Tag: ALOT

Help me confirm if my reads are properly normalized and transformed or do I need to re-do

Help me confirm if my reads are properly normalized and transformed or do I need to re-do 0 Hello, can you help me confirm whether or not my reads dataset were normalized properly prior to my work on them? The data source is 40 florets from Arabidopsis for 3 replicates…

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r – How to export data from Odoo to RStudio

My company has just started using Odoo services and I’m also quite new to it and I’ve seen that it uses alot of Python and Javascript (which im not too familiar with). I use RStudio for a lot of my data gathering and analysis. Is there a way to automatically…

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ChAMP can’t be found in Bioc3.18?

ChAMP can’t be found in Bioc3.18? 1 @8df9ba1f Last seen 6 hours ago Ireland Hi I am on Debian 12 (stable) and just installed R-4.3.2 and Bioconductor v3.18 successfully and then installed alot of my favourite Bioconductor packages. However with ChAMP, the DNA methylation package, it said it couldn’t be…

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python – Better way to load data onto the GPU in pytorch

I am trying to do a comparative study across different image classification models, so I plan on training them all on the same dataset. I was wondering if there is a method in which I load the entire dataset onto the GPU once and use that to train all the…

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Neymar injured lagi

TSCeDhhVss Yesterday, 09:55 AM, updated 17h ago Al Hilal could receive millionaire compensation from FIFA for Neymar’s injury. Eduardo Carlezzo, a specialist in Sports Law, explains that the Saudi club can resort to the Club Protection Program, which pays teams when a player is injured for his country’s main team…

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QC cut off for snRNAseq data

QC cut off for snRNAseq data 1 Hi all, Apologies if this is a silly question as I am very early on in my bioinformatics journey! I have been playing with an snRNAseq dataset in Seurat and I am currently performing QC on the dataset. Alot of the profiles look…

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fastq – Parameter optimisation of minimap2

I’m leveraging minimap2 to map select genes from short-read microbial fastq metagenomics zip files. minimap –heap-sort=yes –splice-flank=no metagenome.fastq.gz fastaDB.fas What I noticed is the low tolerance of mismatch when I need to maximise mismatch because microbes have loads of genetic diversity. Thus the collection of references sequences are never really…

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Chapter 5 Data visualisation | bookdown-demo.knit

geom_point data(iris) # import the data to your global environment ggplot(iris, aes(x = Petal.Length, y = Sepal.Width)) + geom_point()+theme_bw() # cusomtize your x and y axis -We can also add color to our scatter plot ggplot(iris, aes(x = Petal.Length, y = Sepal.Width, colour = Species)) + geom_point()+theme_bw() Or even change…

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Contig labels in BAM off by 1, how do I fix it?

Contig labels in BAM off by 1, how do I fix it? 0 After alot of hairpulling over why strelka wouldn’t run on my bam files, I found that for 18 contig labels were wrong, and they’re off by one (picture below). I’ve figured out which labels should be changed…

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Fine tuning text-bison model – Google Cloud Community

Hi everyone I currently have a pipeline using OpenAI where I pass information about my internal company database tables as a prompt, and then ask a user defined question, and then get an SQL query and a response. As you might have guessed, this takes alot of tokens since I…

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Rarefaction curve of microbiome study

I don’t know why my rarefaction curve for most samples does not reach saturation. Please how can I improve te curve? The curve does not look like most rarefaction curves I see in publications, Please help and I am relatively new to microbiome study. Below is the code I used:…

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How to discard alignments from SAM/BAM file that have mismatches

How to discard alignments from SAM/BAM file that have mismatches 0 Hi all, I have sequenced the mRNA of a heterologous library expressed in human cells using nanopore. Then I mapped the reads from the fastq files to the reference database of the library using the minimap. Then I filtered…

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A Beginner’s Guide to Perform Molecular Dynamics Simulation of a Membrane Protein using GROMACS — GROMACS tutorials https://tutorials.gromacs.org documentation

Building the protein-membrane system in CHARMM-GUI We are now ready to embed the protein structure in the membrane in the proper location and orientation and construct the membrane composition we desire. To do this, we utilized the CHARMM-GUI input Generator, a handy web-based tool to generate GROMACS inputs for the…

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Exploring using YOLOv8n with PyTorch Mobile (Android) | by Stephen Cow Chau | May, 2023

Given the previous experience on using YOLOv8 on Android through converting it from ONNX exported => Tensroflow => Tensorflow Lite (plus the realization on ditching tflite support object detection API and use plaint interpretor), there are following items that I am wondering if directly using PyTorch mobile would be a…

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Query in indexing human genome

Hello , I have to do RNAseq analysis of human cancer cell lines , for that I need to index human genome , as a refrence genome. I index the human genome gff file from thr NCBI.. during some lecture I have heard that ncbi human genome file has some…

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Phyloseq Introduction and Import | Loading Microbiome Data

Phyloseq and Microbiome analyzed in R Data Import and Exploration There are a number of packages advanced in R that make microbiome analysis easy and erzeugt greater figures. At is by times an lot of overlap between this analyse and QIIME – and the choice is yours. Personally I consider…

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The Road To ggplot2 In WebR, Part 1: The Road Is Paved With Good Base R Plots

I have graphics working in Vanilla JS WebR, now, and I’ll cover the path to that in two parts. The intent was to jump straight into ggplot2-land, but, as you saw in my previous post, WASM’d ggplot2 is a bear. And, I really didn’t grok what the WebR site docs…

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Scope for making LAMMPS Automatically Differentiable – LAMMPS Development

Dear LAMMPS developers, With the growing use of machine learning and optimization techniques (that are powered by automatic differentiation Automatic differentiation – Wikipedia), and their adoption and use in the field of molecular modelling, I thought it could be worth discussing whether making LAMMPS – a very efficient, flexible, and…

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Beginner in Data Science? Focus on Basics with Kaggle Titanic Dataset | by Neet Madan | Feb, 2023

Beginner in Data Science? Focus on Basics with Kaggle Titanic Dataset Start with The Tip of the Iceberg — Titanic Machine Learning Dataset on Kaggle For a beginner, starting a career in data science can be overwhelming. Whether it is showcasing your business acumen, programming skills, exploratory data analysis skills,…

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Add Information to Protein Fasta Headers

Add Information to Protein Fasta Headers 1 Hi, I have protein fasta file whose headers look like ‘>evm.model.chr.9.52’. There are almost 30k+ proteins. I have performed functional annotations and also added every information to gene structure we get from EVM. The thing is, in that files I had columns so…

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Filteration of uniquely mapped reads

Filteration of uniquely mapped reads 2 Hello I have BAM-full file with reads mapped to “human and mouse” chromosome file. Now I would like to extract reads mapped only to “mouse” (means not mapped to human chromosome”. This is the protocol I am using : From BAM-full, extract reads mapped…

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Galaxy Genome [Space Sim] HACK/MOD Unlocked All vVaries with device

Download Galaxy Genome [Space Sim] Mod Varies with device for android apk & iphone ios 4.4 and up Galaxy Genome is an open world sci-fi space simulator. You can upgrade your ship and customize each component as you hunt, explore, fight, mine, smuggle, trade and survive in a brutal galaxy….

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Install pytorch in jetson nano

install pytorch in jetson nano Done! Getting Started with Jetson Nano In this tutorial, you will learn how to set up the NVIDIA ® Jetson ™ Nano and install everything you need to use the full power of the tiny embedded board. Git – Version Contol…

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Best Launch Options For Gmod

The -safe launch option will cause the game to launch with minimal video settings, in windowed mode and with a x resolution. This can be helpful for solving video configuration problems. Jonah’s O5 Application – Whitelist Applications – Werwolf This can be helpful for solving video configuration problems.  I finally…

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gmod prop hunt not working

I’ve let the server stay open so you can join it and test for yourself. Game Garry’s Mod. It’s just textures (and maps, if you need it) for use as an addon to Garry’s Mod. From hunting down everyday objects in Prop Hunt to strangling and trampling pigs in Open…

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miRNAseq analysis not shown adapter sequence and huge N’s content

miRNAseq analysis not shown adapter sequence and huge N’s content 0 Hi there, This is my third time doing miRNA sequencing analysis, so i do not have huge experience on this… So, i have 18 human semen samples, (also no experience in this type samples) i have been reading alot…

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