Category: Research

r – Can I analyze RNAseq data from two different cell types using the design matrix model.matrix(~0 + group + celltype)?

I have two cell types(11C and 13C) and two groups (KO and CTRL). sample celltype group 11C-17 11C KO 11C-84 11C KO 11C-C 11C CTRL 13C-17 13C KO 13C-84 13C KO 13C-C 13C CTRL As shown in the PCA plot, the cell type is the dominant difference. But, I’d like…

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Creative Biogene Launches Synthesized siRNAs to Accelerate the Pace of Gene Research

Creative Biogene announced the release of its C. elegans RNAi service to study the mechanism of RNAi and accelerate the pace of gene research. New York, USA – January 28, 2022 – C. elegans platform, the division of Creative Biogene, is dedicated to providing high-quality products and services in order…

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Frequencies and characteristics of genome-wide recombination in Streptococcus agalactiae, Streptococcus pyogenes, and Streptococcus suis

1. Parte, A. C. LPSN–list of prokaryotic names with standing in nomenclature. Nucleic Acids Res. 42, D613-616 (2014). CAS  PubMed  Google Scholar  2. Krzyściak, W., Pluskwa, K. K., Jurczak, A. & Kościelniak, D. The pathogenicity of the Streptococcus genus. Eur. J. Clin. Microbiol. Infect. Dis. 32, 1361–1376 (2013). PubMed  PubMed…

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Technological Advances in RNA Stabilization & Delivery

RNA therapeutics is a rapidly expanding field of next-generation medicine. RNA therapy typically comprises 4 different classes of molecules: non-codingRNA (ncRNA), antisense oligonucleotide (ASO), messengerRNA (mRNA), and RNA aptamer. New York, Jan. 27, 2022 (GLOBE NEWSWIRE) — Reportlinker.com announces the release of the report “Technological Advances in RNA Stabilization &…

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16S rRNA gene sequence diversity in Faecalibacterium prausnitzii-complex taxa has marked impacts on quantitative analysis

doi: 10.1093/femsec/fiac004. Online ahead of print. Affiliations Expand Affiliations 1 Department of Food, Aroma and Cosmetic Chemistry, Faculty of Bioindustry, Tokyo University of Agriculture, 099-2493 Hokkaido, Japan. 2 Functional Food Forum, University of Turku, 20014 Turku, Finland. 3 Department of Microbiology and Biochemistry of Dairy Products, IPLA-CSIC, 33300 Villaviciosa, Spain….

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Scikit Learn Minmaxscaler – January 2022

Sklearn Preprocessing Minmaxscaler – XpCourse Posted: (7 days ago) Scikit_Learn preprocessing.MinMaxScaler example. class sklearn.preprocessing.MinMaxScaler (feature_range=0, 1, *, copy=True, clip=False) [source] Transform features by scaling each feature to a given range. This estimator scales and translates each feature individually such that it is in the given range on the training set,…

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In Brief This Week: Innovent, Senhwa Biosciences, Oric Pharmaceuticals, Dizal Pharmaceutical

NEW YORK – Innovent this week said that pemigatinib (Pemazyre) was approved in Hong Kong as a treatment for locally advanced or metastatic cholangiocarcinoma with an FGFR2 fusion or rearrangement. The approval was based on the Phase II FIGHT-202 study, which showed a 37 percent response rate for cholangiocarcinoma patients treated…

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Paid research study for DLBCL patients and caregivers : lymphoma

I want to thank the community members who have already participated in this research and shared their insight and experiences. There are still spots available – please reach out or fill out the form below if you are interested. Help Us Better Understand Diffuse Large B-Cell Lymphoma (DLBCL) Pinpoint Patient…

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Slurm environment variable for requested time

For a slurm job, the environment variable $SLURM_JOB_NUM_NODES gives the number of nodes requested. Is there a similar variable that gives the run time requested? I couldn’t find the answer and I have tried $SLURM_JOB_TIME, $SLURM_TIME and $SLURM_SUBMIT_TIME, but none of these works. Ultimate goal is to let the script…

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Scipio Bioscience Bets on Hydrogel Tech to Differentiate New Single-Cell RNA-seq Kit

NEW YORK – Paris-based Scipio Bioscience this week announced the European launch of its Asteria hydrogel-based single-cell RNA-seq kit. With less reliance on equipment and reagents, the RNA-seq library preparation kit provides researchers with a flexible benchtop protocol for labeling, isolating, and lysing cells, and recovering labeled mRNA. The Asteria kit comes…

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[lammps-users] moving graphene as rigid – LAMMPS Mailing List Mirror

Hello LAMMPS users, I am using windows 30 july 2021. units are real. I have a query regarding rigid command. I want to move graphene as a rigid body. For this I have created two groups. One group is fixedatoms (purple colored) and the second group is rigidcarbonatoms (grey color)….

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[gmx-users] Regarding combination rules in gromos53a6 ff

Dear GROMACS users,I want to use the geometric mean of both sigma (sigma i sigmaj)andepsilon(epsilon i epsilon j) as a combination rule in my simulation.According to the combination rules in the manual, the combination 3incorporates Vii=sigma and Wii= epsilon along with geometric mean of Ci(6)Cj(6) and Ci(12)Cj(12) terms.So can I…

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Astronomers close in on new way to detect gravitational waves

Supermassive black holes orbiting each other very closely are expected to produce gravitational waves.Credit: NASA’s Goddard Space Flight Center/Science Photo Library Astronomers could be on the verge of detecting gravitational waves from distant supermassive black holes — millions or even billions of times larger than the black holes spotted so…

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import – How to make a python module accessible to multiple editors?

I am learning biopython and would like to use Visual Studio Code (VSC—my favorite editor so far) to do coding exercises on the topic. However, the module does not show up when I try to import using VSC. In fact, for my computer the biopython module only works in Spyder….

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[BioC] limma, remove two type of batch effect

Hi All, In my analysis, I want to find the different expression genes betweendissese A and B. There are two type of batch effect in my analysis. Iwant to use limma to remove two type of batch effect, one is gender,another is tissue type. I do as fellow. But I…

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DESeq2 contrast multiple treated conditions versus multiple control conditions

I have 4 treated and 2 control samples each 3 reps. I would like to contrast treated 1,2,3 against 2 controls, and treated 4 against 2 controls. (condition <-factor(c(“treated1″,”treated1″,”treated2″,”treated2″,”treated3″,”treated3″,”treated4″,”treated4″,”control1″,”control1″,”control2″,”control2”))) (coldata <- data.frame(row.names=colnames(txi.g), condition)) dds <- DESeqDataSetFromTximport(txi.g, colData=coldata, design=~condition) dds <- DESeq(dds) res <- DESeq2::results(dds, contrast = list(c(“treated1″,”treated2″,”treated3”),c(“control1″,”control2”)), listValues = c(3,-3/5)…

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Assistant Professor of bioinformatics and ancient metagenomics – University of Copenhagen – job portal

Job Portal The GLOBE Institute at the Faculty of Health and Medical Sciences, University of Copenhagen seeks to appoint a temporary assistant professor of bioinformatics and ancient metagenomics to commence 1 May 2022 or soon as possible thereafter. Information on the department can be found at: ?url=https%3A%2F%2Fglobe.ku.dk&module=jobs&id=2223594″ target=”_blank” rel=”nofollow”>globe.ku.dk Job…

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Bioinformatics Scientist Job Opening in Seattle, WA at Alpine Immune Sciences

Job Posting for Bioinformatics Scientist at Alpine Immune Sciences Alpine Immune Sciences is applying our platform discovery technology to bring innovative new therapies to people living with serious or life-threatening illnesses or conditions, such as cancer and autoimmune/inflammatory diseases. Exciting challenges lie ahead—guided by our core values, we’ll…

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Confident chemistry | Scientific Computing World

OpenEye Scientific develops and offers large-scale molecular modelling applications and toolkits, primarily aimed at drug discovery and design. ‘Although our tools are used by a wider industrial sector, from large pharma and small biotechs, through to agrochemicals and materials scientists,’  commented Ashutosh Jogalekar, associate director – applications science at  OpenEye Scientific. OpenEye…

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Split multiallelic SNPs to biallelic from vcf

Dear all, I have a particular vcf file like this, chrX 29 . G A,T . PASS AC=1,1;AN=3 GT:DP:HF:CILOW:CIUP:SDP 0/1/2:4839:0.003,0.001:0.002,0.0:0.005,0.003:14;0,4;2 I tried various tools to split this, but I get the following results, so the FORMAT and INFO lines are identical. chrX 29 . G A . PASS AC=1,1;AN=3;OLD_MULTIALLELIC=chrM:899:G/A/T GT:DP:HF:CILOW:CIUP:SDP…

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scrnaseq – Integrating scRNA-seq data using raw data

I believe when you say alignment, you mean aligning reads to a genome (sometimes to transcriptome) and count these to get count matrices. In the aforementioned paper, however, what is meant is “bringing different data sets to a level where they can be compared/integrated/…”. Basically scRNA-seq data are heavily prone…

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UMItools dedup deduplication taking too much time + RAM

I have some RNAseq data from miRNAs that I have processed with Bowtie2 (aligning to miRBase). Now, when doing the deduplication with umi_tools dedup I find that some of the files take a lot of time+RAM to finish (some files take around 3-4 minutes and 4-5GB of RAM and some…

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How to plot common y-axis text for combined figure (ggplot2)

I’m a beginner in R (and ggplot2). I’m trying to make 1×3 figure, and scale of y axis is same for all three figures. Also, I want to remove text and title of y axis for second and third plot. However, I realized that width of first figure become narrow…

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r – Where does ggplot set the order of the color scheme?

I think this is a reproducible example of what you’re seeing. In the diamonds dataset, the mean price of “Good” diamonds is actually higher than the mean for “Very Good” diamonds. library(dplyr) diamonds %>% group_by(cut) %>% summarize(mean_price = mean(price)) # A tibble: 5 x 2 cut mean_price <ord> <dbl> 1…

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JupyterHub on Host Network with HTTPS failing with 503: Service Unavailable – Zero to JupyterHub on Kubernetes

Hi All, Hope everyone is well! I have been working on a small project for an internal network to get JupyterHub running. I have gotten pretty far in the development, but now stuck on getting HTTPS working with the host network option. JupyterHub is running on internal VMs and thus…

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identify and remove adapter sequence

identify and remove adapter sequence 2 Hi all, I am trying to identify the adapter sequences of my ATAC-sequencing data. The way I tried to achieve this was to send the fastq file to FastQC. Hoping the sequence would be picked and showed in the report. In the report, there…

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RStudio is slow when loading a project / package in development

I have recently experienced a serious problem with Rstudio when developing a package. Whenever, I open an existing project with Rstudio where versions are controlled with Git, it takes so long for it to respond to any command. It is also impossible to type something in the console (e.g. 1+1)…

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New method and model address blindspot toward

New method and model address blindspot towards uncommon species in mixed samples For higher accuracy and more effective microbial diagnostics, researchers at the Earlham Institute have evaluated a new approach to analyse metagenomic samples that may contain low numbers of certain species – helping to prevent crucial genomic information from…

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A Novel Tenorrhaphy Suture Technique with Tissue Engineered Collagen Graft to Repair Large Tendon Defects

In this paper, we present an in vitro and in situ protocol to repair a tendon gap of up to 1.5 cm by filling it with engineered collagen graft. This was performed by developing a modified suture technique to take the mechanical load until the graft matures into the host…

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Multi-organoid system to simulate human liver

image: Enlarged view of the co-culture system view more  Credit: Advanced Science Type 2 diabetes (T2DM) is a systematic multi-organ metabolic disease, which is characterized by dynamic interplay among different organs. Pancreatic islet-liver axis is closely associated with normal glucose regulation and homeostasis maintenance. The dysfunction of the interplay between these…

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Mitochondrial DNA variation across 56,434 individuals in gnomAD

Genomic databases of allele frequency are extremely helpful for evaluating clinical variants of unknown significance; however, until now, databases such as the Genome Aggregation Database (gnomAD) have focused on nuclear DNA and have ignored the mitochondrial genome (mtDNA). Here we present a pipeline to call mtDNA variants that addresses three…

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Comparison of circulating DNA in malignant neoplasia from diverse locations: Investigating a diagnostic role

Context: Circulating free DNA (cfDNA) analysis has emerged as novel noninvasive diagnostic biomarker in several solid tumors. Raised levels have been reported in several malignancies and may correlate with clinicopathological and treatment response. The current study was designed to assess the diagnostics of cfDNA in different tumor types of malignancies…

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A simple, unofficial implementation of MAE using pytorch-lightning

A simple, unofficial implementation of MAE (Masked Autoencoders are Scalable Vision Learners) using  pytorch-lightning. Currently implements training on CUB and StanfordCars, but is easily extensible to any other image dataset. Setup # Clone the repository git clone github.com/catalys1/mae-pytorch.git cd mae-pytorch # Install required libraries (inside a virtual environment preferably) pip…

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Active Motif Incorporated Announces the Acquisition of Amaryllis Nucleics and their proprietary RNASeq workflow

CARLSBAD, Calif., Jan. 27, 2022 /PRNewswire/ — Active Motif Incorporated, a company with the vision of bringing epigenetics more deeply into precision medicine, announced that it has purchased Amaryllis Nucleics, a Bay Area-based start-up company focused on proprietary RNA Sequencing methods. Amaryllis Nucleics provides Active Motif with a streamlined, low-cost…

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A high-throughput assay for directly monitoring nucleolar rRNA biogenesis

doi: 10.1098/rsob.210305. Epub 2022 Jan 26. Affiliations Expand Affiliations 1 Department of Molecular Biophysics and Biochemistry, Yale School of Medicine, 333 Cedar Street, New Haven, CT, USA. 2 Yale Center for Molecular Discovery, Yale University, West Haven, CT, USA. 3 Department of Genetics, Yale School of Medicine, New Haven, CT,…

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In Rett Models, Regulatory RNAs Appear To Be Altered

Regulatory RNAs involved in nerve cell signaling and structure were altered in cell and mouse models of Rett syndrome, with these changes also evident in tissue from deceased patients, a study reported. These findings aid in understanding the biological processes impaired in Rett and may reveal potential biomarkers to help…

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Python skicit-learn k-nearest neighbors – 3d distance matrix ( Python, Scikit Learn )

Problem : ( Scroll to solution ) I’m working on the distances of thousands sphere shaped objects in a 3D environment. I used numpy to create a distance matrix between the spheres and would initially like to pick out certain distances, e.g. the nearest 5, of all objects within the…

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How to fix deeptoolsintervals fatal error: python.h? ( Python, Python 3.X )

Problem : ( Scroll to solution ) I tried installing pip3 install deeptoolsintervals the error is: deeptoolsintervals/tree/tree.c:1:20: fatal error: Python.h: No such file or directory compilation terminated. error: command ‘/usr/bin/x86_64-linux-gnu-gcc’ failed with exit code 1 I have Ubuntu 16.04.7 and Python versions installed: ls /usr/bin | grep python dh_python2 dh_python3…

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Clinical manifestations of diffuse large B-cell lymphoma that exhibits initial symptoms in the maxilla and mandible: a single-center retrospective study | BMC Oral Health

Table 1 summarizes the clinical findings at the initial examination. History of treatment before the initial examination Sixteen patients (59.3%) had previously undergone diagnosis and treatment of the site at a previous dental clinic or another Department of Oral Surgery prior to the initial examination at our department. Tooth extraction…

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ZP77 – YFull YTree Info

R-ZP77 – YFull YTree Info SNPs currently defining R-ZP77 ZP77 / FGC6562     Sample ID Country / Language Info Ref File Testing company Statistics Status YF008362 —— R-ZP77* —— Hg19 .BAM FTDNA (Y500) 41X, 13.8 Mbp, 165 bp YF067652 Unknown R-BY40744 —— Hg38 .BAM FTDNA (Y700) 36X, 18.7 Mbp, 151…

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parallel processing – Forcing subsequent SLURM jobs to wait until first job is done?

I am running 1000 jobs on a cluster, using a sbatch job array. I’ve set up my code such that if the job array index is set to 0, precomputations are executed and saved to file; the jobs 1-999 then access these precomputations. The precomputations in job 0 take much…

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Petabase-scale sequence alignment catalyses viral discovery

Serratus alignment architecture Serratus (v0.3.0) (github.com/ababaian/serratus) is an open-source cloud-infrastructure designed for ultra-high-throughput sequence alignment against a query sequence or pangenome (Extended Data Fig. 1). Serratus compute costs are dependent on search parameters (expanded discussion available: github.com/ababaian/serratus/wiki/pangenome_design). The nucleotide vertebrate viral pangenome search (bowtie2, database size: 79.8 MB) reached processing rates…

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python – How can I fix the dash bio error: devtools cannot load source map dashbio@1.0.1 bundle.js.map?

I am implementing a website in Python with Django framework and using django-plotly-dash to display data. I am trying to use dash_bio’s IGV feature to display some chromosome data, but when I attempt to call the functionality, I receive the following errors and the callback that returns ‘dashbio.igv’ is unable…

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DNA Labs International Launches the Newest Technology for Forensic Genetic Genealogy

MiSeq FGx platform by Verogen DEERFIELD BEACH, Fla. (PRWEB) January 26, 2022 DNA Labs International, which specializes in forensic DNA analysis including forensic genetic genealogy (FGG) for law enforcement agencies, government forensic labs, and attorneys, is announcing the release of their newest technology, Single Nucleotide Polymorphism (SNP) testing with…

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Rise in Incidence of Genetic Diseases & Immediate Measures

Genotyping is a specific technology used for identifying the genetic variations in an individual’s genomic sequence or allelic genes by comparing them to the reference sequence. Genotyping generally helps to explore the genetic variants such as structural changes in the DNA and single nucleotide polymorphism (SNPs). Genotyping assay verifies the…

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[lammps-users] How to built lamps for organic molecular crystals using GAFF face field from cif file – LAMMPS Mailing List Mirror

LAMMPS generally does not support importing topology and parameter data from other simulation tools and instead depends on external tools to generate data or input files.A few, simple tools that were contributed by LAMMPS users are in the LAMMPS tools folder, but most of those are unmaintained and untested by…

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Test if a gene is NOT differentially expressed in DESeq2?

Test if a gene is NOT differentially expressed in DESeq2? 1 @pennylane-21859 Last seen 1 day ago United States First, my apologies if this has been covered already. I thought for sure it would have been, but I can’t find the relevant info with my searches. It’s pretty obvious from…

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Data Scientist – Molecular Biology job with SRG

Data Scientist London (hybrid, some remote working is possible) Permanent Up to £40k per annum I’m partnering with an exciting and revolutionary MedTech organisation based in London who are hiring for a Data Scientist to join their assay development team. The organisation has developed unique wearable, personalised technology to inform…

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Postdoctoral Fellow (Bioinformatics) – Jos Melenhorst Lab

Highly motivated individuals with a PhD or MD/PhD in relevant area are encouraged to apply. This training position, under the direct supervision of a Cleveland Clinic Principal Investigator will provide practical training and experience in a research setting. This position is appointed through the Lerner Research Institute. The successful applicant…

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Scientists identify promising transmission chain breakers in the fight against malaria

Credit: CC0 public domain Blocking important proteins found in Anopheles gambiensis, the leading carrier of malaria transmission to humans in Africa, blocks malaria parasite transmission and parasite humans, according to researchers at Johns Hopkins Malaria Research. You can prevent infection to. Johns Hopkins Bloomberg Institute for Public Health School. and…

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CIBERSORTxFractions ERROR: Could not read /src/outdir//temp.Fractions.simfracs.tsv

Hello, can anyone offer any insight into the following problem? I am trying to run the following CIBERSORTx function locally: docker run -v /media/mark/seagate2/data/CIBERSORTx_GC:/src/data -v /media/mark/seagate2/data/CIBERSORTx_GC:/src/outdir cibersortx/fractions –username <my_user_name> –token <my_token> –single_cell TRUE –refsample reference.txt –mixture rsem_mixture_TPM.tsv –fraction 0 –rmbatchSmode TRUE I get the following output to the terminal: >Running…

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Identification of Novel Diagnostic Biomarkers in Prostate Adenocarcinoma Based on the Stromal-Immune Score and Analysis of the WGCNA and ceRNA Network

This article was originally published here Dis Markers. 2022 Jan 15;2022:1909196. doi: 10.1155/2022/1909196. eCollection 2022. ABSTRACT Prostate cancer is still a significant global health burden in the coming decade. Novel biomarkers for detection and prognosis are needed to improve the survival of distant and advanced stage prostate cancer patients. The…

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Novel diagnostic biomarkers for keloid based on GEO database

Introduction Keloid is excessive fibrosis of the skin that extends beyond the area of injury and does not regress.1 Keloid can occur in the joints and mouth after several years of severe injury, including burns, chemical injury, wound, and surgical incision.2 Keloids on the joints affect the quality of life,…

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How to draw x and y axis in ggplot2 r? ( R, Ggplot2 )

Problem : ( Scroll to solution ) So, I’d like to draw x and y axis using ggplot2. I managed to draw x axis with a function: fun = function{x} {x* 0 }, but I don’t know how to do the same with y axis. If I use built in…

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Changing legend title in ggplot changes the shown legend aesthetic

I make some plot with ggplot2 like this: library(ggplot2) ggplot(df, aes(x, y, col= col)) + geom_point() Everything is good but as soon I set another legend title as shown here, the continuous colour gradient changes to some points in the legend: library(ggplot2) ggplot(df, aes(x, y, col= col)) + geom_point() +…

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LKML: Yong Wu: [PATCH v4 16/35] iommu/mediatek: Add IOMMU_TYPE flag

From Yong Wu <> Subject [PATCH v4 16/35] iommu/mediatek: Add IOMMU_TYPE flag Date Tue, 25 Jan 2022 16:56:15 +0800 Add IOMMU_TYPE definition. In the mt8195, we have another IOMMU_TYPE:infra iommu, also there will be another APU_IOMMU, thus, use 2bits for theIOMMU_TYPE.Signed-off-by: Yong Wu <yong.wu@mediatek.com>Reviewed-by: AngeloGioacchino Del Regno <angelogioacchino.delregno@collabora.com>—drivers/iommu/mtk_iommu.c | 12…

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r – How to change the resolution of animated plots (gif) in RStudio Viewer?

I guess those plots shown in the gganimate article were created on a Linux platform. gganimate by default uses the ‘png’ device for rendering the single frames. png() on windows however by default uses the Windows GDI which is not available on Linux (cairographics is used). This is (probably) why…

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Droplet Genomics Debuts New Microfluidic Screening Platform, Touting Throughput, Flexibility

NEW YORK – Droplet Genomics, a European technology company headquartered in Vilnius, Lithuania, is rolling out a new droplet microfluidic platform for high-throughput screening for a variety of research applications. CEO Juozas Nainys said the firm delivered the first of the instruments to customers at the end of 2021 after having…

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Transverse Sectioning of Mature Rice (Oryza sativa L.) Kernels for Scanning Electron Microscopy Imaging Using Pipette Tips as Immobilization Support

This protocol allows for the preparation of transverse sections of cereal seeds (e.g., rice) for the analysis of endosperm and starch granule morphology using scanning electron microscopy. This protocol allows seeds to be sliced intact so they don’t crumble, permitting visualization of starch granules in any seed that can fit…

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IDbyDNA Appoints Susan E. Daniels, Ph.D., as Vice President of R&D and Member of Executive Committee

Susan E. Daniels, Ph.D. Precise insights for better health. SALT LAKE CITY, Jan. 24, 2022 /PRNewswire/ — IDbyDNA, a precision metagenomics company offering next-generation-sequencing-based infectious disease testing and anti-microbial resistance profiling, today announces that it has appointed Susan (Siw) E. Daniels, Ph.D., as Vice President of R&D and a member…

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ZJRen9/CRISPR_screen_effective_m6ASite: CRISPR screen sgRNA analysis pipeline

GitHub – ZJRen9/CRISPR_screen_effective_m6ASite: CRISPR screen sgRNA analysis pipeline You can’t perform that action at this time. You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. Read more here: Source link

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[Bug 1786013] Autopkgtest regression report (linux-meta-hwe-5.13/5.13.0.28.31~20.04.15)

All autopkgtests for the newly accepted linux-meta-hwe-5.13 (5.13.0.28.31~20.04.15) for focal have finished running. The following regressions have been reported in tests triggered by the package: nvidia-graphics-drivers-340/340.108-0ubuntu5.20.04.2 (amd64) systemd/245.4-4ubuntu3.15 (amd64, s390x, ppc64el) Please visit the excuses page listed below and investigate the failures, proceeding afterwards as per the StableReleaseUpdates policy regarding…

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bcftools merged vcf file assigns all variants to one sample

bcftools merged vcf file assigns all variants to one sample 0 I’ve made one vcf file for each of three samples. I then combined them using bcftools, like so: # Make a list of vcf files to merge cat “${OUT}/results/variants/vcf_list” /mnt/gpfs/live/rd01__/ritd-ag-project-rd018o-mdflo13/data/test/manual/results/variants/3a7a-10.vcf.gz /mnt/gpfs/live/rd01__/ritd-ag-project-rd018o-mdflo13/data/test/manual/results/variants/MF3.vcf.gz /mnt/gpfs/live/rd01__/ritd-ag-project-rd018o-mdflo13/data/test/manual/results/variants/R507H-FB_S355_L001.vcf.gz Then merge the list: bcftools merge -l…

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Genomics Beyond Health Care: Future Uses and Considerations of Genome Science

A major new report, Genomics Beyond Health, released today by the Government Office for Science, explores how genomics could play a role in our lives in the future, from sports to education and the fight against crime. Until now, genomics has been used primarily in healthcare and medical research where…

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convolutional neural networks – What the specific dimensions in Pytorch torch.Conv2D mean?

This post is about specific software, hardware, datasets, or pre-trained models. Want to improve this question? Update the question so it’s on-topic for Artificial Intelligence Stack Exchange. Closed yesterday. This post was edited and submitted for review 6 hours ago. x =…

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VCV001120242.1 – ClinVar – NCBI

Likely pathogenic (Jun 01, 2021) criteria provided, single submitter (ACMG Guidelines, 2015) Method: research Postaxial polydactyly type A1 (Autosomal dominant inheritance) Affected status: yes Allele origin: germline Institute for Medical Genetics and Human Genetics, Charité – Universitätsmedizin Berlin Additional submitter: CUBI – Core Unit Bioinformatics,Berlin Institute of Health Accession: SCV001653577.1…

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What is the molarity of a solution made from 325.4 g of AlCl 3 with enough water to make 500.0 mL?

What is the molarity of a solution made from 325.4 g of AlCl3 with enough water to make 500.0 mL? This is a List of Available Answers Options : 0.651 M 4.880 M 1.22 M 2.44 M The best answer is B. 4.880 M. Reported from teachers around the world….

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Novel gene rearrangement in the mitochondrial genome of Anastatus fulloi (Hymenoptera Chalcidoidea) and phylogenetic implications for Chalcidoidea

1. Osellame, L. D., Blacker, T. S. & Duchen, M. R. Cellular and molecular mechanisms of mitochondrial function. Best Pract. Res. Clin. Endocrinol. Metab. 26, 711–723 (2012). CAS  PubMed  PubMed Central  Google Scholar  2. Bernt, M., Braband, A., Schierwater, B. & Stadler, P. F. Genetic aspects of mitochondrial genome evolution….

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In-Depth Analysis of Bacillus anthracis 16S rRNA Genes and Transcripts Reveals Intra- and Intergenomic Diversity and Facilitates Anthrax Detection

Various ratios of 16S-BA/BC-alleles constitute possible explanations for differences in FISH signals of cells of diverse B. anthracis strains (Fig. 1). Indeed, we found a significant correlation between 16S-BA/BC-allele ratios in sequenced genomes and mean intensities of the Cy3 FISH signals targeting the16S-BA-allele (tested with the cor.test function in R, Pearson’s…

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Random Forest Classifier Sklearn Python

Random Forest Classifier in Python | by Joe Tran | Towards … Posted: (5 days ago) Data Preprocessing. import pandas as pd. import numpy as np. import matplotlib.pyplot as … Train the RF classifier. Let’s first create our first model. Of course one can start with … Evaluate the classifier….

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Creative Bioarray Built Professional Cell Reprogramming Services with Cutting-edge Technologies to Accelerate Drug Development and Research

Creative Bioarray announced the release of its professional cell reprogramming services with cutting-edge technologies to accelerate drug development and research. New York, USA – January 24, 2022 – Cell culture platform, the division of Creative Bioarray, focuses on developing complete cell culture solutions with plenty of choices for the next…

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Front-Line Treatment of DLBCL – NewsBreak

Dr. Lenz on the Rationale for the CheckMate 9X8 in Metastatic CRC Heinz-Josef Lenz, MD, FACP, discusses the rationale for the phase 2/3 CheckMate 9X8 trial in metastatic colorectal cancer. Heinz-Josef Lenz, MD, FACP, associate director, Clinical Research, J. Terrence Lanni Chair in Gastrointestinal Cancer Research, co-director, University of Southern…

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How do I save print statements when running a program in SLURM?

By default, print in Python is buffered, meaning that it does not write to files or stdout immediately, and needs to be ‘flushed’ to force the writing to stdout immediately. See this question for available options. The simplest option is to start the Python interpreter with the -u option. From…

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GitHub – jmp448/sc-dynamic-eqtl

GitHub – jmp448/sc-dynamic-eqtl You can’t perform that action at this time. You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. Read more here: Source link

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How to convert transcript-relative coordinates to genomic coordinates?

How to convert transcript-relative coordinates to genomic coordinates? 0 I have queried using Entrez Utilities (efetch: www.ncbi.nlm.nih.gov/books/NBK25499/) and obtained annotations for transcripts like the following: >Feature ref|NM_152486.3| 1 2557 gene gene SAMD11 gene_syn MRS gene_desc sterile alpha motif domain containing 11 db_xref GeneID:148398 db_xref HGNC:HGNC:28706 db_xref MIM:616765 How/what database should…

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Where can I find an annotation table for human gencode ensemble gene ids to gene name/description?

Where can I find an annotation table for human gencode ensemble gene ids to gene name/description? 1 BioMart –> Ensembl Genes –> Human Genes –> Attributes (in left column) –> Select Gene Stable ID, Gene Name, Gene Description (or anything else you want, right pane) –> Hit Count –> 68005…

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Comprehensive summary of mitochondrial DNA alterations in the postmortem human brain: A systematic review

Summary Background Mitochondrial DNA (mtDNA) encodes 37 genes necessary for synthesizing 13 essential subunits of the oxidative phosphorylation system. mtDNA alterations are known to cause mitochondrial disease (MitD), a clinically heterogeneous group of disorders that often present with neuropsychiatric symptoms. Understanding the nature and frequency of mtDNA alterations in health…

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sankaranlab/SCAVENGE: SCAVENGE is a method to optimize the inference of functional and genetic associations to specific cells at single-cell resolution.

GitHub – sankaranlab/SCAVENGE: SCAVENGE is a method to optimize the inference of functional and genetic associations to specific cells at single-cell resolution. You can’t perform that action at this time. You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or…

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Seven technologies to watch in 2022

The Telomere-to-Telomere Consortium is sequencing whole chromosomes.Credit: Adrian T. Sumner/SPL From gene editing to protein-structure determination to quantum computing, here are seven technologies that are likely to have an impact on science in the year ahead. Fully finished genomes Roughly one-tenth of the human genome remained uncharted when genomics researchers…

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bio-alignment from masyagin1998 – Github Help

Implementation of Needleman-Wunsch, Smith-Waterman, Hirschberg and affine bioinformatics algorithms for alighning biological sequences. Tech Algorithm is coded in pure C89 without any dependencies. Installation bio-alignment requires only C89-compatible compiler and make utility. $ cd bio-alignment $ make $ ./bin/bio-alignment –help $ ./bin/bio-alignment -i data/in.fasta -o out.fasta -s blosum62 -g -5…

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taxonomy – Assign multiple taxids to a sequence when constructing a local BLAST database

I recently had a script fail due to poor handling of BLAST output. The BLAST -outfmt staxids field usually returns a single taxid, but occasionally it returns two or more taxids separated by a semicolon, such as 556514;701533. Fixing the script to handle this should be fairly straightforward. But the…

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[lammps-users] Relative energy-well depths of Gay-Berne potential – LAMMPS Mailing List Mirror

Dear lammps user, My lammps version is 29 OCt 2020 . I am interested in simulating ellipsoid particles. However, for some reasons at the moment I am interested in setting all relative energy-well depths to be 1 , i.e., epsilon_x = epsilon_y=epsilon_z = 1 . With these settings, the matrix…

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[gmx-users] Is such hardware suitable for gromacs

Your mail looks like spam at first glance. Surely. They can be used to run Gromacs. In fact, Gromacs welcomes bothIntel and AMD’ modern CPU with SIMD capability. To build a small cluster, you also need some networking devices: a GBether switch and some good cables. Rest is software installation…

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Bioconductor – cleaver

    This package is for version 2.13 of Bioconductor; for the stable, up-to-date release version, see cleaver. Cleavage of polypeptide sequences Bioconductor version: 2.13 In-silico cleavage of polypeptide sequences. The cleavage rules are taken from: web.expasy.org/peptide_cutter/peptidecutter_enzymes.html Author: Sebastian Gibb [aut, cre] Maintainer: Sebastian Gibb <mail at sebastiangibb.de> Citation (from…

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AiThority.com Interview with Nicolas Gaude, CTO at Prevision.io

AiThority.com Interview with Nicolas Gaude, CTO at Prevision.io We store cookies on your computer to improve your experience and provide more personalized services, both on this website and on other sites. For more information about the cookies we use, see our Privacy Policy. We won’t track your information…

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Large DE LogFC range

Large DE LogFC range 1 @3d20f23f Last seen 1 hour ago Italy I’m working with DESeq2 to make a DE analysis between samples in two different conditions. During the analysis, I identified a batch effect due to the sequencing time modelled as a covariate in the design formula. From the…

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The Fabrication and Operation of a Continuous Flow, Micro-Electroporation System with Permeabilization Detection

Current therapeutic innovations, such as CAR-T cell therapy, are heavily reliant on viral-mediated gene delivery. Although efficient, this technique is accompanied by high manufacturing costs, which has brought about an interest in using alternative methods for gene delivery. Electroporation is an electro-physical, non-viral approach for the intracellular delivery of genes…

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Discovery Life Sciences hiring Bioinformatics Scientist in Huntsville, Alabama, United States

The Bioinformatics Scientist will take lab-generated data and create computational models that allow further manipulation and experimentation, perform incremental analysis required to process large amounts of data generated in a high-throughput Next Generation Sequencing (NGS) laboratory devoted to analysis of genomics data with a focus on long- and short-read sequencing…

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Senior Bioinformatics Software Developer – Bethesda

Medical Science & Computing, (MSC), a Dovel company, is seeking skilled Senior Bioinformatics Software Developers to join our team supporting our client, NCBI at the National Institutes of Health, (NIH) in Bethesda, MD. The National Center for Biotechnology Information (NCBI) is part of the National Library of Medicine (NLM) at…

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Newly discovered protein essential for CRISPR/Cas3 genome editing

24 January 2022 A hidden component of the CRISPR/Cas3 genome editing system, which is essential for it to work, has been discovered by scientists. The CRISPR/Cas3 family of genome editing systems is similar to other CRISPR families but can uniquely make larger and more accurate changes to DNA (see BioNews…

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Flow Cytometry Technique Enables High-Speed Cell Sorting | Research & Technology | Jan 2022

FRANKLIN LAKES, N.J., Jan. 24, 2022 — A study led by global medical technology company BD (Becton, Dickinson, and Co.), in collaboration with the European Molecular Biology Laboratory (EMBL), has demonstrated an innovation in flow cytometry that adds fluorescence imaging and image-based fluorescence to sort individual cells at exceptionally high…

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RNA-Seq, mutation , copy numnber

RNA-Seq, mutation , copy numnber 0 0 Entering edit mode 2 hours ago Rob &utrif; 80 Hi friends how do you interpret this plot? and how you see the role EGFR in cancer? this image from cBioportal RNA-Seq • 25 views ADD COMMENT • link 2 hours ago by Rob…

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Blood drive at Town Center

Posted By: Larry Felton Johnson January 24, 2022 Town Center at Cobb is hosting a blood drive. The details are in the press release reprinted below: Town Center at Cobb will host the American Red Cross for a blood driveon Wednesday, Feb. 2 and Thursday, Feb. 3 from noon-5 p.m….

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r – ggplot multiple legends into one box

I am trying to combine multiple partial legends (i.e. for two different features of one plot) legends into one box. My real-life data is a plot made with geom_sf() with fill colors for polygons and a specific border highlighted made with geom_sf()with a line. Since the line is only one…

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UC San Diego’s Jupyterhub Platform Aids Students With Data-Intensive Computing Needs | Computing

Jan. 24, 2022 — In basic UC San Diego trend, an overheard dialog at a campus espresso cart has changed into an interdisciplinary mission that’s making computing-intensive coursework extra thrilling whereas saving properly over $1 million {dollars} thus far. The effort offers UC San Diego graduate and undergraduate college students—and…

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r – Importing huge SAS database to Rstudio

I have a huge dataset in SAS (about 14 gb) that I am trying to import to R-studio for some analysis. However, nothing is working for importation. I tried ‘haven’, ‘sas7bdat’, ‘foreign’ but nothing. I converted the file to csv (became about 7gb) and tried read.csv, fread..but nothing again. R-studio…

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Surgical Techniques to Optimize Ovarian Reserve during Laparoscopic Cystectomy for Ovarian Endometrioma

This protocol presents techniques to laparoscopically excise ovarian endometrioma, to perform adhesiolysis with sparing electrosurgical application, and to employ intraoperative chromopertubation to assess for genital tract patency. This systematic approach will facilitate optimal endometriosis management, guide concomitant adnexal surgeries, and enhance post-surgical fertility outcomes. Surgical techniques to optimize ovarian reserve…

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Increasingly efficient production of human pluripotent stem cells

Reliable production of high-quality iPS cells enables their increasingly efficient utilization in biomedical applications. Credit: Ras Trokovic, University of Helsinki Researchers at the University of Helsinki have developed a new, faster and more reliable technique for reverting human cells to the stem cell state. Pluripotent stem cells are a key…

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Multi-organoid system to simulate human liver-islet axis in normal and type 2 diabetes

Schematic of hiPSCs derived multi-organoid-on-chip system to model human liver-pancreatic islet axis in vitro. Credit: Tao Tingting Type 2 diabetes (T2DM) is a systematic multi-organ metabolic disease, which is characterized by dynamic interplay among different organs. Pancreatic islet-liver axis is closely associated with normal glucose regulation and homeostasis maintenance. The…

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The website is currently not available

The website you want to visit is currently not available. This may be due to that the website is being developed, that maintenance is underway or that the website is closed due to some other reason. Domain owner, please see your contact address (email) or contact support@loopia.com for more information….

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