Categories
Tag: PCA
Mitochondrial DNA damage triggers spread of Parkinson’s disease-like pathology
Lack of IFNβ/IFNAR signaling causes mtDNA oxidization and mutation in a hotspot in complex I respiratory chain subunits mimicking PD brain pathology We analyzed transcriptomic datasets from sPD patients [28] to identify molecular pathways related to the disease pathology. Dysregulated oxidative phosphorylation (OXPHOS) emerged as the top-ranked pathway in sPDD, patients with…
Filter, Plot, and Explore with Seurat in RStudio
First thing’s first, we need to load the packages we will be using. In order to use any functions of a package, we must first call the library of that package. In your console (likely in the lower left corner of your RStudio window), run the following lines of code…
IJMS | Free Full-Text | The Effect of Gene Editing by CRISPR-Cas9 of miR-21 and the Indirect Target MMP9 in Metastatic Prostate Cancer
Gene Editing with CRISPR/Cas9 We inserted sgRNAs into the PX-330 plasmid and sequenced them to validate the construct (Figure 1A). Before transfecting the plasmids into PC-3 and DU145 cell lines, we performed a puromycin dose–response curve and observed that 150 µg/mL for 10 days was the ideal concentration and time…
This dataset is from the US Arrests Kaggle challenge
This dataset is from the US Arrests Kaggle challenge (link). A description of the data is given as: “This data set contains statistics, in arrests per 100,000 residents, for assault, murder, and rape in each of the 50 US states in 1973. Also given is the percent of the population…
Solved Plot the data in the first two principal variables
Transcribed image text: Plot the data in the first two principal variables plt.figure() plt.plot (pdata [:,0],pdata[:,1], “o”, alpha=0.1) plt. show() plt.figure() plt.plot (pdata [:,0], pdata [:,1], “o”, alpha=0.1) plt.show() Your final task in this topic will be to generate random data (an artificial sample) and apply…
Subclustering of intergated cells from scRNA-seq data
Subclustering of intergated cells from scRNA-seq data 1 I used SCTnormalization and Seurat integration to integrate 3 scRNA-seq datasets. After manual annotation using RNA assay, I have one particular cluster of cells with overexpressed different T cells markers. So, to find heterogeneity of T cells I subclustered that particular cluster:…
Number of accessible regions included by DESeq2 to generate the PCA plot with the nf-core ATACseq pipeline ?
Number of accessible regions included by DESeq2 to generate the PCA plot with the nf-core ATACseq pipeline ? 2 Hello everyone, I launched an analysis of some ATACseq data across different conditions. I launch the cf-core ATACseq pipeline v 1.2.1: nf-co.re/atacseq/2.1.2/docs/output In the output I have a PCA generated by…
comparision of umap single cell
comparision of umap single cell 0 Dear Fellow, I’m currently learning to analyze single cell RNAseq and compare my result with the analysis by bioinformatician. We analyzed the same data of 9 individual patients from 10X. His UMAP looks nice, but mine looks a bit messy and aggregated together. I…
Genes Linked to Aggressive Prostate Cancer
Researchers say they have identified genes that should be considered for gene panel testing in prostate cancer. The researchers found evidence to suggest that variants in BRCA2, ATM, NBN, MSH2, XRCC2, and MRE11A are associated with aggressive prostate cancer. These findings were published in JAMA Oncology. For this study, researchers…
AB99. Association of mitochondrial DNA copy number in peripheral blood leukocytes with risk and prognosis of prostate – Zhou
Department of Urology, the Third Xiangya Hospital of Central South University, Changsha 410013, China Objective: To investigate the relationship between mitochondrial DNA (mtDNA) copy number in peripheral blood leukocytes (PBLs) and the risk and the prognosis of prostate cancer (PCa). Methods: In a case-control study of 196 PCa patients and…
Bioconductor – scPCA
DOI: 10.18129/B9.bioc.scPCA Sparse Contrastive Principal Component Analysis Bioconductor version: Release (3.17) A toolbox for sparse contrastive principal component analysis (scPCA) of high-dimensional biological data. scPCA combines the stability and interpretability of sparse PCA with contrastive PCA’s ability to disentangle biological signal from unwanted variation through the use of control…
r – How to adjust labels of loadings in ggplot?
I can’t get the labels to go at the end of the arrows instead of the base: here is the exact code I used: ggplot <- ggplot(data=sep_total_raw_data, aes(x=pc1t, y=pc2t))+geom_point(alpha=0.8, size=1,aes(colour=Data_Type, shape=Data_Type))+xlab(“PC1 (53.83%)”)+ylab(“PC2 (26.3%)”)+guides(colour=guide_legend(title=”Data_Type”))+geom_mark_hull(concavity=5, expand=0, radius=0, aes(fill=Data_Type))+theme(panel.grid = element_blank(), panel.border = element_rect(fill = “transparent”))+geom_text(aes(label=Code, fontface=”bold”, colour=Data_Type)) ggplot + geom_segment(data = PCA_loadings,…
r – ggplot combine layer and keep legend group
I want to create a PCA plot with different legend title data: dataWithLang <- data.frame( PC1 = rnorm(100), PC2 = rnorm(100), PopLang = sample(c(“A”, “B”, “C”), 100, replace = TRUE), Label = sample(1:3, 100, replace = TRUE) ) dataWithLocang <- data.frame( PC1 = rnorm(50), PC2 = rnorm(50), PopLoc = sample(c(“X”,…
Dingoes found to have more harmful mutations than most inbred dog breeds
(a) The scatter graph showing the results from the principal component analysis (PCA) using the whole genomes of dogs, dingoes, and wolves. (b) The proportion of genetic admixture in each canine genome is shown. This analysis was performed assuming four ancestries for canines (K = 4). Credit: Ecology and Evolution (2023). DOI:…
Total Flavonoids of Rhizoma Drynariae Treat Osteoarthritis
Introduction Osteoarthritis (OA) is a common degenerative joint disease characterized by chronic pain and ambulation limitation, affecting about 250 million people worldwide.1 With increased aging population, the OA incidence rapidly increases and OA has become a major cause of disability.2,3 The morbidity of OA is closely related to articular cartilage,…
Adding a control sample to bulk RNA-seq
Adding a control sample to bulk RNA-seq 0 Hello Biostars, I have a control with another technical replicate then I try to down load a biological replicate to make the statistics more robust. I looked at the raw count and there is big different between the biological replicate and the…
Association analysis of agronomic traits and construction of genetic networks by resequencing of 306 sugar beet (Beta vulgaris L.) lines
Genome resequencing approach for genotyping 306 sugar beet germplasm resources In this study, we performed high-depth genome-wide resequencing of 306 sugar beet accessions using an Illumina HiSeq 2000 sequencer, obtaining 1977.12 Gb of sequencing data. This collection included 72 endemic accessions from Northeast China (Harbin), 114 endemic accessions from North China…
Aedes aegypti Argonaute 2 controls arbovirus infection and host mortality
Generation and characterization of Ago2 knockout mutants To demonstrate the essential function of Ago2 in the Ae. aegypti siRNA pathway, we used CRISPR/Cas9 to knock out Ago2 and then investigated its role in defending against arbovirus infection (Fig. 1a). Ae. aegypti Ago2 (AeAgo2) has four exons and four predicated functional domains,…
Add samples IDs to Seurat object when integrating different samples to do differential expression analysis
I have scRNAseq data and I am trying to do differential comparing 2 conditions (for each condition I have 3 samples). to do so I am using Seurat R package and to integrate the samples I used the following code. the part1 has code only for 1 sample (for other…
Batch effect consideration (re-seq the same sample twice)
Batch effect consideration (re-seq the same sample twice) 1 Hello, I would like to know how you guys address batch effects on re sequence on the same samples (Fastq files). Our client targeted 20 million reads for all of her samples. However, in the first run, we generated less than…
Metabolite interactions in the bacterial Calvin cycle and implications for flux regulation
Cultivations and harvest Cupriavidus necator strain DSMZ 428 was grown in Ralstonia Minimal Media (RMM) with 100 mM HEPES pH 7.5 under chemostat conditions in a Photon Systems Instruments Multi-Cultivator MC-1000 OD. Each reactor tube was set up to a volume of 55 mL, OD600 0.05 and 3.5 g/L fructose. Once growth ceased,…
Systemic epigenome-wide association study of elk treponeme-associated hoof disease
Study samples were obtained from Rocky Mountain elk collected in Washington, Idaho, and South Dakota and from Roosevelt elk from Washington, Oregon, and California. Only cases with required metadata (location of collection and sex) and confirmed diagnosis of TAHD present or not detected were included in the analysis. Treponeme-associated hoof…
r – ggplot2: Fill isn’t working for ellipses using geom_polygon()
I’m working on a new version of the ggbiplot package in this github repo and have a problem with filling data ellipses for the points in various groups. This is described in this issue. Perhaps someone here can see what the problem is and how to solve it. In ggbiplot.r…
Comparative evaluation of 16S rRNA metagenomic sequencing in the diagnosis and understanding of bacterial endophthalmitis
Introduction Endophthalmitis is a severe infection in the eye that can occur as a consequence of intraocular surgery, intraocular injections, trauma, the presence of a central venous catheter and systemic infectious diseases such as sepsis, abscesses or urinary tract infection.1 2 Acute bacterial endophthalmitis represents a significant ocular pathology that…
Section 2: ggplot2 Functions (2 pts) In this section,
Transcribed image text: Section 2: ggplot2 Functions (2 pts) In this section, you will be asked to explain the purpose of various ggplot2 functions and their syntax. Each question has two parts, A and B. We’re looking to evaluate if you understand the use and syntax of the functions. Please…
How to compared two groups out of twelve in DESeq2
How to compared two groups out of twelve in DESeq2 1 @27433c91 Last seen 10 hours ago United States I have a data set in which we are comparing RNA seq data collected from twelve different mouse strains. I have figured out how to run the DESeq2 analysis, but I…
A novel multi-epitope vaccine targeting extracellular proteins of Chlamydia pneumoniae
In a recent study published in Scientific Reports, a group of researchers designed and evaluated a multi-epitope vaccine targeting the main outer membrane protein (MOMP) protein of Chlamydia pneumoniae (C. pneumoniae; Cpn) using immunoinformatics. They assessed the vaccine’s interaction with immune receptors and expressed it in silico on a baculovirus…
Cell-free DNA and tumor exosome cargo as diagnostic and prognostic marker for prostate cancer
Abstract: According to the Global Cancer Statistics 2020, prostate cancer (PCa) is the second most commonly diagnosed male cancer and second leading cause of cancer death among men globally. Prostate cancer is known to be more aggressive among men of African origin with reasons not fully known. Previous studies…
Phage-microbe dynamics after sterile faecal filtrate transplantation in individuals with metabolic syndrome: a double-blind, randomised, placebo-controlled clinical trial assessing efficacy and safety
Study design We set up a prospective, double-blinded, randomised, placebo-controlled intervention study that was performed in our academic hospital, the Amsterdam University Medical Centres location AMC in the Netherlands. After passing screening, 24 subjects with MetSyn were randomised to receive a sterile FFT from a lean healthy donor or a…
Morphological and physiological adaptations of psychrophilic Pseudarthrobacter psychrotolerans YJ56 under temperature stress
Bacterial isolation from Antarctic soil Soil samples were collected from the Cape Burk area (1: 74° 45′ 19.6″ S, 136° 48′ 44.6″ W)51. The soil (1 g) was inoculated in a Reasoner’s 2A (R2A) liquid (composed of 0.5% proteose peptone, 0.05% casamino acid, 0.05% yeast extract, 0.05% dextrose, 0.05% soluble starch,…
low counts too many genes
DESEq2 results : low counts too many genes 1 My deseq2 results shows as follows : out of 55357 with nonzero total read count adjusted p-value < 0.1 LFC > 0 (up) : 0, 0% LFC < 0 (down) : 12, 0.022% outliers [1] : 0, 0% low counts [2]…
Solved Alpha and beta diversity analyses of (i) unassembled
Transcribed image text: Alpha and beta diversity analyses of (i) unassembled short and long reads and (ii) open reading frames (ORFs) extracted from long-read, short-read, and hybrid assemblies. (A) Shannon diversity values calculated from unassembled reads. (B) Principal-component analysis of metagenome taxonomic composition calculated from unassembled reads. (C) Shannon diversity…
machine learning – Training a neural network without collapsing
I am trying to train a pytorch neural network to map from image space to 2D. I have the condition that I only want to use the ReLU activation function, linear layers, conv2d layers, and avgpool2d layers. I have created my dataset by taking a single (32,32,3) image and rotating…
Converting scMultiome data to loom using SEURAT
I’m using scMultiom data with the CCAF tool to predict cell cycle phases. CCAF : github.com/plaisier-lab/ccAF CCAF requires a loom file as input. I converted the output h5 file from cellranger-arc and atac_fragment.tsv.gz to a loom file using Seurat’s code. library(Seurat) library(Signac) library(EnsDb.Hsapiens.v86) library(dplyr) library(ggplot2) library(SeuratDisk) inputdata.10x <- Read10X_h5(“D:/Halima’s Data/Thesis_2/1_GD428_21136_Hu_REH_Parental/outs/filtered_feature_bc_matrix.h5”)…
UMAP graph using DimPlot pre/post integration
UMAP graph using DimPlot pre/post integration 1 Hello all, I have a seurat object containing 3 different samples. Before integration with harmony, I can run: pbmc_harmony <- NormalizeData(pbmc_harmony, verbose = F) pbmc_harmony <- FindVariableFeatures(pbmc_harmony, selection.method = “vst”, nfeatures = 2000, verbose = F) pbmc_harmony <- ScaleData(pbmc_harmony, verbose = F) pbmc_harmony…
Single-cell transcriptomes reveal a molecular link between diabetic kidney and retinal lesions
Animals The animal experiments were approved by the Institutional Animal Care and Use Committee of Jinling Hospital (Nanjing, China), in accordance with the approved guidelines of the Institutional Animal Care and Use Committee of Jinling Hospital. 7 weeks old male wild-type (wt) and leptin receptor-deficient (db/db) mice on the C57BLKS/J…
ERS Genomics & AlgenScribe Enter Into CRISPR/Cas9 Licensing Agreement
License allows AlgenScribe to expand its research and development activities using CRISPR/Cas9. DUBLIN and NICE, France, Sept. 5, 2023 /PRNewswire/ — ERS Genomics Limited (‘ERS’) is pleased to announce a new license agreement with AlgenScribe SAS (‘AlgenScribe’). This is a non-exclusive licensing agreement granting AlgenScribe access to the ERS CRISPR/Cas9 patent portfolio. …
Docker Registry Paths and Example Code for Asia Pacific (Melbourne) (ap-southeast-4)
The following topics list parameters for each of the algorithms and deep learning containers in this region provided by Amazon SageMaker. AutoGluon (algorithm) SageMaker Python SDK example to retrieve registry path. from sagemaker import image_uris image_uris.retrieve(framework=’autogluon’,region=’ap-southeast-4′,image_scope=”inference”,version=’0.4′) Registry path Version Job types (image scope) 457447274322.dkr.ecr.ap-southeast-4.amazonaws.com/autogluon-training:<tag> 0.7.0 training 457447274322.dkr.ecr.ap-southeast-4.amazonaws.com/autogluon-inference:<tag> 0.7.0 inference 457447274322.dkr.ecr.ap-southeast-4.amazonaws.com/autogluon-training:<tag>…
TimeTalk uses single-cell RNA-seq datasets to decipher cell-cell communication during early embryo development
Curation of early-embryo development single-cell RNA-seq data sets for studying cell-cell communication To identify and study eLRs, we collected public early embryo development scRNA-seq datasets from the mouse MII-oocyte stage to the late blastocyst stage to ensure that scRNA-seq datasets represented every stage of early embryo development. In addition, to…
Multiomic interpretation of fungus-infected ant metabolomes during manipulated summit disease
Infection mortality, observations of manipulation, and LC–MS/MS Similar to previous laboratory infections with O. camponoti-floridani24, we collected C. floridanus displaying manipulated summiting between four hours before (zeitgeber time, ZT 20) to half an hour after dawn (ZT 0.5), beginning three weeks after infection (Fig. 1). Sham-treated healthy ants showed no mortality…
Getting Started with Python for Data Science
Image by Author Summer is over and it’s back to studying or working on your self-development plan. Many of you may have had the summertime to think about what your next steps will be, and if that involves anything to do with Data Science – you need to read…
Screening non-conventional yeasts for acid tolerance and engineering Pichia occidentalis for production of muconic acid
Screening non-conventional yeast strains for organic acid tolerance To build a library of non-conventional yeasts for screening prospective acid tolerant hosts, we surveyed public culture repositories for non-Saccharomyces strains, selecting strains with reported acid tolerance where available. In total, 153 strains from 83 distinct species were obtained, of which 124…
Single-cell massively-parallel multiplexed microbial sequencing (M3-seq) identifies rare bacterial populations and profiles phage infection
Bacterial strains and growth conditions for eBW1 B. subtilis 168 and E. coli (MG1655) were streaked out from a frozen glycerol stock onto an LB plate and grown overnight at 37 °C. Following a night of growth, a single colony was picked and inoculated into 5 ml of LB broth and grown…
How should I adjust covariates in eQTL analysis with an interaction term?
How should I adjust covariates in eQTL analysis with an interaction term? 0 Hello, I’m trying to perform eQTL analysis using an interaction term. (maybe with MatrixEQTL) My purpose is to get eQTLs having different effects according to the gender. In my case, it’s impossible to perform analyses separately for…
Question about umap using different numbers of pca components as initialization
Question about umap using different numbers of pca components as initialization 0 I am new to the scRNA-seq field and I have been doing some experiments of visualization of UMAP using different numbers of PCA components for initialization. The process involves projecting scRNA-seq data (count matrix) onto various numbers of…
Transcriptome-based prediction of drugs, inhibiting cardiomyogenesis in human induced pluripotent stem cells
Directed differentiation of hiPSCs (SBAD2) towards cardiomyocytes after exposure to teratogens and non-teratogens To study the early events of the process of cardiomyogenesis, we used a cell monolayer-based directed hiPSC differentiation protocol, designated as the UKK2 cardiotoxicity test (UKK2-CTT), which is based on the sequential activation and inhibition of Wnt/β-catenin…
Read data file and produce RPKM in edgeR
This post is in response to a number of emails and posts asking about reading data into edgeR and producing RPKM. Suppose we start with a tab-delimited file counts.txt like this: To read this into edgeR: library(edgeR) Data <- read.delim(“counts.txt”, sep=”\t”, row.names=1) y <- DGEList(Data, annotation=”Length”) To normalize the library…
Bioconductor Biovi
Comment: Handle zero effective gene length when tximport RSEM results by swbarnes2 ★ 1.3k Are you sure that those genes with size < 1 have non-zero counts? Comment: P-value inflation? by James W. MacDonald 63k The table indicates that you have – 9122 genes with p>0.05 and FDR >0.1 –…
Speeding up large scale scRNAseq analyses in R and improve memory
Hi everyone, My apologies if the question is rather broad, but I am looking for a general solution. I am analysing several datasets in the ballpark of 500k cells, and possibly would like to integrate them. However, analysing even one of these datasets takes days even to finish. My attempts…
PCA proteomic DEP
Hello everyone, I hope everyone of you had some fun in this summer time. I am back to work and I’m having some issue with DEP tool for proteomic. I have to make a PCA plot, and for some reason I don’t see my all my samples in the plot…
Problems using ERCC spike-ins for normalization in DESeq2
Hello everyone, I’m analyzing some RNA-seq datasets for differential expression. We did not run the experiments ourselves, but the database where I got them from indicates that they were done adding additional spike-ins (ERCC92) for normalization. Originally, I did not use these spike-ins, and just went along with the default…
Genome-wide analysis of circRNA regulation during spleen development of Chinese indigenous breed Meishan pigs | BMC Genomics
Overview of the sequencing information To explore the presence of circRNAs during spleen development, we assessed circRNAs expression in the spleen tissues of Meishan pigs at various developmental stage. We prepared and sequenced ribo-depleted total RNA-seq libraries, as shown in the flow chart (Fig. 1). Table S2 presents our rudimentary sequencing…
Topology evaluation of models for difficult targets in the 14th round of the critical assessment of protein structure prediction (CASP14).
Abstract This report describes the tertiary structure prediction assessment of difficult modeling targets in the 14th round of the Critical Assessment of Structure Prediction (CASP14). We implemented an official ranking scheme that used the same scores as the previous CASP topology-based assessment, but combined these scores with one that emphasized…
Solved (0) Unsupervised Machine Learning:Hi. I would like to
(0) Unsupervised Machine Learning: Hi. I would like to get a solution to this task. This has been asked before but the question was not answered in full. can you please assist with a detailed feedback as per question requirements? Thank you in advance Compulsory Task 1: This dataset is…
Advances in methylation analysis of liquid biopsy in early cancer detection of colorectal and lung cancer
Study participants Whole blood samples were collected from 327 participants consisting of 102 with colorectal cancer, 99 with lung cancer, and 126 healthy controls. After excluding 6 patients who withdrew consent to participate and two patients with QC-failed samples, the final analysis included 96 patients with colorectal cancer, 95 with…
PCA percent variance DESeq2
PCA percent variance DESeq2 0 @6d1ed6fa Last seen 14 hours ago United States I saved ‘pcaData’ as a data frame for future use. I ran the following to get vector ‘percentVar’, however, it is empty. Do I need the data in a different format to extract percent variance? > pcaData…
Leveraging SageMath and ChatGPT for (orthogonal) diagonalization and singular value decomposition
[1] S. Andrilli, D. Hecker, Elementary Linear Algebra, Sixth edition, Academic Press, Cambridge, Massachusetts, US, 2022. doi.org/10.1016/C2019-0-03227-X [2] H. Anton, C. Rorres, Elementary Linear Algebra: Applications Version, 12th edition, John Wiley & Sons, New York, US, 2013. …
Principal component analysis (PCA) from Desmond output file
Principal component analysis (PCA) from Desmond output file 0 Hi All, I have the output (-out.cms) file of the protein ligand simulation from Desmond. Now I want to perform principal component analysis (PCA) for the same. How to perform PCA on Desmond trajectory using prody? Can you please suggest any…
Platelet factors attenuate inflammation and rescue cognition in ageing
Animal models The C57BL/6 mouse line was used for all of the experiments (The Jackson Laboratory and National Institutes of Aging). Homozygous Pf4-KO mice were previously generated and characterized as described48. Pf4-KO mice were a gift from M. Anna Kowalska. Heterozygous mice were bred to generate Pf4-KO and WT littermate…
Nuclear genetic control of mtDNA copy number and heteroplasmy in humans
Overview of mtSwirl Here we develop mtSwirl, a scalable pipeline for mtCN and variant calling which makes calls relative to an internally generated per-sample consensus sequence before mapping all calls back to GRCh38. In addition to GRCh38 reference files and WGS data, the mtSwirl pipeline takes as input nuclear genome…
What are the reasons to find so few Differentially expressed genes (DEGs)?
What are the reasons to find so few Differentially expressed genes (DEGs)? 1 HI, After the differential gene expression analysis, I had got only 15 genes with logFC < 1.5. Is it because of the Transcriptome reference annotation, expression quantification method, and DEG detection methods which are affecting the optimal…
What is the best way to combine machine learning algorithms for feature selection such as Variable importance in Random Forest with differential expression analysis?
NB – this answer has been updated January 28th, 2020 Update: It is important to point out that the assumptions of RandomForest® differ from those of, e.g., a regression model. So, RandomForest® and other classification algorithms certainly must be considered. Just use my general pointers here as just that, i.e.,…
LD pruning Archives | The Golden Helix Blog
Pruning your data based on Linkage Disequilibrium (LD) values is an important quality assurance step for GWAS analysis. In particular, some tests such as Identity by Descent Estimation (IBD), Inbreeding Coefficient Estimation (f) and Principal Component Analysis (PCA) will…
Taraxasterol suppresses the proliferation and tumor growth of androgen-independent prostate cancer cells through the FGFR2-PI3K/AKT signaling pathway
All experimental protocols were approved by Dali University. All methods were performed in accordance with relevant guidelines and regulations. Reagents and chemicals MEM medium, RPMI-1640 medium, fetal bovine serum (FBS), phosphate-buffered saline (PBS), and penicillin–streptomycin (Pen Strep) were purchased from Biological Industries (Israel). CCK-8 reagent was purchased from Proteintech (Wuhan,…
Unreprogrammed H3K9me3 prevents minor zygotic genome activation and lineage commitment in SCNT embryos
doi: 10.1038/s41467-023-40496-3. Ruimin Xu # 1 2 3 , Qianshu Zhu # 3 4 , Yuyan Zhao 1 , Mo Chen 2 5 , Lingyue Yang 1 2 , Shijun Shen 3 4 , Guang Yang 3 4 , Zhifei Shi 1 , Xiaolei Zhang 1 , Qi Shi 1 2 , Xiaochen Kou …
t-SNE plot dots that are close together assigned to different clusters.
Hi, I have been having trouble to understand why some dots are so close together in t-SNE plot but they are assigned to different clusters in FindNeighbors() and FindClusters()? For example below plot: The most of the cluster 0 (red dots) are in bottom right but there are some are…
Unsupervised clustering on gene expression data
Clustering is a data mining method to identify unknown possible groups of items solely based on intrinsic features and no external variables. Basically, clustering includes four steps: 1) Data preparation and Feature selection, 2) Dissimilarity matrix calculation, 3) applying clustering algorithms, 4) Assessing cluster assignment I use an RNA-seq dataset…
Error in h(simpleError(msg, call)) in monocle2
Error in h(simpleError(msg, call)) in monocle2 0 Want to run monocle2 for a single cell RNAseq data processed using Seurat, but encountering following problem. library(monocle) Seurat An object of class Seurat 41445 features across 55683 samples within 1 assay Active assay: RNA (41445 features, 1850 variable features) 4 dimensional reductions…
How to preprocess and visualize beautifully scRNA-seq with omicverse?
Omicverse is the fundamental package for multi omics included bulk and single cell RNA-seq analysis with Python. To get started with omicverse, check out the Installation and Tutorials. For more details about the omicverse framework, please check out our publication. The count table, a numeric matrix of genes\u2009\u00d7\u2009cells, is the…
Question with manipulating OD gene list when running PCA
Hello, I am using Seurat 4.9.9.905 and Pagoda2 1.0.10 to do sc clustering on an integrated object. I integrated two merged sample sets with var features and normalization applied to each of the two merged objects. I would like to do the clustering in Pagoda. This is my integration script:…
DESEQ2 analysis – PCA plot
DESEQ2 analysis – PCA plot 1 I am not getting a lot of genes from my DESEQ2 analysis hence I was checking the PCA plot and this is how it looks like.Any suggestions how to mitigate this ? RNA-seq differential-expression deseq2 • 84 views • link updated 13 minutes ago…
Functional divergence of CYP76AKs shapes the chemodiversity of abietane-type diterpenoids in genus Salvia
Phylogenetic relationships within Salvia To characterize chemical diversity and phylogenetic relationships within the genus Salvia, 77 species, including six outgroups (Melissa officinalis L., Mentha spicata L., Clinopodium polycephalum (Vaniot) C.Y.Wu & S.J.Hsuan, Origanum vulgare L., Nepeta cataria L., and Prunella vulgaris L.), were sampled for analyses (Supplementary Data 1), covering the…
Cell-free DNA in the management of prostate cancer: Current status and future prospective
Objective: With the escalating prevalence of prostate cancer (PCa) in China, there is an urgent demand for novel diagnostic and therapeutic approaches. Extensive investigations have been conducted on the clinical implementation of circulating free DNA (cfDNA) in PCa. This review aims to provide a comprehensive overview of the present state…
Direct inference and control of genetic population structure from RNA sequencing data
In this study, we constructed the RGStraP pipeline to calculate RG-PCs from genetic variants called from RNAseq data. RGStraP relies on GATK for its variant calling suite, as well as PLINK and flashPCA to filter the SNPs and calculate genetic principal components from them, respectively (Methods). We make RGStraP available…
Day 17 Dimensionality Reduction by Muhammad Dawood
Python for Data Science Day 17: Dimensionality Reduction Welcome to Day 17 of our Python for data science challenge! Dimensionality Reduction is a powerful technique used to simplify high-dimensional data while preserving essential information. Today, we will explore dimensionality reduction techniques, including Principal Component Analysis (PCA) and t-distributed Stochastic Neighbor…
Machine learning prediction and classification of behavioral selection in a canine olfactory detection program
2013 TSA cohort traits The traits scored in the cohort represent measures of confidence/fear, quality of hunting related behaviors, and dog-trainer interaction characteristics19,20. The traits Chase/Retrieve, Physical Possession, and Independent Possession were measured in both the Airport Terminal and Environmental tests whereas five and seven other traits were specific to…
Study Finds Link Between Baseline Uric Acid Levels and Prostate Cancer Prognosis
Past research has shown that higher uric acid (UA) levels contribute to cancer growth in patients with prostate cancer (PCa), and a recent study published in Cancer Medicine demonstrated a link between PCa mortality and above or below average UA levels. Researchers examined health data from patients with PCa who…
Seurat IntegrateData function returning an error
Hello, I am trying to integrate the data by correcting for batch effects per patient and I’m running into this error while executing the IntegrateData function, how do I fix this? Is it because the sepsis2HTO_HAB3 (7th dataset) has too few samples (66) to be properly integrated? analyseFinalList = function(objlist,…
Transcriptomic analysis of neutrophil apoptosis induced by large B-cell lymphoma
introduce Difuse large B-cell lymphoma is the most common subtype of non-Hodgkin lymphoma, accounting for 30 percent of new cases in NHL each year. Although approximately 50-60% of human patients are cured by R-CHOP immunochemotherapy, more than 30% of patients are refractory to these regimens or relapse after remission, and…
plink QC
plink QC 0 we perpose in identify rick factor snp in my alzhimer’s disease dataset in GWAS analysis case and control study. i don’t understand plink gwas, any one explain and any workflow give me. what type of qc step i’m do it. pls any one help me. which perpose…
Gut microbiota analyses of inflammatory bowel diseases from a representative Saudi population | BMC Gastroenterology
Study populations Between 2015 and 2019, stool samples and data were collected from 219 IBD subjects (CD or UC) attending the Internal Medicine Clinics, King Fahd Hospital of the University, Al-Khobar and King Fahad Hospital, Alhafof, Saudi Arabia. Diagnosis of IBD was based on endoscopy (for CD) or colonoscopy (for…
Senior Bioinformatics Scientist – Enhanc3D Genomics
VACANCY – Senior Bioinformatics Scientist About Enhanc3D Genomics Enhanc3D Genomics is a functional genomics spinout company from the Babraham Institute (Cambridge, UK) leveraging a disruptive technology to profile interactions of gene promotors with distal DNA regulatory elements that allow unbiased allocation of enhancers to their target genes across the genome….
A universal tool for predicting differentially active features in single-cell and spatial genomics data
singleCellHaystack methodology For a detailed description of the original singleCellHaystack implementation (version 0.3.2) we refer to Vandenbon and Diez19. In brief, singleCellHaystack uses the distribution of cells inside an input space to predict DAFs. First, it infers a reference distribution \(Q\) of all cells in the space by estimating the…
Upcycling rice yield trial data using a weather-driven crop growth model
Phenotype data We obtained yield datasets for rice (Oryza sativa L.) from 207,331 trials with 8524 cultivars during the 38 years from 1980 to 2017. The data were obtained from field trials at 110 public agricultural experimental stations in Japan conducted by the Institute of Crop Science of the National…
Effects of Candidatus Liberibacter asiaticus infection on metagenome of Diaphorina citri gut endosymbiont
Psyllid sampling, tissue collection and DNA isolation Adult D. citri newly emerged (five days old) was initially harvested from Citrus Tachibana uninfected CLas in 2020 at Guangxi province, China, and was successively reared on Murraya paniculata at Guangxi Special Crops Research Institute for more than 15 generations. All cages and…
Antiviral HIV-1 SERINC restriction factors disrupt virus membrane asymmetry
Constructs and expression of human SERINC proteins SERINC3 The gene that encodes human SERINC3 (Genscript-OHu02717D) was inserted upstream of a thrombin protease cleavable linker (LVPRGS) and Strep II epitope (WSHPQFEK) in a modified pFastBac vector by In-Fusion cloning (Clontech). Mutagenesis using the QuikChange Site-Directed Mutagenesis kit (Agilent) was performed to…
BigData and ChIP-seq workshop | Master2 GenE2
The Big Data workshop is dedicated to biology and medicine students who wants to acquire skills in NGS data manipulation, treatment and statical analysis. This training is for beginners, no previous training in computer required. In addition to this, you will need to know more about it. Through this workshop,…
smallRNA-seq analysis batch correction in limma
Good morning, I am currently trying to analyse a small-RNA sequencing dataset using limma package and the voomLmFit function. However, I am experiencing some issues with the p-value distribution, with some of the comparisons I am testing showing odd p-value distribution. This probably indicates that there is some kind of…
How to analyze heterogenous forms of experimental data (not sequencing based)?
How to analyze heterogenous forms of experimental data (not sequencing based)? 0 Hello all- looking for some general tips/inquiring about feasibility for analyzing heterogenous biological data that may/may not have a sequencing component. I have been tasked with analyzing various forms of data from the same experiment, including: -Imaging data…
Ancient dolphin genomes reveal rapid repeated adaptation to coastal waters
Ethics We confirm our research complies with all relevant ethical regulations and was approved by the animal ethics committee of the School of Biology at the University of St Andrews on 26 July 2018 www.st-andrews.ac.uk/research/environment/committees/awerb/. The three new contemporary dolphin samples analysed in this study were collected under the relevant…
ChatGPT meets DNA: DNAGPT, The Ultimate Tool for Multitasking DNA Sequence Analysis!
Motivated by the success of the GPT (Generative Pre-trained Transformer) model, researchers from the Southern University of Science and Technology, Tencent AI Lab, Shenzhen, China, and the City University of Hong Kong have developed DNAGPT, a generalized foundation model capable of simultaneously processing multiple DNA sequences from various species. Its…
Seurat clustering and classification
Seurat clustering and classification 0 Hi All, I have a seurat object, but now i want to subset that on the basis of few genes only (almost 250 genes). These 250genes I got from a published paper showing different macrophae annotations (7 annotated clusters). The idea is to see if…
Anatomical and molecular characterization of parvalbumin-cholecystokinin co-expressing inhibitory interneurons: implications for neuropsychiatric conditions
Genetic targeting of CCK+ interneurons restricted by the Dlx5/6 driver line in mouse hippocampus and neocortex CCK isoforms and their preprohormone can be expressed in excitatory neurons in addition to GABAergic interneurons [28]. In order to target CCK+ inhibitory interneurons only, we employed an intersectional genetic strategy by simultaneous co-expression…
integration downstream analysis and identification genes altered in one condition
scRNAseq: integration downstream analysis and identification genes altered in one condition 0 Hi, I am new to scRNAseq and I am very confused about few things when it1s time to integrate two datasets/conditions (control vs treated). So I “characterized” each dataset (control or treated) and identified the various clusters (which…
Can Pre-Op MRI Staging Help Predict Prostate Cancer Recurrence after a Prostatectomy?
Emerging research suggests that pre-operative magnetic resonance imaging (MRI) findings may have comparable predictive efficacy to post-prostatectomy pathologic staging in assessing the risk of biochemical recurrence (BCR) of prostate cancer (PCa). For the retrospective study, recently published in the American Journal of Roentgenology, researchers assessed findings of extraprostatic extension (EPE)…
Kaggle competition, enzyme stability prediction, machine learning in life sciences, protein engineering, ML6
When Christmas is nearing, everybody is looking forward to the Christmas tree, maybe snow, presents, Santa Claus and the new year. For us at ML6, there is something more! We get some time off our regular projects and get to spend time exploring new horizons for ML6: new tech, new…
what is gene synthesis used for
As the resulting plasmid contains the original prefix and suffix sequences, it can be used to join with more BioBricks parts. The development of the Golden Gate assembly methods and its variants has allowed researchers to design tool-kits to speed up the synthetic biology workflow. By using the BsaI restriction…
Principal component analysis (PCA) for studying mutation effect – User discussions
GROMACS version: 2023.1GROMACS modification: No Hi everyone,I need to investigate the effects of a single-point mutation on my protein structure. I would like to run a free energy landscape analysis but first I need to compute PCA and I was starting with this command: gmx covar -f md_noPBC.xtc -s md.tpr…
Global within-species phylogenetics of sewage microbes suggest that local adaptation shapes geographical bacterial clustering
Predominant bacteria in sewage do likely not originate from the human gut To identify bacterial genomes from sewage across the world, we used a combination of two different metagenomics genome binners (VAMB24 and MetaBAT225). From 757 samples across 101 different countries (Fig. 1a and Supplementary Fig. 1), we were able to create…
A Power Duo for Advanced Machine Learning
Hello fellow coders, seasoned developers and data enthusiasts! Welcome aboard on this deep dive into machine learning using Python, with a special focus on the Scikit-learn library. This guide is designed to level up your understanding of machine learning with some serious hands-on learning. Machine Learning and Python: A Powerful…