Tag: CLUE

I have a dataframe like df: df <- structure(list(VarBinariaY = c(“1”, “1”, “0”, “1”, “0”, “1”, “1”, “1”, “1”, “1”), VarContinuaX = c(0.42125112307258, 0.403089860687032, 0.501541076926515, 0.285735354525968, 0.838761311257258, 0.728340754751116, 0.547309613088146, 0.758638551225886, 0.664854867151007, 0.730170585680753 ), VarContinuaY = c(0.62294910964556, 0.153794215992093, 0.173481315141544, 0.441902326885611, 0.556428883690387, 0.300496574025601, 0.778148024342954, 0.358530796831474, 0.163795455591753, 0.658571016974747)), row.names = c(NA, 10L), class…

Hi.I’m having troubles with torch on my Jetson Orin NanoWhen I try to import it in python the interpreter crashes.I tried to run it with the fault handler here is the output: python3 -q -X faulthandler >>> import torch Fatal Python error: Segmentation fault Current thread 0x0000ffff8411c010 (most recent call…

Hi everyone First of all thank you for making rna-seq data much more accessible to an average clinical doctor through the DEseq2 packages and vignettes. I am though running into some trouble: I have a dataset of Nanostring mRNA-data from clinical study, which later was followed up. I therefore have…

Introduction Sarcoidosis is a multisystem inflammatory disease of unknown aetiology that is characterised by non-caseating epithelioid granulomatous lesions (aggregates of lymphocytes, macrophages, epithelioid cells, and giant cells).1 Typical clinical features include bilateral hilar lymph node lesions, pulmonary infiltration, and eye and skin lesions. Some patients may also have neurological and…

A new study conducted by researchers at the University of Eastern Finland discovered that the APP A673T genetic variant, which protects against Alzheimer’s disease (AD), alters levels of several proteins and peptides linked to amyloid-beta metabolism in human biofluids and cell culture models, including amyloid beta itself.  These new data…

GROMACS version: 2020.4GROMACS modification: No I have been running simulations of small proteins in water. Nothing fancy. Have been doing them without a hitch for awhile now. This last one I tried to do, however, behaved very strangely. The simulation seems to run for 125ns without any problems, but when…

S amnii is an important but underappreciated pathogen affecting women’s health because of its complex nutritional requirements, slow growth patterns, and requirement of anaerobic conditions. S amnii causes bacterial vaginosis and poor reproductive and perinatal outcomes. Sneathia species (spp.) have been identified as members of Community State Type IV (CST-IV)…

Many human cancers arise in this manner during cell division, when chromosomes get rearranged and awaken dormant cancer genes that can trigger tumor growth. One such chromosomal scramble can occur when a chromosome breaks, and a second copy of the broken chromosome is made before the break gets fixed. Then,…

Bacterial metatransciptome antimicrobial resistance genes workflow? 0 Hi everyone! I’m trying to analyse some metatranscriptomics data from different samples, the final goal is to determine wether one group of samples has a higher expression of antimicrobial resistance genes. I’m completely new to RNAseq and I have no clue where to…

Overview of the droplet-based snRandom-seq method for FFPE tissues The main workflow of snRandom-seq is shown in Fig. 1. For single nucleus isolation of FFPE tissues, the areas of interest of banked FFPE tissue block were first selected and placed into tubes. Deparaffinization and rehydration were carried out with standard xylene…

My pipelines and schedulers were running smoothly without any problems. After I went out to lunch, I changed the number of epochs a Neural Network would run, save the .yaml file again and leave it in the bucket named “budgetff”. Afterwards, everything stopped working. There are the errors and I…

Hello everyone! My name is Jacob and this is my first ML project that I’m doing on my own. It’s also my first blog post, hope you will like it. This project comes from Kaggle’s competition “Titanic – Machine Learning from Disaster”. Here is the link to the competition: www.kaggle.com/competitions/titanic/data…

Clinical and biochemical characteristics of parathyroid carcinoma In total, 50 thyroid tissues were collected from three groups, 12 parathyroid carcinomas, 28 parathyroid adenomas, and 10 normal parathyroid tissues, for genomic and transcriptomic profiling (Fig. 1). The detailed protocols and quality control procedures are described in the Materials and Methods section….

Enlarge / After Balto died in 1933, his taxidermy mount was put on display at the Cleveland Museum of Natural History. Cleveland Museum of Natural History In 1925, a sled dog named Balto led his plucky canine team on the last leg of a grueling 127-hour dogsled relay across Alaska…

In a recent study published in the Eurosurveillance Journal, researchers detected a cryptic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lineage on mink farms in Poland. Study: Cryptic SARS-CoV-2 lineage identified on two mink farms as a possible result of long-term undetected circulation in an unknown animal reservoir, Poland, November 2022…

Is third-generation sequencing/long-read-sequencing the only way to identify the full length sequence of a novel transcript? 0 Thanks for your attention, TLDR: How to get the full length sequence of a novel transcript? Details: There is a novel transcript A I identified using short-read sequencing, through assembly. It contains an…

I have a dataset, and I am trying to make another dataset that is based on the previous dataset. Obviously, I will use a for loop to do that! Below is the data set used, and represented by the variable data. So I want to use rows 1 to 501…

Willa Rubin is a 26-year-old high school teacher in San Antonio, Texas, and like millions of other women, she suffers from recurrent urinary tract infections. “It’s really painful. It’s one of these situations that you just can’t really ignore. It’s sort of on the front of your mind until it…

The search for life beyond Earth “follows the water,” reports the Economist (since water is vital for earth’s lifeforms, and the laws of chemistry are universal). “For most of the space age that insight led scientists to Mars.” But… More and more, though, planetary scientists are following the water to…

Q. BioPython: CodeML FileNotFoundError: [WinError 2] 0 I’m trying to run codeml in Biopython, following by Biopython cookbook. But it doesn’t work with an FileNotFoundError: [WinError 2]. I found ctl file does not contain file’s full path, like seqfile = seq2.phy outfile = result.out treefile = template.tree Files are on…

David Ashley, MD, PhD, the Rory David Deutsch Distinguished Professor of Neuro-Oncology and director of the Preston Robert Tisch Brain Tumor Center at Duke, calls his choice to focus his career on brain cancers “a compulsion to defeat this terrible problem.”   “When I was 23 years old, my father…

Transcribed image text: Perform the following Expasy analyses. Provide screenshots of analyses for both translate and protparam calculations. a) Translate the recA gene sequence to protein using “EXPASY: translate” tool. Copy and paste the RecA protein sequence into your answer sheet. (1 point) b) Use “EXPASY Protparam” tool to calculate…

Transmictomic analysis with draft reference genome 1 Hello, ultra noob here but is it possible to perform a transcriptome analysis but using a draft genome as a reference? I’m working with an assembled draft genome (a fasta file with a bunch of contigs) and I have no clue if bowtie…

At the start your career, entering the world of work may seem daunting. The requirements of the jobs market always appear to be changing, thanks to technological shifts, while application processes can feel inscrutable and building up your skills from a limited foundation looks like an uphill battle. If you…

Credit: Pixabay/CC0 Public Domain Why do some people with a genetic mutation associated with leukemia remain healthy, while others with the same mutation develop the blood cancer? In a new study published in Blood, scientists from the USC Stem Cell laboratory of Rong Lu discovered a mechanism that linked a…

How to extract proteins from PCs in plot_pca in DEP package? 1 I am using DEP package to analyze proteomics data. I did PCA for my samples (see the following plot) and wish to extract proteins in PC1 for further analysis. However, the objects x and y generated by the…

Dead, and in a jacket and tie. That’s how he was on 1 December 1948, when two men found him slumped against a retaining wall on the beach at Somerton, a suburb of Adelaide, Australia. The Somerton Man’s body was found on a beach in 1948. Nobody came forward to…

But because viruses don’t survive in the environment outside of their hosts for long, finding so much of the genetic material from the virus intermingled with genetic material from raccoon dogs is highly suggestive that they could have been carriers, according to scientists who worked on the analysis. The analysis…

Keep asking why. For months, Dynamo export tests have been intermittently failing with “AssertionError: whole graph export entails exactly one call”. Flaky tests that you can’t reproduce are pretty difficult to debug, since you can’t easily make a change and see if it fixes the problem or not. So when…

Get average base quality of bases in a read 1 Hi all! Given a BAM, I want to plot the insert size of a read pair vs average base quality of bases in a read I’ve actually got the insert size data point by filtering my BAM using: samtools view…

Advances in DNA sequencing methods have helped law enforcement catch perpetrators and given rise to genealogy research whereby people learn more about their ancestry. But did you know researchers at the UWI St Augustine Cocoa Research Centre (CRC) are using DNA sequencing to offer a Cocoa DNA Fingerprinting service to…

“Golden mitochondria” by National Institutes of Health(NIH) is licensed under CC BY-NC 2.0. A controversial embryo engineering technique turns out not to work as planned. It is touted as a way to prevent the births of children with mitochondrial disease, and a few fertility clinics have been using it – without much evidence…

We do know of one case in which it does not seem to have worked. A baby was born from an embryo that PGT revealed to have around 12% of the mother’s “bad” mtDNA. But by the time the baby was born, the proportion had shot up to around 50%….

03 Mar 2023 Of the dozens of loci genome-wide association studies have linked to Alzheimer’s, most are mysterious to scientists. How do they contribute to disease? Much work focuses on changes in expression of individual genes, but as reported in a preprint posted to medRxiv on February 8, scientists led…

Africa, where humans first evolved, today remains a place of remarkable diversity. Diving into that variation, a new analysis of 180 indigenous Africans from a dozen ethnically, culturally, geographically, and linguistically varied populations by an international scientific team offers new insights into human history and biology, and may inform precision…

Summary of a Single-cell Guided Pipeline to Aid Repurposing of Drugs Using scRNA-seq data, ASGARD repurposes drugs for disease by fully accounting for the cellular heterogeneity of patients (Fig. 1, Formula 1 in “Methods” section). In ASGARD, every cell cluster in the diseased sample is paired to that in the normal…

Hi,we’ve been looking everywhere how to get the id_token JWT when using Google Authenticator in jupyterhub (on kubernetes).We get the access_token and other user info, but not that one. It seems the authenticator code is not requesting for it, and so it doesn’t end up in the auth_state. Anybody doing…

Hi, I am working on TCGA-LUSC methylation analysis using TCGABiolinks, but I am unable to find out the groupCol and groups for differential methylation analysis (for TCGAanalyze_DMC function). When I looked into the object, it contains no info regarding methylation. My sequence of commands is as: query.met.lusc <- GDCquery( project…

image: Epigenetic Age and Lung Cancer Risk in the CLUE II Prospective Cohort Study view more  Credit: 2023 Michaud et al. BUFFALO, NY- February 16, 2023 – A new research paper was published in Aging (listed as “Aging (Albany NY)” by MEDLINE/PubMed and “Aging-US” by Web of Science) Volume 15, Issue…

eduseb (Eduardo) February 13, 2023, 5:01pm 1 Hello everyone! I’m currently trying to run dada2 denoise-paired. However, it results in the following error: “Plugin error from dada2:An error was encountered while running DADA2 in R (return code 1), please inspect stdout and stderr to learn more.” Anyone has a clue…

(00:00):Segments in DNA are so good today, I’m going to give you two for just watching one video (00:14):Howdy, I’m Andy Lee with his fanatics, and this is a segment of DNA. Be sure to subscribe to our channel line. Click on that bell if you wanna be notified about…

Hello! I ran the following command qiime feature-classifier classify-consensus-blast \ –i-query OTUs/rep-seqs.qza \ –i-reference-reads Classifier/silva-138-99-seqs.qza \ –i-reference-taxonomy Classifier/silva-138-99-tax.qza \ –o-classification Taxonomy/taxonomy.qza \ –verbose rep-seqs.qza (431.3 KB) and received the following error message Running external command line application. This may print messages to stdout and/or stderr. The command being run is…

I’ve been using the library / package ‘brazilmaps’ in order to graphically represent the area that has been affected by deforestation in Amazonia. With the help of the aforementioned library, I’ve managed to get a visualisation of those Brazilian states that are closer to the river; hence, affected by deforestation…

I have a reference genome explained by accession number instead of chromosome number. Any clue how to convert it into a chromosome number in the Linux terminal? Any suggestion is kindly appreciated. 0 I have a reference genome explained by accession number instead of chromosome number. Any clue how to…

Job Posting for Scientist II, Bioinformatics at PTC Therapeutics, Inc. Job Description Summary: The Scientist II, Bioinformatics is responsible for planning and performing scientific experiments that contribute to PTC’s research and drug discovery activities. The Scientist II is also responsible for communicating experimental results to his/her supervisor and…

GDCPrepare error (No such process) 0 Hi, I am trying to do mutation analysis from TCGA data, and I am doing it using a simple process like this: query.met <- GDCquery( project = project, data.category = “Simple Nucleotide Variation”, access = “open”, data.type = “Masked Somatic Mutation”, workflow.type = “Aliquot…

image: Fanflow4Insects consists of three pipelines. view more  Credit: Hidemasa Bono, Hiroshima University (CC-BY 4.0) Genome sequencing, where scientists use laboratory methods to determine a specific organism’s genetic makeup, is becoming a common practice in insect research. A greater understanding of insect biology helps scientists better manage insects, both those that…

A Segment-ology TIDBIT Genetic Genealogy has two main parts: genetic – the Shared DNA Segments; and genealogy – the Most Recent Common Ancestor (MRCA) with a Match. In a perfect world we link a Match and his/her Shared DNA Segment to the MRCA who passed it down to both of…

DOI: 10.18129/B9.bioc.ComplexHeatmap     This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see ComplexHeatmap. Make Complex Heatmaps Bioconductor version: 3.14 Complex heatmaps are efficient to visualize associations between different sources of data sets and reveal potential patterns. Here the ComplexHeatmap package provides a highly…

Introduction Breast cancer (BC) is the most commonly diagnosed cancer in women, and it is the main cause of cancer mortality in women around the world.1 Although standard treatments for breast cancer, including surgery, radiotherapy, chemotherapy, endocrine therapy, targeted therapy, and immunotherapy, have greatly improved during the last few decades.2,3…

Sequence Duplication Levels failed FastQC Report 1 Hi all, I’m checking quality for my RNA-Seq through FastQC and all my fastq failed on “Per base sequence content” and “Sequence Duplication Levels”, besides warning on “Overrepresented sequences” only for read 1 files (it’s paired-end; the sequences match between samples). Below is…

This is the first post in a two-part series. Read Part 2 here. Around the same time that Alan Turing was shaping his theories of machine intelligence in Manchester, another future giant of the computing world, Douglas Engelbart, was developing an alternative computing paradigm over 5,000 miles away in…

Genetic Affairs has created a new version of AutoKinship at GEDmatch. The new AutoKinship report adds new features, allows for more kits to be included in the analysis, and integrates multiple reports together: AutoCluster – the autoclusters we all know and love AutoSegment – clusters based on segments AutoTree –…

Spectroscopic studies The binding and interactive mode of flavonoid trans-resveratrol with HSA was investigated before its use as a dislodging agent for HSA bound AFB1. The binding behavior was studied using spectroscopic tools like fluorescence spectroscopy and UV–visible spectroscopy. UV-absorption spectroscopy was used to ascertain the structural changes induced by…

I tried to build a model using lightgbm with the dataset of kaggle’s competition, which is www.kaggle.com/c/ubiquant-market-prediction, on google colaboratory. I wrote codes to build a model by reference to some notebook and it works on kaggle notebook, but it doesn’t work on google colaboratory. The following lines were outputted….

When I make the following, I want just to compare the three years not to sum them. And the actual code sums them even if I don’t tell it to do it. Any clue? hoteles <- tibble::tribble( ~Hotel , ~Año, ~Ingresos , “Hawaiian Club” , “1993”, 450000 , “Hawaiian Club”…

Take a trip to the marvelous world of microbes, where bacteria breathe electricity, neon-yellow slime molds forage for snacks on the forest floor, and thousands of mysterious viruses hang out in your guts. This year, scientists made a slew of fascinating discoveries about the microscopic organisms living in and all…

Installing Bio::DB::Big::File on Ubuntu (Building and testing…) 0 Hi everyone, I’m trying to install VEP, I already downloaded all the recommended PERL libraries/dependencies/modules But I still have a problem with Bio::DB::Big::File and Bio::DB::Big::AutoSQL They asked for lib big wig. I’ve found three ways to install this (in my understanding): sudo…

The evolutionary biologist Jochen Wolf was working from home when we first spoke, in April, 2020. Germany was under lockdown, and his lab, at Ludwig Maximilian University, in Munich, had been closed for weeks. Still, a reminder of his research had followed him from the office. “I have a crow…

Which AWS instance type for peak calling with ChIP-seq data? 0 We have generated ChIP-seq and RNA-seq datasets and are considering using Amazon’s AWS cloud computing service to run various peak calling programs, assess peak reproducibility between replicates, and genome browser visualization. AWS offers several instance types and I have…

Advanced Duplicator 2 is a Garry’s Mod addon which implements a tool similar to the Duplicator, but with many added features. Yeah no problem mate, thanks for the response. I’m done with gmod and I don’t take requests, so please stop spamming the comment section. “Originally published in single magazine…

rsem-calculate-expression with STAR takes forever but without error 1 Hi all, I am running rsem-calculate-expression after succesfully generating the reference files with rsem-prepare-reference. However, the command never proceeds past: “started mapping” like in the example below Sep 16 08:44:43 ….. started STAR run Sep 16 08:44:43 ….. loading genome Sep…

Ensembl VEP Plugin not working 0 Hi all… I’m using SubsetVCF plugin to extract some fields from my VCF file when using VEP annotator. I’ve noticed that using VCFv4.1, the plugin works fine but not with VCFv4.2. Are there any limitations to the VCF version that impacts the plugin? Does…

Introduction Coronary artery disease (CAD) is a complex pathology associated with behavioral and environmental factors.1–3 CAD shows high prevalence and is associated with a high fatality rate among cardiovascular diseases. The main manifestations of CAD are stable or unstable angina pectoris and identifiable or unrecognized myocardial infarction.4 The main risk…

It was a game where you had a less colorful UI than the current and no random generated names. You’d be around much more Clue like environments such as a dark storming island with a spooky huge mansion on it. People would all have guns I believe maybe no body…

Aurich Lawson | Getty Images In the US, September is National Prostate Cancer Awareness Month. This feature highlights why catching prostate cancer early can be critical, and what researchers are doing to improve the odds of controlling the disease once it’s found. Prostate cancer is a paradox. It has one…

In a 2014 interview with Lossip, the girl group couldn’t help but gush about Grande and how amazing of a friend she is. Food blogger Alexa Luria (born December 25, 1993) is an American food blogger. Ariana Grande. This is in a large format, it’s appropriate for all ages. So…

LAKE SUPERIOR — Choppy, windswept waves slap at the hull as our boat nears the last known location of the Lucerne, a schooner that sank to the bottom of Lake Superior in 1886. The wreck, just off a narrow sand peninsula jutting from the northern tip of Wisconsin, doubles as…

Different Gene Lengths and Expected Gene Lengths from Sample to Sample 0 Hi all, I have come across something I have never seen before. I am working with some data from an outside source which appears to be processed RNA-seq files. Like other processed RNA-seq files I have ran into…

The open oceans are harsh and hostile environments where insects might not be expected to thrive. In fact, only one insect group, ocean skaters, or water striders, has adapted to life on the open seas. How these insects evolved to conquer the high seas, however, was not known. Now, a…

Hi everybody! I have uploaded on R a list of 9K fasta sequences, on which 40K SNPs map to – which means, some sequence host 1+ SNP. I have a R object (and a vcf as well) with the fasta sequences names and the SNP positions and I want to…

DOI: 10.18129/B9.bioc.Single.mTEC.Transcriptomes     This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see Single.mTEC.Transcriptomes. Single Cell Transcriptome Data and Analysis of Mouse mTEC cells Bioconductor version: 3.8 This data package contains the code used to analyse the single-cell RNA-seq and the bulk ATAC-seq data…

How do I start clue GO in R using the cytoscape REST API? 0 Hi there, I am trying to connect to open the Clue GO application in R using cytoscape REST API. I have the following code: port.number = 1234 host.address <- “localhost” cytoscape.base.url = paste(“http://”,host.address,”:”, toString(port.number), “/v3.11.1″, sep=””)…