Tag: sample

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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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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Their DNA Hides a Warning, but They Don’t Want to Know What It Says

“I was like, wait a minute. Where is this information going? How will it be utilized?” she later asked. “I don’t know if there are any implications for life and health insurance for me or my family, but why risk it?” What should happen when researchers, while sequencing a participant’s…

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Which method works best for analysing ONE sample of scRNA-seq data?

Which method works best for analysing ONE sample of scRNA-seq data? 1 Hello, I currently have a single-cell RNA-seq (scRNA-seq) data of a single person (sample) and i want to perform DE analysis. However, when I run the DESeq() in the DESeq2 package, it shows an error about only one…

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ggplot2 – Create graphs by group using ggplot in R

I’m relatively new to using ggplot2 in R and have been struggling with this for awhile. I have figured out how to get everything from one data frame on a graph (that is pretty easy…), and how to write a loop function to get each observation (id in the example…

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Fixing abrupt changes/transitions in animated ggplot

I was wanting to make an animated ggplot of daily values for countries over the course of a year. I was able to do that thanks to some helpful questions/answers here. While the code below successfully makes a gif, the changes/transitions when countries move up or down/overtake one another is…

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hash – SHA256 digest disagrees in Python vs. mbedTLS (STM32)

Problem: I am trying to compute the SHA256 digests of single blocks (512 bit) on an STM32L552ZE-Q using mbedTLS. Unfortunately, the digest doesn’t agree with that of Python’s SHA256 implementation, even for a single block of all-zeros. Sample output: Python: f5a5fd42d16a20302798ef6ed309979b43003d2320d9f0e8ea9831a92759fb4b mbedTLS, data-type= 1 bit: B20941D6177356919BCDF1F716029D5F53C81932439D59B98F04A5EE0E192A25 mbedTLS, data-type != 1…

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Combining multiple 10x scRNAseq datasets

Hi everyone, Wondering if someone can provide me with some guidance. I have previously sequenced 4 skin cancers using 10X chemistries and I would like to combine them into one dataset. My research question is to look at cancer stem cell populations, so I will need sensitivity. I have done…

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Samtools flagstat confusing result of a merged bam file

Hi, I am a bioinformatics student and I am struggling with an issue, I had paired-end fastq files for one sample with some low-quality bases at the end and adapter contamination, so I went and I trimmed my reads with trimmomatic, it gave me 4 files that I used for…

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Senior Bioinformatics Scientist, Assay Development Analytics Job in California

About KariusKarius is a venture-backed life science startup focused on transforming the way infectious diseases are diagnosed. Combining Next-Generation Sequencing and proprietary data analysis, we can identify over 1,000 pathogens from a single blood sample with typical turnaround time in one business day. By unlocking the information present in…

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Writing ggplot custom geometry function

stat_accum <- function(mapping = NULL, data = NULL, geom = “point”, position = “stack”, …, show.legend = NA, inherit.aes = TRUE) { layer( data = data, mapping = mapping, stat = StatAccum, geom = geom, position = position, show.legend = show.legend, inherit.aes = inherit.aes, params = list( na.rm = na.rm,…

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NuProbe Technology Showcases Quantitative PCR for

Houston, January 18, 2022 (GLOBE NEWSWIRE) – NuProbe, a genomics and molecular diagnostics company that develops ultra-sensitive tests for precision cancer research, today released research demonstrating new technology to qualitatively and quantitatively detect multiple low-grade variants frequency in a quantitative PCR (qPCR reaction). The new allele-specific BDA technology (As-BDA) uses…

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Comethyl: a network-based methylome approach to investigate the multivariate nature of health and disease

This article was originally published here Brief Bioinform. 2022 Jan 17:bbab554. doi: 10.1093/bib/bbab554. Online ahead of print. ABSTRACT Health outcomes are frequently shaped by difficult to dissect inter-relationships between biological, behavioral, social and environmental factors. DNA methylation patterns reflect such multivariate intersections, providing a rich source of novel biomarkers and…

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rna seq – How does DESeq2 “collapseReplicates” work on read counts data?

Comparing read counts from an RNA-seq experiment for a couple select genes before and after using DESeq2’s collapseReplicates function yields interesting results: Before: Geneid foo1.1 foo1.2 foo2.1 foo2.2 foo3.1 foo3.2 bar1.1 bar1.2 bar2.1 bar2.2 bar3.1 bar3.2 baz1.1 baz1.2 baz2.1 baz2.2 baz3.1 baz3.2 WASH7P 6 5 0 2 7 3 1…

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Got `AttributeError` from `from_pymc3` of ArviZ

You are passing return_inferancedata=True to pm.sample(), which according to the PyMC3 documentation will return an InferenceData object rather than a MultiTrace object. return_inferencedatabool, default=False Whether to return the trace as an arviz.InferenceData (True) object or a MultiTrace (False) Defaults to False, but we’ll switch to True in an upcoming release….

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Functioning induced liver cells from skin tissue

Figure 1. Urea metabolism is impaired in patient-derived human-induced pluripotent stem cells (hiPSCs) differentiated into hepatocytes (hiPSC-Heps). (A) Scheme showing the urea cycle detoxifying ammonia (NH4+) into nontoxic urea in five consecutive urea cycle enzyme (UCE)–mediated reactions in mitochondria in hepatocytes. (B) Urea secretion in four control hiPSC-Hep lines (Ctrl_1-4)…

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A Clinical and Immunohistochemical Study

Diffuse large B cell lymphoma is the most common type of lymphoma in Egypt with an unfavorable prognosis. The tumor microenvironment is rich in immune response either T cells or macrophages. The current study is aimed at testing CD4, CD8, CD68, and MMP9 immunohistochemistry of DLBCL activities with the prognosis…

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Failure to detect mutations in U2AF1 due to changes in the GRCh38 reference sequence

Materials and Methods Genomic data was collected as part of the MDS National History Study or The Cancer Genome Atlas project and consented appropriately under those protocols 8 Sekeres M.A. Gore S.D. Stablein D.M. DiFronzo N. Abel G.A. DeZern A.E. Troy J.D. Rollison D.E. Thomas J.W. Waclawiw M.A. Liu J.J….

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gromacs 2021.5 – Download, Browsing & More

gromacs 2021.5 – Download, Browsing & More | Fossies Archive “Fossies” – the Fresh Open Source Software Archive Contents of gromacs-2021.5.tar.gz (14 Jan 16:58, 38023772 Bytes) About: GROMACS performs molecular dynamics, i.e. simulates the Newtonian equations of motion for systems with hundreds to millions of particles (designed for biochemical molecules…

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Process Development for the Production and Purification of Adeno-Associated Virus (AAV)2 Vector using Baculovirus-Insect Cell Culture System

In this protocol, AAV2 vector is produced by co-culturing Spodoptera frugiperda (Sf9) insect cells with baculovirus (BV)-AAV2-green fluorescent protein (GFP) or therapeutic gene and BV-AAV2-rep-cap infected Sf9 cells in suspension culture. AAV particles are released from the cells using detergent, clarified, purified by affinity column chromatography, and concentrated by tangential…

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An intronic transposon insertion associates with a trans-species color polymorphism in Midas cichlid fishes

Conflicting results suggest a missing variant In order to narrow down candidates for the causal genetic variant, we performed genome-wide association mapping separately in individual lake populations (previously, association mapping was only performed across the whole species flock5). Interestingly, despite clear association peaks in the crater lakes (Fig. 1a, b), the…

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GWAS and ExWAS of blood Mitochondrial DNA copy number identifies 71 loci and highlights a potential causal role in dementia

Background: Mitochondrial DNA copy number (mtDNA-CN) is an accessible blood-based measurement believed to capture underlying mitochondrial function. The specific biological processes underpinning its regulation, and whether those processes are causative for disease, is an area of active investigation. Methods: We developed a novel method for array-based mtDNA-CN estimation suitable for…

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python xarray – PyMC3/Arviz: CDF value from trace

I have a sample from PyMC3 and I’m trying to get a cumulative probability from it, e.g. P(X < 0). I currently use this: trace = pymc3.sample(return_inferencedata=True) prob_x_lt_zero = (trace.posterior.X < 0).sum() / trace.posterior.X.size Is there a better way to do this, either with some helper function from Arviz or…

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downloading RNA seq data

downloading RNA seq data 0 Hi friends I am using the following code to get the data from TCGA. I want to have only one allocate of each person then I will have unique patients ID. Is there any line of code that I should add to this to get…

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Genetic diversity and selection in Puerto Rican horses

Horses have been considered one of our most prized possessions, used for travel, work, food, and pleasure for at least five and a half millennia17,18,19,20. Nevertheless, the ancestry of various horse breeds and their characteristic traits remains unclear21. In this paper, we describe the patterns and the origins of genetic…

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A tiny, pedagogical neural network library with a pytorch-like API

A tiny, pedagogical implementation of a neural network library with a pytorch-like API. The primary use of this library is for education. Use the actual pytorch for more serious deep learning business. The implementation is complete with tensor-valued autodiff (~100 lines) and a neural network API built off of it…

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Predicting sepsis severity at first clinical presentation: The role of endotypes and mechanistic signatures

Summary Background Inter-individual variability during sepsis limits appropriate triage of patients. Identifying, at first clinical presentation, gene expression signatures that predict subsequent severity will allow clinicians to identify the most at-risk groups of patients and enable appropriate antibiotic use. Methods Blood RNA-Seq and clinical data were collected from 348 patients…

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CNV calling for wgs of S. pombe

CNV calling for wgs of S. pombe 0 Hi, Can anyone help to do CNV calling of WGS data of S.Pombe? I have 1 normal sample and 3 samples treated with a suppressor. I used Control-FREEC but did not get the right result. Can anyone help, how to do germline…

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Estimating individual mtDNA haplotypes in mixed DNA samples by combining MinION and MiSeq

doi: 10.1007/s00414-021-02763-0. Online ahead of print. Affiliations Expand Affiliations 1 Department of Forensic Medicine, Juntendo University School of Medicine, 2-1-1, Hongo, Bunkyo-Ku, Tokyo, 113-8421, Japan. hnakani@juntendo.ac.jp. 2 Department of Forensic Medicine, Saitama Medical University, 38 Morohongo, Moroyama, Saitama, 350-0495, Japan. 3 Department of Forensic Medicine, Juntendo University School of Medicine,…

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Genome research: Finding the invisible

Fig. 1: Ladder-seq uses mRNA length information to aid transcriptome reconstruction. Credit: DOI: 10.1038/s41587-021-01136-7 LMU researchers have developed a method to extract more information from sequencing data. This will afford deeper insights into biology. Higher organisms store their genetic material in the nuclei of cells as deoxyribonucleic acid (DNA). In…

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combine OTU and tax table and replace actual sequences with OTU ids (Phyloseq/dada2)

This is to the part of the question “replace actual sequences with OTU ids (Phyloseq/dada2)?” I contacted the phyloseq/dada2 developers and based on Susan Holmes’ reply (github.com/joey711/phyloseq/issues/1030) I came up with this piece of code to replace the amplicon sequences with a numbered OTU header. Further discussion can be found…

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Microtubule Plus-End Dynamics Visualization in Huntington’s Disease Model based on Human Primary Skin Fibroblasts

This protocol is dedicated to the microtubule plus-end visualization by EB3 protein transfection to study their dynamic properties in primary cell culture. The protocol was implemented on human primary skin fibroblasts obtained from Huntington’s disease patients. The Huntington’s disease, HD, is an incurable, neurodegenerative pathology caused by a mutation in…

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EPCAM – PrimePCR Assay and Template | Life Science

Control assays and synthetic DNA templates were designed to facilitate the assessment of the key experimental factors impacting your real-time PCR results. DNA Contamination Control AssayUse the PrimePCR DNA contamination control assay to determine if genomic DNA (gDNA) is present in a sample at a level that may affect PCR…

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Description, Programming Languages, Similar Projects of Gpt 2 Pytorch

GPT2-Pytorch with Text-Generator Better Language Models and Their Implications Our model, called GPT-2 (a successor to GPT), was trained simply to predict the next word in 40GB of Internet text. Due to our concerns about malicious applications of the technology, we are not releasing the trained model. As an experiment…

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Running Jobs on Titan

Running Jobs on Titan Table of Contents Titan’s Job Scheduler – SLURM Documentation Translating to SLURM commands from other workload managers Basic SLURM Commands squeue sinfo scontrol sbatch scancel Titan’s Environment Module System – LMOD Listing all available modules on Titan Loading a module into your environment Listing all modules…

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Radboud University Medical Center Increases HiFi Sequencing Capacity with PacBio’s Sequel IIe

Added whole genome sequencing capacity enables the SOLVE-RD research program to significantly increase sample throughput MENLO PARK, Calif., Jan. 07, 2022 (GLOBE NEWSWIRE) — PacBio (Nasdaq: PACB), a leading developer of high-quality, highly accurate sequencing platforms, today announced Radboud University Medical Center (Radboudumc) in Nijmegen, the Netherlands will increase their…

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Ggplot: heatmap based on two vectors ( R, Ggplot2 )

Problem : ( Scroll to solution ) I am trying to plot data as a heat map in ggplot2. I understand that you’d normally have to have x, y, and z coordinated to plot x against y and then color by z. I have found plenty of heat map examples…

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Identification of missed viruses by metagenomic sequencing of clinical respiratory samples from Kenya

The detection of viruses As shown in Table 1, viral NGS identified at least one syndrome-associated mammalian virus in 35 of 95 Kilifi County Hospital (KCH) inpatient samples (36.8%) and 23 of 95 household cohort (study investigating Who-Acquires-Infection-From-Whom, WAIFW) samples (24.2%), leading to an overall 30.5% “missed virus detection rate”….

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Comparison of CNV analysis methods: Array CGH vs NGS

Rare genetic disorders are caused by variants in major functional genes. Most are SNV or INDEL variants, but SVs, such as CNVs or chromosomal variants, can also be the cause. Recently, a large-scale study has also been published showing that CNVs were identified in 11-12% more infants and children with…

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Protocols

normalization data transformation protocol 10X Genomics Visium sequencing data were aligned and quantified using the Space Ranger Software Suite (version 1.0.0, 10x Genomics Inc) using the GRCh38 human reference genome (official Cell Ranger reference, version 3.0.0). Spots were manually aligned to the paired H&E images by 10x Genomics. nucleic acid…

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python – Creating batches of sequences for pytorch LSTM

I’m currently working on a LSTM Autoencoder using pytorch. I have a big amount of samples. Each sample contains 120 features. For now, I’m creating sequences of length 1, batch_size is equal to 1 and everything is working fine. I first convert my data array to a list and then…

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The Genetic Architecture of Sleep Health Scores in the UK

Introduction Sleep is a complex neurological and physiological state. It is defined as a natural and reversible state of reduced responsiveness to external stimuli and relative inactivity, accompanied by a loss of consciousness.1 Sleep disorders can be classified as seven major categories: insomnia disorders, sleep-related breathing disorders, central disorders of…

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Bioinformation Analysis Reveals IFIT1 as Potential Biomarkers in Centr

Introduction Tuberculosis (TB) is considered to be one of the top ten causes of death in the world, about a quarter of the world’s population is infected with M. tuberculosis.1 The World Health Organization (WHO) divides tuberculosis into pulmonary tuberculosis (PTB) and extra-pulmonary tuberculosis (EPTB). Although breakthroughs have been made…

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Variant calls of published already assembled genomes

Variant calls of published already assembled genomes 0 I have a set of short read sequencing for the 172 KB Epstein-barr virus genome. We successfully called our variants using GATK to a reference genome. A publication linked below from a different population compared variants (also from short read sequencing) to…

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python – Missing input files after defining them in function

I am trying to do QC on RNAseq data that is tarballed. I am using Snakemake as a workflow manager and am aware that Snakemake does not like one-to-many rules. I defining a checkpoint would fix the problem but when I run the script I get this this error message…

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metagenome low alignment rate

metagenome low alignment rate 1 I have 20 metagenome samples which need to be analyzed. I started with one sample for the time being with the below tools/pipelines. After assembling first sample I mapped its reads back to contigs but the alignment rate is pretty low, What could be the…

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Digital Droplet PCR Method for the Quantification of AAV Transduction Efficiency in Murine Retina

This protocol presents how to quantify AAV transduction efficiency in mouse retina using digital droplet PCR (dd-PCR) together with small scale AAV production, intravitreal injection, retinal imaging, and retinal genomic DNA isolation. In this video, we will show how to quantify AAV transduction in mouse retina using digital droplet PCR…

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why my VCF file generated with manta is missing genotype information

Hi, everybody, I am pretty new to coding and bioinformatics. I am using Manta as a tool to infer somatic structural variants (SVs) from a paired tumor/normal sample call. However, my somaticSV.vcf.gz file does not contain information about the genotype nor the genotype quality (there is a dot instead of…

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[FIXED] Information Gain calculation with Scikit-learn ~ PythonFixing

I am using Scikit-learn for text classification. I want to calculate the Information Gain for each attribute with respect to a class in a (sparse) document-term matrix. The Information Gain is defined as H(Class) – H(Class | Attribute), where H is the entropy. Using weka, this can be accomplished with…

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Do VQSR for HaplotypeCaller calls – Sarek

Expected Behavior Filter the calls from HaplotypeCaller with Variant Quality Score Recalibration according to GATK best practise (Tools VariantRecalibrator, ApplyRecalibration, see gatkforums.broadinstitute.org/gatk/discussion/39/variant-quality-score-recalibration-vqsr or a more recent version) Current Behavior Variant quality score recalibration currently not included. Asked Jan 26 ’18 at 08:25 malinlarsson 1 Answer: Keep in mind, that you’d…

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Mendelian randomization analyses support causal relationships between blood metabolites and the gut microbiome

1. Wang, J. & Jia, H. Metagenome-wide association studies: fine-mining the microbiome. Nat. Rev. Microbiol. 14, 508–522 (2016). CAS  PubMed  Google Scholar  2. Moschen, A. R. et al. Lipocalin 2 protects from inflammation and tumorigenesis associated with gut microbiota alterations. Cell Host Microbe 19, 455–469 (2016). CAS  PubMed  Google Scholar …

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Toll-like receptor 2/4 in Chinese patients with sepsis

Introduction Sepsis is a life-threatening organ dysfunction that results from an exaggerated host immune response to disseminate infection.1 Despite improvements in treatment strategies, sepsis remains a leading cause of death in critically ill patients worldwide.2 Low platelet number, known as thrombocytopenia, is common in infectious diseases (also sometimes referred to…

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RedChIP identifies noncoding RNAs associated with genomic sites occupied by Polycomb and CTCF proteins

Abstract Nuclear noncoding RNAs (ncRNAs) are key regulators of gene expression and chromatin organization. The progress in studying nuclear ncRNAs depends on the ability to identify the genome-wide spectrum of contacts of ncRNAs with chromatin. To address this question, a panel of RNA–DNA proximity ligation techniques has been developed. However,…

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Change size of label annotations in a ggplot

I am trying to change text label sizes inside my plot (not the axes, rather the label annotations) I am working with a phyloseq object but I don’t think that matters. Here is the code and the output. Any suggestions? plot_ordination(prokaryote_ra, ordBC, color = “Stage”, label=”SampleID”) + ggtitle(“PCoA: Bray-Curtis”) graph…

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Stan vs PyMC3 vs Bean Machine

I have been a light user of Stan and RStan for some time and while there are a lot of things I really like about the language (such as the awesome community you can turn to for support and ShinyStan for inspecting Stan output) there are also a few things…

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swagger – How to integrate openapi specifications from different APIs?

This bounty has ended. Answers to this question are eligible for a +50 reputation bounty. Bounty grace period ends in 15 hours. cah1r wants to draw more attention to this question: Needing a good solution on how to solve this problem I wanted to ask if…

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Tensorflow realizes kaggle cat and dog recognition (network design step by step)

This article is tensorflow edition ,pytorch The version will be given in the next blog Friendship tips : Try GPU, Blogger CPU Run on one VGG16 It took 1.5h… Tensorflow Realization kaggle Cat and dog recognition Online disk download link :pan.baidu.com/s/1kqfkr2X7mMkuFXb6C3KgTgExtraction code :xzyh kaggle Download it on the official website…

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Using DESeq2 to analyse multi-variate design resulting in testing the wrong parameter

Enter the body of text here Hi, I am analysing a RNA Seq dataset coming from 3 independent cell isolates (isolate1, isolate2, isolate3), each given 3 different treatments (control, drug1, drug2). We are testing drug 1 against control in the first instance: We also observed that there is some variation…

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Classification Problem using Pymc3 – Questions

Hello everyone!I am trying to figure out how to do a classification task using the pymc3 library. I have read an amazing article on how to achieve that but the article caters to the classification problem having only two features (target variable included). In the article, the author samples one…

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Sr. Manager of Manufacturing – Resumetojobs.com

NuProbe USA is seeking an experienced Sr. Manager, In-Vitro Diagnostics Operations who will be responsible for all aspects of manufacturing, including design transfer of newly developed products from research & development. The successful candidate will control production planning, scheduling and forecasting. The candidate will lead continuous improvements in manufacturing as…

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Bioconductor – ChIPQC

    This package is for version 3.1 of Bioconductor; for the stable, up-to-date release version, see ChIPQC. Quality metrics for ChIPseq data Bioconductor version: 3.1 Quality metrics for ChIPseq data Author: Tom Carroll, Wei Liu, Ines de Santiago, Rory Stark Maintainer: Tom Carroll <tc.infomatics at gmail.com>, Rory Stark <rory.stark…

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DNA-Tethered RNA Polymerase for Programmable In vitro Transcription and Molecular Computation

We describe the engineering of a novel DNA-tethered T7 RNA polymerase to regulate in vitro transcription reactions. We discuss the steps for protein synthesis and characterization, validate proof-of-concept transcriptional regulation, and discuss its applications in molecular computing, diagnostics, and molecular information processing. We propose a method for regulating polymerase activity…

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RNA-seq analysis cloud server

RNA-seq analysis cloud server 1 Hi all, I have some RNA-seq of mice (around 200GB) and I want to perform a RNA-seq analysis (including QC, mapping, quantification, differential expression analysis). But I don’t know how to choose a server. Could anyone can tell me to process such a dataset, how…

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What is SNP array testing?

What is SNP array testing? The SNP array test looks for changes in specific areas of a person’s chromosomes, such as gains (duplications) or losses (deletions). These gains or losses result in extra or missing copies of genetic material. How does SNP array work? SNP array is a type of…

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how to align paired and unpaired fastq files of a sample using STAR?

how to align paired and unpaired fastq files of a sample using STAR? 2 Hi all I’m new to using STAR aligner. I have PE sequencing fastq files which have forward and reverse pairs and forward and reverse unpairs reads (4 files). In the manual of this tool, it seems…

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Characterization of Blood- Based Molecular Profiling in Pancreatic Adenocarcinoma

Introduction Most cases of pancreatic adenocarcinoma (PDAC) are diagnosed in the metastatic or locally advanced stage. It is the fourth leading cause of cancer death in the United States,1,2 with a 5-year overall survival (OS) around 10% in this country2 despite years of research and therapeutic development. For those patients…

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sequence alignment – Help with MinION sequencing data species identification

Hi I’m new to bioinformatics and have just completed my first run on the MinION (long read sequencing Oxford Nanopore Technologies). I was hoping someone could direct me towards R packages, workflow, tutorials or guides that will help me identify species that are present in my sample mainly for fungi…

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Omics advanced 07 | transcriptome mRNA | miRNA | lncrna

A brief introduction mRNA,miRNA,lncRNA And circRNA Principle of genome sequencing 、 Routine analysis of Shengxin . Catalog Introduction to transcriptome sequencing mRNA|miRNA|lncRNA|circRNA Introduction to analysis mRNA Group miRNA Group lncRNA Group circRNA Group mRNA|miRNA|lncRNA|circRNA Correlation analysis Reference Introduction to transcriptome sequencing Transcriptome (Transcriptome) Is a single or group of cells…

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CRISPR/Cas12a Powered DNA Framework-Supported Electrochemical Biosensing Platform for Ultrasensitive Nucleic Acid Analysis

Nucleic acid analysis using ultrasensitive and simple methods is critically important for the early-stage diagnosis and treatment of diseases. The CRISPR/Cas proteins, guided by a single-stranded RNA have shown incredible capability for sequence-specific targeting and detection. Herein, in order to improve and expand the application of CRISPR/Cas technology to the…

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Scientists Develop $10 Per Genome Approach for Large-Scale Bacterial Sequencing

A worldwide consortium of scientists, led by the Earlham Institute and the University of Liverpool, has developed an efficient, inexpensive approach to large-scale bacterial genome sequencing that could equip researchers in low- and middle-income countries (LMICs) with cheap and accessible methods for sequencing large collections of bacterial pathogens—at a cost…

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Can an enzyme have multiple EC numbers?

Can an enzyme have multiple EC numbers? 2 Can an enzyme have multiple EC numbers? I have used run_dbcan and taken the hotpep output to identify all carbohydrate active enzymes in my metagenomic sample. I have more unique EC numbers than enzymes in the output when those EC numbers are…

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python – How to implement Bayesian Inference correctly with pymc3?

I have been working with pymc3 for a while and I was observing the several tutorials with examples. However, I am not sure if I am approaching the Bayesian InFerence method correctly. Find below my approach: from pymc3.distributions import Interpolated import numpy as np # import warnings # import sys…

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Automation Hub Open API Power Query Data Parsing

Parsing the data from the Automation Hub API can sometimes prove to be challenging, especially if you are consolidating a very complex report. In this page, we are presenting a couple of tips and tricks that can be used to improve the overall data parsing process. The page contains: The…

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Which is @RG read group in the head of bam files?

Which is @RG read group in the head of bam files? 1 I am not sure which part of the head of bam files is @RG read group. I am curious why all of my samples have the sameA01494:44:H53Y7DMXY:1 part? Are they read groups? samtools view -S Sample_7R-MDV_IGO_09530_H_1_dedup.bam | head…

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tensorflow – Why is the Accuracy Different in my PC From Kaggle When Using the Same Code

I am writing a watermark detection algorithm, and I’ve tried a code from Kaggle which fine-tunes a ResNet, but when I run the same code in Jupyter notebook, I get 50% accuracy when the sample code in Kaggle has around 97% accuracy. I don’t have a GPU installed on my…

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vRhyme enables binning of viral genomes from metagenomes

Abstract Genome binning has been essential for characterization of bacteria, archaea, and even eukaryotes from metagenomes. Yet, no approach exists for viruses. We developed vRhyme, a fast and precise software for construction of viral metagenome-assembled genomes (vMAGs). vRhyme utilizes single- or multi-sample coverage effect size comparisons between scaffolds and employs…

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faq – What should I do when my neural network doesn’t learn?

There’s a saying among writers that “All writing is re-writing” — that is, the greater part of writing is revising. For programmers (or at least data scientists) the expression could be re-phrased as “All coding is debugging.” Any time you’re writing code, you need to verify that it works as…

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ddPCR allows 16S rRNA gene amplicon sequencing of very small DNA amounts from low-biomass samples | BMC Microbiology

1. Lane DJ, Pace B, Olsen GJ, Stahl DA, Sogin ML, Pace NR. Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses. Proc Natl Acad Sci U S A. 1985;82(20):6955–9. PubMed  PubMed Central  CAS  Google Scholar  2. Vos M, Quince C, Pijl AS, de Hollander M, Kowalchuk GA. A…

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10q26 FGFR2 Break Apart FISH Probe Kit

1 0q26 FGFR2 Break Apart FISH Probe Kit For Research Use Only Not for Use in Diagnostic Procedures 0q26 FGFR2 Break Apart FISH Probe Kit 09N /R2 Key to Symbols Used 09N /R2 Reference Number Lot Number Global Trade Item Number Centromere D0S294 0q26. Region FGFR2 5 ATE SHGC-529 Telomere…

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[100% Off UDEMY Coupon] – Molecular Dynamic Simulation on Gromacs Software –

Using this 100% off UDEMY Free Coupon Code, you can able to enroll the course: Molecular Dynamic Simulation on Gromacs Software for Free on Udemy.This is a UDEMY Free Promo Code this is totally Free for a Limited Time so enroll soon as possible Molecular Dynamics Simulations ,Gromacs Software ,MD…

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Science snapshots from Berkeley Lab

image: 3D image of melanin in a zebrafish sample captured by micro-computed tomography. view more  Credit: Spencer R. Katz and Daniel J. Vanselow, Penn State College of Medicine) Adapted from a UC Berkeley news release To date, CRISPR enzymes have been used to edit the genomes of one type of cell…

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Adrenal aldosterone-producing adenoma | IJGM

Background Primary hyperaldosteronism (PA) is characterized by spontaneous secretion of excessive aldosterone and inhibition of plasma renin activity.1 The pathogenesis of adrenal aldosterone-producing adenoma (APA) involves the abnormal proliferation of adrenal cortex cells and the excessive secretion of aldosterone, accounting for nearly 30% of PA. Excessive secretion of aldosterone can…

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RStudio AI Weblog: Picture segmentation with U-Internet

Certain, it’s good when I’ve an image of some object, and a neural community can inform me what sort of object that’s. Extra realistically, there is perhaps a number of salient objects in that image, and it tells me what they’re, and the place they’re. The latter process (referred to…

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Systems biology analysis of human genomes points to key pathways conferring spina bifida risk

Significance Genetic investigations of most structural birth defects, including spina bifida (SB), congenital heart disease, and craniofacial anomalies, have been underpowered for genome-wide association studies because of their rarity, genetic heterogeneity, incomplete penetrance, and environmental influences. Our systems biology strategy to investigate SB predisposition controls for population stratification and avoids…

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Integrating Bulk RNA-seq data with Single cell RNA seq data

Integrating Bulk RNA-seq data with Single cell RNA seq data 0 Hello all, recently, I had been trying to integrate bulk RNAseq data into single-cell data where I treat each sample in my bulk RNAseq data as a single cell and integrate it into the single-cell data based on the…

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Benchmarking the NVIDIA Clara Parabricks germline pipeline on AWS

This blog post was contributed by Ankit Sethia, PhD, and Timothy Harkins, PhD, at NVIDIA Parabricks, and Olivia Choudhury, PhD,  Sujaya Srinivasan, and Aniket Deshpande at AWS. This blog provides an overview of NVIDIA’s Clara Parabricks along with a guide on how to use Parabricks within the AWS Marketplace. It…

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Index of /~psgendb/doc/bioLegato/blreads

Name Last modified Size Description Parent Directory   –   SOAPdenovo2.hints.html 2019-05-04 15:52 3.9K   Trimmomatic.hints.html 2019-05-20 13:32 6.3K   Trinity.hints.html 2019-04-23 11:39 2.4K   adaptercheck.hints.html 2021-05-13 12:27 8.0K   adaptercheck.html 2021-05-12 17:45 4.9K   adaptercheck_output.png 2021-05-12 17:17 51K   fastq_pair.hints.html 2019-04-05 13:16 3.4K   gffcompare.hints.html 2018-07-18 14:05 3.2K  …

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Very important pharmacogene variants in the Blang population

Introduction The use of drugs should be different among diverse ethnic groups because of differences in ethnicity, age, sex, environmental factors and genetic factors. If these differences are ignored, then drug sensitivity, metabolic rate, and adverse reactions are affected, which influences the curative effect of drugs and aggravates the illness…

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samtools mpileup error – 1 samples in 1 input files

samtools mpileup error – 1 samples in 1 input files 0 Hi All, I have relatively new to bioinformatics and have encountered an issue when trying to generate an mpileup file with samtools. I have entered the following command samtools mpileup -f /home/path_to_reference/nCoV_Jan31.fa.fasta sorted_sample1.sam > sample.mpileup The message returned is…

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bcftools merge of over 9000+ vcf files

Hi all, I have around 9000+ vcf files that I’m trying to merge using bcftools merge. They are all located in their own folder so essentially I have a folder containing 9000+ separate folders, each containing one vcf.gz file. I have tried out the following code via this tutorial bcftools…

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r – ggplot2 Set geom_point Size according to a Factor

I am trying to set the size of geom_point according to a factor. I know it is not advised, but my data is extremely unbalanced (the minimum value is 6 while the maximum is larger than 10,000). I am trying to make the size of the points reflect the total…

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Import problem: Not a(n) QIIME1DemuxFormat file – Technical Support

Hi @emiliomastriani, Did you download the sequences form sra?This previous question may give you some help: Hi there, I am familiar with QIIME1 but relatively new with QIIME2. I have gotten my raw file in the past from a facility in the CASAVA pair ended demultiplexed format and I had…

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Omicron Threat: Kerala Reports First Case of New Variant, India’s Tally Touches 38 | Key Points

Thiruvananthapuram: Kerala on Sunday reported its first case of COVID-19 Omicron variant. The new variant was detected in a man who flew in to Kochi from the United Kingdom, state Health Minister Veena George said. “High-risk passengers who were seated next to him have been informed. There is no need…

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laboratory jobs in germany

We wish you a good luck and have a prosperous career. Working at Labcorp | Jobs and Careers at Labcorp 15 GNeuS Postdoc Positions in Neutron Science of 24 Months Each (Full-time Job) FZJ – Forschungszentrum Jülich. What other similar jobs are there to Laboratory jobs in Germany? Clinical Laboratory…

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Roche launches AVENIO Edge System to simplify and automate next-generation sequencing sample preparation, reduce human error and advance precision medicine

Next-generation sequencing (NGS) can better understand the genetic mechanisms associated with specific diseases and help promote personalise health care Preparing DNA for sequencing library is complicated and prone to human error, which can interfere with accurate sequencing results The new AVENIO Edge system is a fully automated solution for sample…

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Roche launches the AVENIO Edge System to simplify and

Next-generation sequencing (NGS) enables a better understanding of genetic mechanisms linked to specific diseases and is helping drive personalised healthcare Preparing DNA for sequencing libraries is complex and prone to human error, which can interfere with accurate sequencing results The new AVENIO Edge System is a fully-automated solution for the…

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A pandemic-scale phylogenetic analysis tool

Phylogenetics is an analytical tool that quickly analyzes genomic data to provide invaluable insights into the evolution and spread of a pathogen, thereby allowing public health officials and governments to respond to it in a timely fashion. During the coronavirus disease 2019 (COVID-19) pandemic, phylogenetics, like many other pre-pandemic tools,…

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Real-World Study of Tisagenlecleucel in R/R B-Cell Non-Hodgkin Lymphomas Shows Efficacy, Safety

Real-world data on tisagenlecleucel in patients with relapsed/refractory B-cell lymphoma was consistent with the phase 2 JULIET trial, demonstrating favorable efficacy and safety. Real-world data on the use of tisagenlecleucel (Kymriah) showed greater efficacy and a favorable safety profile, according to updated findings from a study of the Center for…

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Addition of Ibrutinib to R-Mini-Chop for Newly Diagnosed DLBCL Shows Promise in an Elderly Population

Adding ibrutinib (Imbruvica) to rituximab (Rituxan) plus mini-CHOP (cyclophosphamide, doxorubicin, vincristine, and prednisone [R-mini-CHOP]) improved progression-free survival (PFS), quality of life (QOL), and function in elderly patients with diffuse large B-cell lymphoma (DLBCL), according to the primary analysis of the Australasian Leukaemia & Lymphoma Group NHL29 Study presented the 63rd…

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16S rRNA gene amplicon sequence data from sunflower endosphere bacterial community

doi.org/10.1016/j.dib.2021.107636Get rights and content Abstract Insights into plant endosphere bacterial diversity and exploration of their bioincentives in the formulation of biofertilizers promise to avert ecological disturbances. Here, we presented the sequence dataset of the endophytic bacterial community from the roots and stems of sunflower obtained from farmlands in Itsoseng and…

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