/third_party/ideep/mkl-dnn/include -I/home/xu/conda_spaces/ipex_cpu/frameworks.ai.pytorch.ipex-cpu/csrc/cpu/tpp -I/home/xu/conda_spaces/ipex_cpu/frameworks.ai.pytorch.ipex-cpu/third_party/libxsmm/include -I/home/xu/conda_spaces/ipex_cpu/frameworks.ai.pytorch.ipex-cpu/build/Release/csrc/cpu/csrc/cpu/cpu_third_party/ideep/mkl-dnn/include -I/home/xu/conda_spaces/ipex_cpu/frameworks.ai.pytorch.ipex-cpu/third_party/ideep/include -I/home/xu/anaconda3/envs/ipex_cpu/include/python3.12 -I/home/xu/anaconda3/envs/ipex_cpu/include -I/home/xu/anaconda3/envs/ipex_cpu/lib/python3.12/site-packages/torch/include/torch/csrc/api/include -I/home/xu/conda_spaces/ipex_cpu/frameworks.ai.pytorch.ipex-cpu/third_party/ideep/mkl-dnn/src/../include -isystem /home/xu/anaconda3/envs/ipex_cpu/lib/python3.12/site-packages/torch/include -fPIC…

DOI: 10.18129/B9.bioc.QTLExperiment   This is the development version of QTLExperiment; for the stable release version, see QTLExperiment. S4 classes for QTL summary statistics and metadata Bioconductor version: Development (3.19) QLTExperiment defines an S4 class for storing and manipulating summary statistics from QTL mapping experiments in one or more states. It…

— editor_options: markdown: wrap: 72 — # **phenomis**: An R package for post-processing and univariate analysis [](https://travis-ci.org/odisce/phenomis) ## Description This package provides methods to perform the statistical analysis of phenomics datasets (e.g. in proteomics and metabolomics). These methods include the reading of datasets (as 3 table *dataMatrix*, *sampleMetadata*…

Explore the free sources that will help to get the datasets for data science projects Data science is a dynamic discipline where analysis, learning, and innovation depend heavily on the availability of diverse and high-quality datasets. This post examines several free resources that serve data scientists and provide a wealth…

A Comprehensive Guide to Building Your Own Text Classifier Understanding language is a complex task, not just for computers, but even for us humans. How do we interpret sentences, categorize news, or even decide if a text is positive or negative? This is the realm of text classification, and today,…

Article Summary Box Familiarize yourself with RStudio’s help system, which is essential for efficient programming. Strategies for accessing detailed documentation for specific R packages directly within RStudio. Leverage RStudio’s advanced search features for streamlining the process of finding relevant help information. Interpreting and utilizing package vignettes and manuals, an often-overlooked…

The Allen Brain Cell Atlas (ABC Atlas) has been updated with new data! Mouse Whole-Brain Transcriptomic Cell Type Atlas Data Updates In conjunction with the publication of an associated paper in Nature, we have made some minor updates to the Merscope and 10x data sets. In addition, 7 new neighborhood…

Several tools can be used to create SDKs from an OpenAPI spec. Let’s use the oapi-codegen Go code generator to create a Go SDK, and then build a client using that SDK. Generate the SDK First, grab the OpenAPI spec. Then install and use the generator to create the SDK….

Hi, I want to perform MMPBSA for complex file Command: gmx_MMPBSA -O -i mmpbsa.in -cs md_100.tpr -ct md_center.xtc -ci index.ndx -cg 1 13 -cp topol.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv Error: [INFO ] Starting gmx_MMPBSA v1.6.2 [INFO ] Command-line gmx_MMPBSA -O -i mmpbsa.in -cs md_100.tpr -ct md_center.xtc -ci index.ndx -cg 1…

Tissue preparation and nucleus isolation All experimental procedures using live animals were approved by the SALK Institute Animal Care and Use Committee under protocol number 18-00006. Adult C57BL/6J male mice were purchased from Jackson Laboratories. Brains were extracted from 56–63-day-old mice and sectioned into 600 µm coronal sections along the anterior–posterior…

Abstract Metagenomics, the whole genome sequencing of microbial communities, has provided insight into complex ecosystems. It has facilitated the discovery of novel microorganisms, explained community interactions, and found applications in various fields. Advances in high-throughput and third-generation sequencing technologies have further fuelled its popularity. Nevertheless, managing the vast data produced…

Article Summary Box Preparing RStudio for package management is pivotal, involving setting up workspace directories and ensuring R version compatibility for optimal package functionality. In Understanding Package Libraries, the intricacies of library paths and package storage locations reveal strategies for streamlined package accessibility and organization. Advanced Techniques for Package Loading…

Article Summary Box RStudio’s Package Manager significantly simplifies the process of installing and managing R packages, enhancing user efficiency. CRAN’s vast repository offers a wide range of R packages, but understanding the nuances of package versions and dependencies is crucial for optimal utilization. Utilizing GitHub for R package installations opens…

Welcome to What’s New in AI, our weekly update where we bring you all the latest AI news, tools, and tips to help you excel in this new brave new AI-driven world. AI in the news: Google dominates once again Last week Google was in the news for the release…

Cohorts Saliva and/or blood samples were collected from consenting individuals among four NCIG-partnered communities: Tiwi Islands (comprising the Wurrumiyanga, Pirlangimpi and Millikapiti communities), Galiwin’ku, Titjikala and Yarrabah, between 2015 and 2019. Non-Indigenous comparison data, generated from unrelated Australian individuals of European ancestry, was drawn from two existing biomedical research cohorts:…

Is Apple planning to enter the AI race? On December 6, 2023, Google shook the tech world with its grand AI ambitions, unveiling Gemini, its largest AI model from the DeepMind division. Not wanting to lag behind, Apple quietly entered the AI arena, introducing its own machine learning (ML) framework…

$30-250 USD Posted about 2 hours ago • Ends in 6 days $30-250 USD Paid on delivery I have a Google Docs API that I will be using in a Custom GPT, to update Google Documents via a Custom GPT. The primary goal is to address existing errors and circular…

We’re happy to announce that Swift OpenAPI Generator just reached the 1.0.0 milestone! Since it went open source in May 2023 with version 0.1.0, Swift OpenAPI Generator merged over 300 pull requests, released 25 updates, and introduced support for several major new features. It wouldn’t be possible without over 25…

Volta Labs is an MIT spin-off that has unlocked powerful new DNA sequencing capabilities by developing novel fluidic technology. Building off of this core technology, Volta has created a product that streamlines DNA sequencing sample prep. Volta is at the forefront of a sequencing revolution, driving sequencing towards seamless ease…