Open Source Biology & Genetics Interest Group

I’m trying to generate a bar chart (using ggplot2) with location estimates data along the y axis and a basic count scale along the x axis. My data is structured like so: Data <- data.frame(locations = c(“A”,”B”,”C”,”D”…), estimates = c(200, 300, 400, 200…) I then used dplyr to arrange my…

Low Mapping/Alignment rates with bowtie2 in mouse reduced genome 0 Hello, I want to perform mapping in two ways. One way is to run bowtie2 with my mouse data in the reference of mm10 and in this case everything works correct. The other way of mapping is to map my…

Catalog R Language gets all Aesthetics( Aesthetic Mapping ) Parameters ： Use long table output 、 Use wide table output #ggplot2 # Get all Geom* function R Language gets all Aesthetics( Aesthetic Mapping ) Parameters # Use long table output # Use wide table output #ggplot2 ggplot2 By Hadley Wickham…

Strain-level metagenome deconvolution. Microbial communities in many environments include distinct lineages of closely related organisms, which have proved challenging to separate in metagenomic assembly. It is difficult to distinguish between read errors and real polymorphisms between bacterial strains, but high-fidelity (HiFi) long reads have the potential to solve this issue….

Strain-level metagenome deconvolution. Microbial communities in many environments include distinct lineages of closely related organisms, which have proved challenging to separate in metagenomic assembly. It is difficult to distinguish between read errors and real polymorphisms between bacterial strains, but high-fidelity (HiFi) long reads have the potential to solve this issue….

1. (25 pts) What data you’ll use and where you’ll get it? If considering a dataset from a site such as kaggle, email me for approval. Otherwise, consider looking at the list I have at the end of this document  – ages.csv  – students.csv  – list.csv …

1. (25 pts) What data you’ll use and where you’ll get it? If considering a dataset from a site such as kaggle, email me for approval. Otherwise, consider looking at the list I have at the end of this document  – ages.csv  – students.csv  – list.csv …

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          Ribosomal RNA (rRNA)   The following texts are the property of their respective authors and we thank them for giving us the opportunity to share for free to students, teachers and users of the Web their texts will…

Affinity Capture-MS An interaction is inferred when a bait protein is affinity captured from cell extracts by either polyclonal antibody or epitope tag and the associated interaction partner is identified by mass spectrometric methods. Related interactions Interaction Experimental Evidence Code Dataset Throughput Score Curated By Notes KRR1 SLX9 Affinity Capture-MS…

Affinity Capture-MS An interaction is inferred when a bait protein is affinity captured from cell extracts by either polyclonal antibody or epitope tag and the associated interaction partner is identified by mass spectrometric methods. Related interactions Interaction Experimental Evidence Code Dataset Throughput Score Curated By Notes KRR1 SLX9 Affinity Capture-MS…

#include “config.h”#include <netinet/in.h>#include <sys/socket.h> This browser is not able to show SVG: try Firefox, Chrome, Safari, or Opera instead. This browser is not able to show SVG: try Firefox, Chrome, Safari, or Opera instead. Implements the parts of the vmdsock.h interface needed for IMD communication. Author Martin Hoefling, Carsten Kutzner…

The Slurm Workload Manager, often called just SLURM, is what a lot of supercomputers and big compute clusters use to manage scheduling and executing all of the jobs that people always want to run on them. However you don’t have to use it in such grand environments, and we use…

Error when trying to use Ensembl virtual machine 0 Hello. After realizing that installing Ensembl-vep on Windows requires installing multiple other programs, I tried using the Ensembl Virtual Machine. I followed the instructions at www.ensembl.org/info/data/virtual_machine.html, and when I ran the virtual machine I got the following error message: I tried…

Error when trying to use Ensembl virtual machine 0 Hello. After realizing that installing Ensembl-vep on Windows requires installing multiple other programs, I tried using the Ensembl Virtual Machine. I followed the instructions at www.ensembl.org/info/data/virtual_machine.html, and when I ran the virtual machine I got the following error message: I tried…

AfghanistanÅland IslandsAlbaniaAlgeriaAmerican SamoaAndorraAngolaAnguillaAntarcticaAntigua and BarbudaArgentinaArmeniaArubaAustraliaAustriaAzerbaijanBahamasBahrainBangladeshBarbadosBelarusBelgiumBelizeBeninBermudaBhutanBolivia, Plurinational State ofBonaire, Sint Eustatius and SabaBosnia and HerzegovinaBotswanaBouvet IslandBrazilBritish Indian Ocean TerritoryBrunei DarussalamBulgariaBurkina FasoBurundiCambodiaCameroonCanadaCape VerdeCayman IslandsCentral African RepublicChadChileChinaChristmas IslandCocos (Keeling) IslandsColombiaComorosCongoCongo, the Democratic Republic of theCook IslandsCosta RicaCôte d’IvoireCroatiaCubaCuraçaoCyprusCzech RepublicDenmarkDjiboutiDominicaDominican RepublicEcuadorEgyptEl SalvadorEquatorial GuineaEritreaEstoniaEthiopiaFalkland Islands (Malvinas)Faroe IslandsFijiFinlandFranceFrench GuianaFrench PolynesiaFrench Southern TerritoriesGabonGambiaGeorgiaGermanyGhanaGibraltarGreeceGreenlandGrenadaGuadeloupeGuamGuatemalaGuernseyGuineaGuinea-BissauGuyanaHaitiHeard Island and McDonald IslandsHoly…

Hello! There are a couple of ways of doing this. The best is what I’ve labelled the “reshape” method, but the “wide data” method also works: library(tidyverse) dat = tribble( ~id, ~blood, ~comp, 1, 90, 112, 2, 115, 130, 3, 100, 90, 4, 50, 70, 5, 120, 10, 6, 70,…

National Center for Biotechnology Information logo The National Center for Biotechnology Information (NCBI) is part of the United States National Library of Medicine (NLM), a branch of the National Institutes of Health. The NCBI is located in Bethesda, Maryland and was founded in 1988. The NCBI houses genome sequencing data…

The number of mentions indicates the total number of mentions that we’ve tracked plus the number of user suggested alternatives. Stars – the number of stars that a project has on GitHub. Growth – month over month growth in stars. Activity is a relative number indicating how actively a project…

The number of mentions indicates the total number of mentions that we’ve tracked plus the number of user suggested alternatives. Stars – the number of stars that a project has on GitHub. Growth – month over month growth in stars. Activity is a relative number indicating how actively a project…

michigan imputation server 0 Hi, I performed imputation on my GWAS data using Michigan imputation server. Now I have two output files: 1).dose.vcf.gz and 2).info.gz Michigan imputation server use mimimac3 (–format GT,DS,GP) and in the output file “.dose.vcf.gz” are present all the three formats. I’m new on this kind of…

michigan imputation server 0 Hi, I performed imputation on my GWAS data using Michigan imputation server. Now I have two output files: 1).dose.vcf.gz and 2).info.gz Michigan imputation server use mimimac3 (–format GT,DS,GP) and in the output file “.dose.vcf.gz” are present all the three formats. I’m new on this kind of…

DNA sequencing is a necessary technique for almost all molecular biology studies including DNA cloning, characterization, mutagenesis, DNA recombination, regulation of gene expression,1-3 and protein expression. There are several well-established methods for nucleic acid sequencing, and in recent years, advances in automated sequencing have made DNA sequence analysis an easy…

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With over 35 nationalities and a range of backgrounds represented in our Benevolent team, we aim to build an inclusive environment where our people can bring their authentic selves to work, be respected for who they are and the exceptional work they do. We welcome and actively encourage applications from…

I can’t install the “dplyr” package on RStudio. When I try, the following warnings appear: > install.packages(“dplyr”) Installing package into ‘C:/Users/elisa/Desktop/OneDrive/Documentos/R/win-library/3.4’ (as ‘ lib ‘ is unspecified) also installing the dependencies ‘ellipsis‘, ‘pillar’ ‘ ‘glue’ ‘ ‘lifecycle’,’ rlang‘,’ tibble‘,’ tidyselect‘,’vctrs ‘ There are binary versions available but the source versions…

One of the positive experiences during two years of pandemic gloom has been the speed of scientific progress in understanding and treating Covid. Many effective vaccines were launched in less than a year and rapid large-scale trials found a cheap and effective drug, dexamethasone, that saved thousands of lives. The…

R: Run plotting code and view svg in RStudio Viewer or web… dsvg_view {ggiraph} R Documentation Run plotting code and view svg in RStudio Viewer or web broswer. Description This is useful primarily for testing. Requires the htmltools package. Usage dsvg_view(code, …) Arguments code Plotting code to execute. … Other…

R: Run plotting code and view svg in RStudio Viewer or web… dsvg_view {ggiraph} R Documentation Run plotting code and view svg in RStudio Viewer or web broswer. Description This is useful primarily for testing. Requires the htmltools package. Usage dsvg_view(code, …) Arguments code Plotting code to execute. … Other…

Review . 2021 Nov 20;13(22):5827. doi: 10.3390/cancers13225827. Affiliations Expand Affiliations 1 Department of Oncology, Barbara Ann Karmanos Cancer Institute, Wayne State University, 4100 John R, HW04HO, Detroit, MI 48201, USA. 2 Department of Hematology and Oncology, St Joseph Mercy Health System, Ann Arbor, MI 48201, USA. Item in Clipboard Review…

You are receiving this mail as a port that you maintain is failing to build on the FreeBSD package build server. Please investigate the failure and submit a PR to fix build. Maintainer: y…@freebsd.org Log URL: beefy12.nyi.freebsd.org/data/130releng-armv7-quarterly/46aef99be2ae/logs/py38-pymc3-3.11.4.log Build URL: beefy12.nyi.freebsd.org/build.html?mastername=130releng-armv7-quarterly&build=46aef99be2ae Log: =>> Building math/py-pymc3 build started at Sat Nov 27…

The number of mentions indicates the total number of mentions that we’ve tracked plus the number of user suggested alternatives. Stars – the number of stars that a project has on GitHub. Growth – month over month growth in stars. Activity is a relative number indicating how actively a project…

A kubernetes openapi unmangler. Creates rust structs from a named crd by converting the live openapi schema. ⚠️ WARNING: ALPHA SOFTWARE ⚠️ Installation Grab a prebuilt musl/darwin binary from the latest release, or install from crates.io: Usage kopium prometheusrules.monitoring.coreos.com > prometheusrule.rs rustfmt +nightly –edition 2021 prometheusrule.rs Output use kube::CustomResource; use…

This article was originally published here Cancers (Basel). 2021 Nov 20;13(22):5825. doi: 10.3390/cancers13225825. ABSTRACT Renal cell carcinoma (RCC) is known for its variable clinical behavior and outcome, including heterogeneity in developing relapse or metastasis. Recent data highlighted the potential of somatic mutations as promising biomarkers for risk stratification in RCC….

How to add a individuals IDs to admixture output? 1 The output of my admixture command looks like that: 0.807781 0.103628 0.000010 0.088581 0.000010 0.340997 0.658983 0.000010 0.043489 0.516310 0.428646 0.011555 0.000010 0.999970 0.000010 0.000010 0.000010 0.297796 0.702184 0.000010 0.999970 0.000010 0.000010 0.000010 0.000010 0.786360 0.213620 0.000010 0.878834 0.056439 0.000010…

How to add a individuals IDs to admixture output? 1 The output of my admixture command looks like that: 0.807781 0.103628 0.000010 0.088581 0.000010 0.340997 0.658983 0.000010 0.043489 0.516310 0.428646 0.011555 0.000010 0.999970 0.000010 0.000010 0.000010 0.297796 0.702184 0.000010 0.999970 0.000010 0.000010 0.000010 0.000010 0.786360 0.213620 0.000010 0.878834 0.056439 0.000010…

References 1. Bräutigam, K. and Cronk, Q. DNA Methylation and the Evolution of developmental complexity in plants. (2018). Frontiers in Plant Sciences.9-1470. 2. Zhou, D.X. and Hu, Y. Regulatory function of histone modifications in controlling Rice gene expression and plant growth. (2010). Rice. 3:103–111. 3. Deng, X., Song, X., Wei,…

Job Overview: The job’s main responsibility is to lead a bioinformatics team to collaborate with cross-functional departmental teams to build and integrate cutting edge computational solutions and applications to improve clinical diagnostics. With both technical and leadership capacities, the Director of Bioinformatics will drive bioinformatics strategy and initiatives in support…

Work from Home jobs – Wanted Pharmacy,Pharmacist,B.Pharm,M.Pharm,D.Pharm,Physiotherapist,BPT,MPT,Physio,Staff nurse,Bsc nursing ,gnm ,dgnm Freshers Skills : Medical Coding , Pharmacy , Physiotherapy , Nursing , Staff Nurse , Biotechnology , Biomedical , Bioinformatics , Biochemistry , Microbiology , Biology , Botany , Pharmacist , Zoology , Nutrition & dietetics , Bhms ,…

Kforce is a Tampa, Florida-based staffing services provider that specializes in technology, and finance & accounting. The 2018 Best of Staffing Award winner’s vision is to have a meaningful impact on all the lives it serves. The company is committed to delivering remarkable quality and service through progressive recruiting strategies…

NEWS Hopefully, finally fix compatibility with tidyeval changes in ggplot2 v2.3.0 Bug fixes Now actually compatible with ggplot2 v2.3.0 Major changes geom_gene_arrow() now supports forward aesthetic (#3 and #5, thanks geom_gene_label added (#3, thanks @adomingues) @adomingues and @jasonserviss) Compatible with ggplot2 v2.3.0 Minor changes Change R version dependency to fix…

I have an example data frame: #Libraries library(tidyverse) #Create example data ex <- data.frame(id = 1:300, event = rep(c(“f”, “s”, “t”), 100), x = rnorm(300, 50, 20)) And I need to make one plot with three horizontal reference lines and one plot with two horizontal reference lines. The plot with…

Examples # NOT RUN { x <- ymd_hms(“2009-08-07 00:00:01”, tz = “America/New_York”) force_tz(x, “UTC”) force_tz(x, “Europe/Amsterdam”) ## DST skip: y <- ymd_hms(“2010-03-14 02:05:05 UTC”) force_tz(y, “America/New_York”, roll=FALSE) force_tz(y, “America/New_York”, roll=TRUE) ## Heterogeneous time-zones: x <- ymd_hms(c(“2009-08-07 00:00:01”, “2009-08-07 01:02:03”)) force_tzs(x, tzones = c(“America/New_York”, “Europe/Amsterdam”)) force_tzs(x, tzones = c(“America/New_York”, “Europe/Amsterdam”), tzone_out…

Abstract The application of quasi-median networks provides an effective tool to check the quality of mtDNA data. Filtering of highly recurrent mutations prior to network analysis is required to simplify the data set and reduce the complexity of the network. The phylogenetic background determines those mutations that need to be…

Abstract Mitochondrial DNA (mtDNA) population data for forensic purposes are still scarce for some populations, which may limit the evaluation of forensic evidence especially when the rarity of a haplotype needs to be determined in a database search. In order to improve the collection of mtDNA lineages from the Iberian…

In this tutorial we learn how to install globus-gram-job-manager-slurm on Ubuntu 18.04. globus-gram-job-manager-slurm is Globus Toolkit – SLURM Job Manager Support Introduction In this tutorial we learn how to install globus-gram-job-manager-slurm on Ubuntu 18.04. What is globus-gram-job-manager-slurm globus-gram-job-manager-slurm is: The Globus Toolkit is an open source software toolkit used for…

I am trying to make an NDMS plot with the plot_ordinate function in phyloseq and I keep getting this error. It worked for me previously. This is my code. dist <- phyloseq::distance(rf.indpig.decomp, method=”bray”) ordination <- ordinate(rf.indpig.decomp, method=”NDMS”, distance=dist) plot_ordination(rf.indpig.decomp, ordination, color=”decomp.stage”,shape=”location”) Error in input$map_loaded : $ operator not defined for…

The number of mentions indicates the total number of mentions that we’ve tracked plus the number of user suggested alternatives. Stars – the number of stars that a project has on GitHub. Growth – month over month growth in stars. Activity is a relative number indicating how actively a project…

Calculating polygenic score using plink 0 Hi I am trying to calculate PRS in test sample after getting best SNPs from PRSice 2 with highest R2 My target data is in the form of bed,bim, fam for 22 chromosomes, I want to use plink for specific p-value threshold in this…

NSW Health Minister Brad Hazzard has made a sobering assessment today bluntly saying it’s possible measures to prevent Omicron may already be useless. NSW Health Minister Brad Hazzard has made the frank declaration that the Omicron variant may already be in the Australian community. “We have to expect Omicron may…

NSW Health Minister Brad Hazzard has made a sobering assessment today bluntly saying it’s possible measures to prevent Omicron may already be useless. NSW Health Minister Brad Hazzard has made the frank declaration that the Omicron variant may already be in the Australian community. “We have to expect Omicron may…

Reads annotation data from TIGR Resourcerer or convert the annotation data into Bioconductor data pacakge. Bioconductor version: 2.6 This package allows user either to read an annotation data file from TIGR Resourcerer as a matrix or convert the file into a Bioconductor annotation data package using the AnnBuilder package. Author:…

Showing : bioc-devel • reset updated 3.1 years ago by shepherl 2.9k • written 3.1 years ago by Tim Triche &starf; 4.2k 14 results • Page 1 of 1 Traffic: 314 users visited in the last hour Read more here: Source link

This article was originally published here J Clin Med. 2021 Nov 22;10(22):5443. doi: 10.3390/jcm10225443. ABSTRACT AIMS: Irreversible electroporation is an ablation technique being adapted for the treatment of atrial fibrillation. Currently, there are many differences reported in the in vitro and pre-clinical literature for the effective voltage threshold for ablation….

Overview Abveris is Boston’s premier antibody discovery company providing contract research services to the biopharma industry. Abveris applies advanced immunization methods combined with B cell screening and hybridoma-based antibody discovery technologies to provide comprehensive gene-to-antibody discovery services. Abveris is developing the next generation of biologics, cell therapies, vaccines, and diagnostics…

Overview Abveris is Boston’s premier antibody discovery company providing contract research services to the biopharma industry. Abveris applies advanced immunization methods combined with B cell screening and hybridoma-based antibody discovery technologies to provide comprehensive gene-to-antibody discovery services. Abveris is developing the next generation of biologics, cell therapies, vaccines, and diagnostics…

finder – How can I prevent file association from resetting: .R <> RStudio – Ask Different …

##Genome-Annotation-Data-START##Annotation Provider::NCBIAnnotation Date::06/25/2014 15:11:26Annotation Pipeline::NCBI Prokaryotic Genome Annotation PipelineAnnotation Method::Best-placed reference protein set; GeneMarkS+Annotation Software revision::2.6 (rev. 438450)Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_regionGenes::2,713CDS::2,629Pseudo Genes::35CRISPR Arrays::3rRNAs::3 (5S, 16S, 23S)tRNAs::45ncRNA::1Frameshifted Genes::29##Genome-Annotation-Data-END## Read more here: Source link

The new COVID-19 ‘variant of concern’ named Omicron by the World Health Organisation has created an atmosphere of uncertainty related to transmissibility, vaccine effectiveness, the risk for reinfections and other properties. The overall level of risk associated with the SARS-CoV-2 variant Omicron is assessed as ‘high’ to ‘very high’.  Scientists are…

Abstract Though being vital for human health, microbial interactions with their host and with each other are still largely obscure for researchers. To deepen the understanding, the analyses based on longitudinal data are a better choice than the cross-sectional data since the information provided by the former is usually more…

Abstract Though being vital for human health, microbial interactions with their host and with each other are still largely obscure for researchers. To deepen the understanding, the analyses based on longitudinal data are a better choice than the cross-sectional data since the information provided by the former is usually more…

In 1997, Niall Ferguson edited a book called Virtual History: Alternatives and Counterfactuals, where experts reflected on what the world would be like today if the American Revolution had never happened, if Hitler had invaded England in 1940 or if JFK had never been assassinated. Yet despite a few such illustrious cases,…

Rstudio`s mission is to create free and open-source software for data science, scientific research, and technical communicationWe do this to enhance the production and consumption of knowledge by everyone, regardless of economic means, and to facilitate collaboration and reproducible research, both of which are critical to the integrity and efficacy…

In the war on wheat, William Davis is the commander of a battalion on the front lines. The Milwaukee-based cardiologist’s 2011 book Wheat Belly along with 2013’s Grain Brain by David Perlmutter, both New York Times best-sellers, were twin bombshells that some argued took up the war against the world’s…

In the war on wheat, William Davis is the commander of a battalion on the front lines. The Milwaukee-based cardiologist’s 2011 book Wheat Belly along with 2013’s Grain Brain by David Perlmutter, both New York Times best-sellers, were twin bombshells that some argued took up the war against the world’s…

So I need to replace aes with aes_string due to failing rcmdcheck(). Original: aes( x = A, y = pmax(B, C, na.rm = TRUE), ), My confusion is regarding B and C. Am I allowed to put quotes around them since they are inside the pmax function? Like so: aes_string(…

Estimate cell types proportion by single cell expressions data and gene markers table 0 Hi! I am trying to figure out how to analyze scRNAseq data correctly. I have a table of gene expression data for several people and manually curated tables with genes and corresponding cell types. I want…

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%PDF-1.4 % 125 0 obj > endobj 137 0 obj >stream Skia/PDF m97 Google Docs Renderer application/pdf Impact of protein conformational diversity on AlphaFold predictions 2021-11-27T16:08:55-08:00 2021-11-27T16:08:55-08:00 2021-11-27T16:08:55-08:00 uuid:16d62b69-1dd2-11b2-0a00-4c09271d5700 uuid:16d62b81-1dd2-11b2-0a00-bf0000000000 endstream endobj 124 0 obj > endobj 2 0 obj > endobj 62 0 obj > endobj 114 0 obj >…

🔮 Full RStudio IDE and Syntax Themes (by gadenbuie) Inspired of the similarly named theme, Horizon is a dark theme created for Obsidian. Compatible with Obsidian Desktop, Mobile, and Publish. (by tylernguyen) Our great sponsors Scout APM – A developer’s best friend. Try free for 14-days Nanos – Run Linux…

🔮 Full RStudio IDE and Syntax Themes (by gadenbuie) Inspired of the similarly named theme, Horizon is a dark theme created for Obsidian. Compatible with Obsidian Desktop, Mobile, and Publish. (by tylernguyen) Our great sponsors Scout APM – A developer’s best friend. Try free for 14-days Nanos – Run Linux…

Name Last modified Size Description Parent Directory   –   Databases.choices 2014-08-07 17:26 2.0K   ModifierFields.txt 2018-07-21 17:35 3.1K   Modifiers.csv 2018-07-21 17:27 1.6K   Modifiers.txt 2018-07-21 17:24 692   gc.choices 2018-07-22 14:23 1.0K   gc.csv 2018-07-22 14:21 913   locations.csv 2018-07-22 15:28 555   makepanels.sh 2018-07-22 19:30 1.2K  …

Hi all, I am trying to train a model for gene prediction of a non model plant species using the data set from arabidopsis thaliana. I am referring this tutorial and trying to follow the steps: Steps followed so far: (1) Download arabidopsis data, as provided by this tutorial; this…

Hi all, I am trying to train a model for gene prediction of a non model plant species using the data set from arabidopsis thaliana. I am referring this tutorial and trying to follow the steps: Steps followed so far: (1) Download arabidopsis data, as provided by this tutorial; this…

In tensorflow, if you have 2 tensors of shape NxTxD and NxDxT respectively (N=batch_size, T=SequenceLength, D=NumberOfFeatures), you can dot them and get an output of NxTxT, as demonstrated below: import tensorflow as tf import numpy as np x1 = np.arange(2 * 4 * 3).reshape(2, 4, 3) x2 = np.flip(np.arange(2 *…

PROGRAM DESCRIPTION The Advanced Biomedical Computing Center (ABCC) is a part of the Biomedical Informatics and Data Science (BIDS) Program at Leidos Biomedical Research, Inc. The ABCC provides technology development, scientific consultation, collaboration and training, and high-performance computing support to the NCI and NIH scientists and staff. KEY ROLES/RESPONSIBILITIES The…

I have built a machine for deep learning with a RTX 3060. However, while running the first test, it seems that the computation on GPU is slower than on CPU. The code and the output is attached below. Note that I don’t measure the time that it takes to move…

About Benson HillBenson Hill empowers innovators to develop more healthy, tasty and sustainable food by unlocking the natural genetic diversity of plants. Benson Hill’s CropOS™ platform combines machine learning and big data with advanced breeding techniques and plant biology to drastically accelerate and simplify the product development process. The CropOS…

Publications PubMed=9081441Shubina N.G., Kolontsov A.A., Malakhova M.S., Makarov V.V.Cell-to cell interactions in cultures of swine bone marrow cells and CPK-66b cells infected with African swine fever virus.Biull. Eksp. Biol. Med. 122:418-424(1996) DOI=10.3103/S1068367415020056Balysheva V.I., Prudnikova E.Y., Galnbek T.V., Balyshev V.M.Immunological properties of attenuated variants of African swine fever virus isolated in…

The Italian Regional Student Group of the ISCB – International Society for Computational Biology is happy to announce that our second event “BIOINFORMATICS CAREERS OUTSIDE ACADEMIA” will take place online next Monday 29/11 from 7-8.15PM! There will be three speakers who are excited to share their experience and to take…

Interfacing single-stranded DNA (ssDNA) with 2D transition metal dichalcogenides are important for numerous technological advancements. However, the molecular mechanism of this process, including the nature of intermolecular association and conformational details of the self-assembled hybrids is still not well understood. Here, atomistic Molecular Dynamics (MD) simulation is employed to study…

1 Introduction Lung cancer is the leading cause of cancer-related deaths worldwide, with adenocarcinoma as the most common histological subtype.1 In recent years, epidermal growth factor receptor-tyrosine kinase inhibitors (EGFR-TKIs), such as gefitinib (first generation) and osimertinib (third generation), have been widely used for lung adenocarcinoma patients harboring activated EGFR…

This article was originally published here J Clin Med. 2021 Nov 13;10(22):5276. doi: 10.3390/jcm10225276. ABSTRACT (1) Background: The aim of our study was to analyze the possible relationship of ABCB1 and CYP1A1 gene variants with susceptibility and outcome of multiple myeloma (MM); (2) Methods: Genomic DNA samples from 110 newly-diagnosed…

This article was originally published here J Pers Med. 2021 Nov 11;11(11):1185. doi: 10.3390/jpm11111185. ABSTRACT Thalidomide analogues (or immunomodulatory imide drugs, IMiDs) are cornerstones in the treatment of multiple myeloma (MM). These drugs bind Cereblon (CRBN), a receptor for the Cullin-ring 4 ubiquitin-ligase (CRL4) complex, to modify its substrate specificity….

Kidney organoids designed with the same mutation as that present in Fabry disease can help investigators better understand how the disease functions, authors suggested. A new report makes the case that stem-cell-derived kidney organoids can provide a meaningful model for understanding how Fabry disease affects the body and for developing…

Introduction UCL-BLIC/rnaseq is a bioinformatics analysis pipeline used for RNA sequencing data, modified to add kallisto. The workflow processes raw data from FastQ inputs (FastQC, Trim Galore!), aligns the reads (STAR or HiSAT2), generates gene counts (featureCounts, StringTie) as well as kallisto abundance files, and performs extensive quality-control on the…

samtools mpileup error 0 I am using samtools function mpileup to get reads in sites. The command I used is: samtools mpileup -l hg19.position -f hg19.fa -Q 20 -q 20 -I file.bam in the command, hg19.position is position-based site file. When running these is an error printed on screen: ……

r – Q: Disjoin data gaps that exceed a certain value (ggplot2) – Stack Overflow …

  This article shows how to create a ggplot2 graphic with a factor on the x-axis in R programming. The tutorial consists of the following: Let’s dive right in…   Example Data & Packages The first step is to create some exemplifying data: data <- data.frame(group = factor(letters[1:5]), # Create…

which value is selected for pearson correlation for cis and trans target gene prediction ? 1 I want to analyses the cis and trans target gene from the RNA-seq data. i had read several paper and it shows that either PCC or spearman’s correlation is used for finding the cis…

R: Grab Bag of GGplot2 Functions. ggallin-package {ggallin} R Documentation Grab Bag of GGplot2 Functions. Description This package consists of some helper functions for working with ggplot2: geoms, transforms, etc., with no real unifying theme among them. Legal Mumbo Jumbo ggallin is distributed in the hope that it will be…

I am trying to configure Jupyterhub with Docker on port 8080 for http and port 8443 for https, and I have set up an AWS ELB that forwards traffic to port 8000. I am currently getting a bad gateway error, but what I am trying to understand is, it seems…

Mitochondrial annotation tools other than MITOS and DOGMA 3 Hi All I am working on de novo mitochondrial genome assembly of trematode species. The size of the assembled genome is ~14kb which is also expected, considering the genome size of the closest reference. I used MITOS for gene prediction, but…

—–BEGIN PGP SIGNED MESSAGE—– Hash: SHA512 Format: 1.8 Date: Tue, 12 Oct 2021 20:08:26 +0200 Source: jupyterhub Binary: jupyterhub Architecture: source all Version: 1.4.1+ds2-1 Distribution: unstable Urgency: medium Maintainer: Debian Python Team <team+pyt…@tracker.debian.org> Changed-By: Roland Mas <lola…@debian.org> Description: jupyterhub – Multi-user server for Jupyter notebooks Changes: jupyterhub (1.4.1+ds2-1) unstable; urgency=medium…

Generate DNA string 0 Q1/we need to ensure that a motif with the same or even larger score is unlikely to occur in a collection of “typical” DNA strings (of the same length). How would you generate these strings? Q2/When using motif software with fixed motif lengths, is it better…

—–BEGIN PGP SIGNED MESSAGE—– Hash: SHA512 Format: 1.8 Date: Fri, 26 Nov 2021 16:53:38 +0100 Source: mbedtls Architecture: source Version: 2.16.11-0.3 Distribution: unstable Urgency: medium Maintainer: James Cowgill <jcowg…@debian.org> Changed-By: Andrea Pappacoda <and…@pappacoda.it> Changes: mbedtls (2.16.11-0.3) unstable; urgency=medium . * Non-maintainer upload * Drop CMAC support as it breaks ABI…

In more ways than one, the process of studying ecology began as early as the first humans came into existence. However, the process of doing it now continues to develop and evolve as we continue to apply technology to the execution of our ideas. Ecology is a structure that shows…

    This package is for version 3.2 of Bioconductor; for the stable, up-to-date release version, see edge. Extraction of Differential Gene Expression Bioconductor version: 3.2 The edge package implements methods for carrying out differential expression analyses of genome-wide gene expression studies. Significance testing using the optimal discovery procedure and…

topGO: Enrichment analysis for Gene Ontology Bioconductor version: 2.6 topGO package provides tools for testing GO terms while accounting for the topology of the GO graph. Different test statistics and different methods for eliminating local similarities and dependencies between GO terms can be implemented and applied. Author: Adrian Alexa, Jorg…

Is there any way to fix the low percentage mapping results ? 0 Hi Guys! Is there any way to fix the low percentage mapping results ? I have some shotgun metagenome data. Before mapping I checked the quality with FAST QC and then trimmed it. Minimum contig length was…