Tag: NA

Error when adding new residue to hdb (CHARMM36) – User discussions

dom June 26, 2022, 2:05am #1 GROMACS version:2022.2GROMACS modification: No I am adding a new protein residue to the CHARMM36 forcefield (July 2021). As per the instructions in the GROMACS manual (“Adding a Residue to a Force Field”), I modified residuetypes.dat, aminoacids.rtp, and aminoacids.hdb with the new residue entry. It…

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extendedSequences length is not the required for DeepCpf1 (34bp)

Hi, I’m using CRISPRseek dev v. 1.35.2, installed from github (hukai916/CRISPRseek). I wanted to calculate the CFD, and the grna efficacy of a Cas12 sgRNA (my_sgrna.fa file) using Deep Cpf1. my_sgrna.fa, TTTT (PAM) + sgRNA (20bp): >sgrna1 TTTTTGTCTTTAGACTATAAGTGC Command: offTargetAnalysis(inputFilePath = “my_sgrna.fa”, format = “fasta”, header = FALSE, exportAllgRNAs =…

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Escherichia coli K-12 substr. MG1655 EC 2.7.1.180

BioCyc ID: RXN-14461 EC Number: 2.7.1.180 Enzymes and Genes: FAD:protein FMN transferase: ftp Reaction Locations: periplasmic space The reaction direction shown is in accordance with the direction in which it was curated. Mass balance status: Balanced. Enzyme Commission Primary Name: FAD:protein FMN transferase Enzyme Commission Synonyms: flavin transferase, apbE (gene…

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python – Matching two files(vcf to maf) using a dictionaries, and appending the contents

annotation_file ##INFO=<ID=ClinVar_CLNSIG,Number=.,xxx ##INFO=<ID=ClinVar_CLNREVSTAT,Number=.,yyy ##INFO=<ID=ClinVar_CLNDN,Number=.zzz #CHROM POS ID REF ALT QUAL FILTER INFO chr1 10145 . AAC A 101.83 . AC=2;AF=0.067;AN=30;aaa chr1 10146 . AC A 98.25 . AC=2;AF=0.083;AN=24;bbb chr1 10146 . AC * 79.25 . AC=2;AF=0.083;AN=24;ccc chr1 10439 . AC A 81.33 . AC=1;AF=0.008333;AN=120;ddd chr1 10450 . T G 53.09…

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ERROR No such moleculetype NA – User discussions

GROMACS version:GROMACS modification: Yes/No I got this errorwhen I run the line: gmx grompp -f em.mdp -c solv_ions.gro -p topol.top -o em.tpr -maxwarn 10in the topol.top there is 3 NA atoms 🙂 GROMACS – gmx grompp, 2020.1-Ubuntu-2020.1-1 (-: GROMACS is written by: Emile Apol Rossen Apostolov Paul Bauer Herman J.C….

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Using element_ Textcustomize text in ggplot2

Ggplot2’s theme system allows us to better control graphicsNon data elementTo enhance the beauty of the image through more subtle modifications,Theme system of ggplot2Self contained multipleelement_function element_text( ) element_line( ) element_rect( ) element_blank( ) This section describes the topic element element_ Text (), which controls many parts of text elements…

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Merge multiple text files to create a combined dataframe and rename columns in R – General

Hi, I have multiple .txt files (each file contains 4 columns; an identifier Gene column, a raw_counts and other columns). I would like to merge those files into a combined dataframe using the common gene column. I was able to import multiple .txt files together, merge based on identifier column,…

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Description, Programming Languages, Similar Projects of ggfx

ggfx is a (currently experimantal) package that allows the use of various filters and shaders on ggplot2 layers. Installation You can install ggfx from CRAN in the usual manner (install.packages(‘ggfx’)) or you can grab the development version directly from github using the devtools package: # install.packages(‘devtools’) devtools::install_github(‘thomasp85/ggfx’) Example The basic…

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python – Scikit optimize with objective function returning None

Can the expensive objective function that is being passed to scikit-optimize return None (NA/NaN/…) type? I would need to optimize simulation parameters and sometimes, the simulation can return a non-feasible result. I could theoretically return some artificially large number (1/ε), but that would probably break the scikit normality assumption. And…

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Breast Reconstruction with Inferior Flap and Fat Transfer as Curative Treatment for BIA-ALCL

Araco A, Gravante G, Araco F, Delogu D, Cervelli V, Walgenbach K. A retrospective analysis of 3,000 primary aesthetic breast augmentations: postoperative complications and associated factors. Aesthet Plast Surg. 2007;31(5):532–9. doi.org/10.1007/s00266-007-0162-8. CAS  CrossRef  Google Scholar  Nahabedian MY, Patel K. Management of common and uncommon problems after primary breast augmentation. Clin…

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Parse a file of strings in python separated by newline into a json array

I don’t see where you’re actually reading from the file in the first place. You have to actually read your path_text.txt before you can format it correctly right? with open(‘path_text.txt’,’r’,encoding=’utf-8′) as myfile: content = myfiel.read().splitlines() Which will give you [‘/gp/oi/eu/gatk/inputs/NA12878_24RG_med.hg38.bam’, ‘/gp/oi/eu/gatk/inputs/NA12878_24RG_small.hg38.bam’] in content. Now if you want to write this…

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Reordering boxplot (ggplot) with scale_x_discrete(limits=(…) results in Warning message: Removed 103 rows containing missing values (stat_boxplot)

Probably a user error but I can’t find it for the life of me. Trying to rearrange the order of factors in a boxplot I am making using ggplot using the, “scale_x_discrete(limits=(…)” function. Doing so results in the following warning message “Warning message: Removed 103 rows containing missing values (stat_boxplot”….

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[Solved] tryCatch not catching error produced by install.packages within RStudio

RStudio does not exectute the normal install.packages but instead does its own thing: look at the code in RStudio: > install.packages function (…) .rs.callAs(name, hook, original, …) <environment: 0x3e4b478> > .rs.callAs function (name, f, …) { withCallingHandlers(tryCatch(f(…), error = function(e) { cat(“Error in “, name, ” : “, e$message, “\n”,…

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[BioC] rtracklayer 1.6: invalid class “ucscCart” object

Dear Bioc, Following the rtracklayer documentation, section 2.2.4, ‘A Shortcut’, I encounter the following error browseGenome (subTargetTrack) Error in validObject(.Object) :invalid class “ucscCart” object: superclass “ANYTHING” not defined in the environment of the object’s class traceback () 13: stop(msg, ” “, errors, domain = NA)12: validObject(.Object)11: initialize(value, …)10: initialize(value, …)9:…

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xml – I am trying to importxml from ENSEMBL using xpath copied from Chrome, but it is not working

I want to use google sheet’s IMPORTXML to extract the gene name (SLC3A1) and ensembl ID (ENSG00000138079) from this URL: asia.ensembl.org/Multi/Search/Results?q=SLC3A1;site=ensembl I tried copying xpath from Chrome and also tried deriving it on my own step by step, but I am only getting a #NA. My xpath: /html/body/div[1]/div/div[2]/div[1]/div[1]/div[2]/div[2]/div[4]/div/div/div[2]/div/div/div[3]/div[2]/div[1]/div[2]/div/div/div/div[1]/div/div[2]/span From Chrome:…

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CYP2D6 antibody | Anti-CYP2D6 | stjohnslabs

Host: Goat Applications: Pep-ELISA, WB Reactivity: Human Note: FOR RESEARCH USE ONLY (RUO). Short Description: Goat polyclonal antibody anti-CYP2D6 (C-Term) is suitable for use in ELISA and Western Blot research applications. Clonality: Polyclonal Conjugation: Unconjugated Isotype: IgG Formulation: 0.5 mg/ml in Tris saline, 0.02% sodium azide, pH7.3 with 0.5% bovine…

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LinkedIn svg{display:block;margin:auto}li-icon[type$=-icon]{width:24px;height:24px}li-icon[type$=-icon][size=small]{width:16px;height:16px}li-icon[type$=-icon]>svg{vertical-align:top}li-icon[type^=nav-]{width:32px!important;height:32px!important}li-icon .inactive-item,li-icon .large-icon{fill:currentColor}li-icon .active-item,li-icon .small-icon{fill:currentColor;visibility:hidden}li-icon[size=small] .inactive-item,li-icon[size=small] .large-icon,li-icon[type^=nav-][active] .inactive-item,li-icon[type^=nav-][active] .large-icon{visibility:hidden}li-icon[size=small] .active-item,li-icon[size=small] .small-icon,li-icon[type^=nav-][active] .active-item,li-icon[type^=nav-][active] .small-icon{visibility:visible}li-icon[type^=app-]{width:40px!important;height:40px!important}li-icon[type=loader]{fill-opacity:1;stroke-opacity:1;fill:transparent;stroke:transparent}li-icon[type=loader][size=small]{fill-opacity:0;stroke-opacity:0;fill:currentColor;stroke:currentColor}li-icon .color-icon,li-icon[color] .solid-icon{display:none}li-icon[color] .color-icon{display:block}li-icon[type^=large-],li-icon[type^=large-][size=small]{width:48px!important;height:48px!important}[dir=rtl] li-icon[type*=arrow],[dir=rtl] li-icon[type*=chevron],[dir=rtl] li-icon[type*=follow],[dir=rtl] li-icon[type=enter-icon],[dir=rtl] li-icon[type=forward-icon],[dir=rtl] li-icon[type=leave-icon],[dir=rtl] li-icon[type=question-pebble-icon],[dir=rtl] li-icon[type=reply-icon],[dir=rtl] li-icon[type=share-ios-icon],[dir=rtl] li-icon[type=share-linkedin-icon],[dir=rtl] li-icon[type=to-end-icon],[dir=rtl] li-icon[type=to-start-icon]{transform:rotateY(180deg)}[dir=rtl] li-icon>svg{float:left}li-icon[type$=-pebble-icon][animate]{transform:scale(.2);animation:b 334ms ease-in-out forwards}li-icon[type$=-pebble-icon][animate] .circle{stroke-dasharray:63;stroke-dashoffset:63;animation:a .5s ease-out forwards;animation-delay:334ms}li-icon[type$=-pebble-icon][animate][size=small] .circle{stroke-dasharray:38;stroke-dashoffset:38}li-icon[type^=premium-]{width:auto;height:16px}li-icon[type^=premium-][type^=premium-app-icon],li-icon[type^=premium-][type^=premium-inverse-app]{height:24px}li-icon[type^=premium-][size=”8dp”]{height:8px}li-icon[type^=premium-][size=”10dp”]{height:10px}li-icon[type^=premium-][size=”12dp”]{height:12px}li-icon[type^=premium-][size=”16dp”]{height:16px}li-icon[type^=premium-][size=”20dp”]{height:20px}li-icon[type^=premium-][size=”24dp”]{height:24px}li-icon[type^=premium-][size=”32dp”]{height:32px}li-icon[type^=premium-] text{font-size:24px;font-weight:600;letter-spacing:4px;dominant-baseline:text-before-edge;font-family:Source Sans Pro,Helvetica,Arial,sans-serif}@media screen and (-ms-high-contrast:white-on-black){li-icon[type=premium-app-icon],li-icon[type=premium-badge]{-ms-high-contrast-adjust:none;background-color:#fff}li-icon[type=premium-app-icon] svg,li-icon[type=premium-badge] svg{height:90%!important;position:relative;top:5%;right:2%}}@media screen and (-ms-high-contrast:black-on-white){li-icon[type=premium-inverse-app-icon],li-icon[type=premium-inverse-badge]{-ms-high-contrast-adjust:none;background-color:#000}li-icon[type=premium-inverse-app-icon] svg,li-icon[type=premium-inverse-badge]…

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Human stem cell modelling for heart disease of long QT syndrome

Abstract Sudden cardiac death (SCD) in otherwise healthy young people is a public health priority. Long QT syndrome (LQTS) is the commonest life-threatening cardiac arrhythmia contributing to SCD under 40 years old with an estimated prevalence of 1:2,000. Cardiac rhythm is driven by coordinated cardiac action potential, which is triggered…

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Unable to open pdf file of volcano plots created using many group comparisons from EnhancedVolcano package in R

Hi, I am working with a dataframe in R containing the quantitative data and trying to plot a volcano plot using library(EnhancedVolcano) package. I am currently analyzing by subsetting based on corresponding matching pairs of “Coef” and “P.value” obtained from limma (for instance; Coef.HC_6h_vs_0h and P.value.HC_6h_vs_0h) individually and export the…

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Endometriosis-related functional modules and hub genes

Introduction Endometriosis (EMS) is a chronic gynecological disease defined as implantation and periodic growth of the endometrial glands and stroma outside the uterine cavity, causing chronic pelvic pain, severe dysmenorrhea, and infertility in 10% reproductive-age women, among which the infertility rate is approximately 30–50%.1,2 Surgical excision is commonly used for…

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Digital Identity Solutions Market In-Depth Analysis including Development Strategy, Regional Analysis, Key Segmentation by Major Companies like IDEMIA, ForgeRock, Imageware Systems, Jumio, NEC, Samsung SDS

“ The global Digital Identity Solutions Market is an information rich representation of the current market developments that echo upward spike in growth numbers. Our team of research experts at Adroit Market Research has relied upon dedicated primary and secondary research methodologies to make accurate deductions of the market developments,…

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r – How to combine two qualitative data to make a bar graph

If you want to make two graphs to display Yesterday and Today in a single ggplot (or want to display both in the same plot) you’ll need to include a pivot_longer Example data df <- as.data.frame(structure(c(1L, 2, 3, 4, 5, 6, “Male”, “Female”, “Female”, “Male”, “Male”, “Female”, “Very good”, “Good”,…

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Pangenome-based genome inference allows efficient and accurate genotyping across a wide spectrum of variant classes

Sequencing data We used publicly available sequencing data from the GIAB consortium45, 1000 Genomes Project high-coverage data46 and Human Genome Structural Variation Consortium (HGSVC)4. All datasets include only samples consented for public dissemination of the full genomes. Statistics and reproducibility For generating the assemblies, we used all 14 samples for…

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r – convert ALL genes from ensembl ID to symbol without NAs

I tried to convert genes with ensembl ID to Symbol I used the “EnsDb.Hsapiens.v86” package using this code: library(“EnsDb.Hsapiens.v86”) mapIds <- mapIds(EnsDb.Hsapiens.v86, keys = genes, keytype = “GENEID”, column = “SYMBOL”) mapIds Results is like that: ENSG00000033327 GAB2 ENSG00000033627 ATP6V0A1 ENSG00000033800 PIAS1 ENSG00000033867 SLC4A7 ENSG00000034063 < NA > ENSG00000034152 MAP2K3…

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Install Bioconductor package using rpy2 in Python Jupyter notebook

This introduction comes from this SO question: “argument is of length zero” is a very specific problem that comes from one of my least-liked elements of R. Let me demonstrate the problem: > FALSE == “turnip” [1] FALSE > TRUE == “turnip” [1] FALSE > NA == “turnip” [1] NA…

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Histograms using ggplot2 within loop

I agree with @GabrielMagno, facetting is the way to go. But if for some reason you need to work with the loop, then either of these will do the job. library(gridExtra) library(ggplot2) df<-matrix(NA,2000,5) df[,1]<-rnorm(2000,1,1) df[,2]<-rnorm(2000,2,1) df[,3]<-rnorm(2000,3,1) df[,4]<-rnorm(2000,4,1) df[,5]<-rnorm(2000,5,1) df<-data.frame(df) out<-list() for (i in 1:5){ x = df[,i] out[[i]] <- ggplot(data.frame(x),…

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How to specify tagging levels when using textual layout in patchwork package? – General

I want to tag the plots: A1, A2, B. I can get A-C and A1-A3 but not what I am after, what am I missing? #Grid layout grid <- ” AABB CCCC ” #the following tags A-C patchwork <- p1 + p2 + p3 + plot_layout(design = grid, guides =…

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Accepted slurm-wlm 21.08.6-1 (source) into unstable

—–BEGIN PGP SIGNED MESSAGE—– Hash: SHA512 Format: 1.8 Date: Tue, 22 Mar 2022 21:59:40 +0100 Source: slurm-wlm Architecture: source Version: 21.08.6-1 Distribution: unstable Urgency: medium Maintainer: Debian HPC Team <debian-…@lists.debian.org> Changed-By: Gennaro Oliva <oliv…@na.icar.cnr.it> Changes: slurm-wlm (21.08.6-1) unstable; urgency=medium . * New upstream release * Remove fix-typos patch included upstream…

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ggplot2 – How To Update R Values

I have the below code which runs a 3 month picture of my metrics. I open the saved code, remove “Nov-21” and add “Feb-22”, then delete the first entry for each metric and add “Feb-22” entry to end of each metric (957L, 1208L, 1054L, 476L). Previously, the 3 month picture…

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Development of Cas12a-Based Cell-Free Small-Molecule Biosensors via Allosteric Regulation of CRISPR Array Expression

In nature, microbes have evolved different systems to sense external stimuli. Synthetic biology approaches (1) repurpose these systems as biosensors to specifically and sensitively detect various targets of interest. Although various highly sensitive and specific laboratory-based analytical methods (including high-performance liquid chromatography and mass spectrometry) can detect small-molecule targets, they…

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Htseq is giving me 0 counts using the GFF3 of miRBase

Hello! I am trying to annotate a miRNA-seq so that it gives me mature miRNAs where I already have 5p and 3p. For this, I have used the index mm10.fa and the miRBase mmu.gff3. I have aligned with HISAT2 and am trying to count with HTSeq, however I get 0…

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A Comprehensive Guide on ggplot2 in R

                                                                  Image source: Author       Introduction Visualization plays an important role in the decision-making process after analyzing relevant data. Graphical representation highlighting the interdependence of key elements affecting performance is important in the above process. There are many libraries in Python and R which provide different options showing…

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Accurate prediction of metagenome-assembled genome completeness by MAGISTA, a random forest model built on alignment-free intra-bin statistics | Environmental Microbiome

Steen AD, Crits-Christoph A, Carini P, DeAngelis KM, Fierer N, Lloyd KG, Cameron TJ. High proportions of bacteria and archaea across most biomes remain uncultured. ISME J. 2019;13:3126–30. PubMed  PubMed Central  Google Scholar  Goh KM, Shahar S, Chan K-G, Chong CS, Amran SI, Sani MH, Zakaria II, Kahar UM. Current…

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r – How to get dates aligned with data points in ggplot()

So I have ran into a problem where I can only get my data points to align with the x-axis labels when I specify in scale_x_date(…, date_breaks = “days”) which misrepresents the data. Could someone please give some indication why they aren’t aligned and how to fix it? tidy_sales$Week_End <-…

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R: PC gamma

PCgamma {GSAgm} R Documentation PC gamma Description For GSA of SNP data, the following two-step procedure is implemented (see Biernacka et al[1] for more details on the method). Step 1: Principal components analysis for SNPs within a gene is completed with the components needed to explain 80 percent of the…

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Notch activation suppresses endothelial cell migration and sprouting via miR-223-3p targeting Fbxw7

Alabi RO, Farber G, Blobel CP (2018) Intriguing roles for endothelial ADAM10/Notch signaling in the development of organ-specific vascular beds. Physiol Rev 98:2025–2061 CAS  Article  Google Scholar  Autiero M, De Smet F, Claes F, Carmeliet P (2005) Role of neural guidance signals in blood vessel navigation. Cardiovasc Res 65:629–638 CAS …

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The epigenetic dimension of protein structure

References [1] Tunyasuvunakool K, Adler J, Wu Z, Green T, Zielinski M, Žídek A, et al. Highly accurate protein structure prediction for the human proteome. Nature. 2021;596:590–6.10.1038/s41586-021-03828-1Search in Google Scholar [2] Hardy J, Allsop D. Amyloid deposition as the central event in the aetiology of Alzheimer’s disease. Trends Pharmacol Sci….

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ggplot2 – How can I directly compute a t-test for proportion in R from a data frame using prop_test?

I have a data frame with n>1000 in which each row includes data for columns Year, which is a numeric year, and Gender, which is either “Male” or “Female”. I want to compute a t-test for the proportion of Gender == “Male” pairwise between Years. I have succeeded in creating…

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r – ggplot2 running for minutes without plotting

I am attempting to plot the below vector, but when I run the function, it just continues to run and does not plot. I have waited 5 minutes before I feel uncomfortable and click stop in the console. Wondering what is going on. Up until this point I have had…

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Fatty infiltration after rotator cuff tear

Introduction Rotator cuff tear (RCT) is a common shoulder disorder causing shoulder pain and disability. The prevalence of full-thickness RCT is 20.7% in the general population, and increased with age.1 Rotator cuff play essential roles in shoulder function and the treatment of proximal humeral fractures.2,3 It is important to repair…

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use tcgabiolinks package to download TCGA data

TCGA Data download in terms of ease of use ,RTCGA The bag should be better , And because it’s already downloaded data , The use is relatively stable . But also because of the downloaded data , There is no guarantee that the data is new .TCGAbiolinks The package is…

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r – Creating legend and defining colours for facetwrap with multiple geoms

I’m creating a faceted plot of each sampling point, and trying to show four variables – a bar (species abundance at each sampling point), a line for water depth at the sampling point, another line for river height (measured elsewhere), and symbols for treatment intervention. My problem is I can’t…

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Estimating prediction accuracy of a Cox survival model using sbrier (R)

You can use the pec package, instead. Example: library(pec) set.seed(18713) library(prodlim) library(survival) dat=SimSurv(100) pmodel=coxph(Surv(time,status)~X1+X2,data=dat) perror=pec(list(Cox=pmodel),Hist(time,status)~1,data=dat) ## cumulative prediction error crps(perror) # between min time and 1 ## same thing: ibs(perror) library(survival) library(ipred) data(“DLBCL”, package = “ipred”) smod <- Surv(DLBCL$time, DLBCL$cens) coxmod <- coxph(smod ~ IPI, data = DLBCL) coxmod Call:…

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Requirement of Xk and Vps13a for the P2X7-mediated phospholipid scrambling and cell lysis in mouse T cells

Significance The extracellular concentration of adenosine triphosphate (ATP) reaches several hundred micromoles in the inflamed tissues or tumor environment. A high concentration of ATP activates P2X7, a purinergic receptor, and induces the formation of a nonselective cation channel, accompanied by reversible phosphatidylserine (PtdSer) exposure, leading to cell lysis. Here, we…

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r – Reorder and split the ggplot heatmap based on the clusters in one of the columns

I generated a heatmap with ggplot, and order the samples by using hclust, However, I still need more reordering to get all the similar values corespondent with one of the samples in the ordered cluster. Here I generate a samples data to explain better. set.seed(99) M <- data.frame(names = paste0(“g”,…

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Quip potential – LAMMPS Development

Hi,I am trying to run quip pair_style in lammps ( 9 Nov 21) to perform MD using my trained gap potential. I trained GAP potential for sodium data using distance_2b and soap as descriptors. But when I run the input file, I get the following warnings and no data are…

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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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ggplot2 – How to wrap graphs by categories while keeping the same width of bars with ggplot in R?

I am struggling with using facet_grid() and facet wrap() with ggplot(). I would like to be able to wrap the different stacked barcharts for every two categories (of the variable Department here) but at the same time have the same width of bars. The first action can be achieved with…

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Plotting date intervals in ggplot2

I have a dataset which has a bunch of date intervals (i.e. POSIXct format start dates and end dates). In the example provided, let’s say it’s each period is associated to when someone was in school or out of school. I’m interested in plotting the data in ggplot2, each row…

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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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ggplot2 – R knitr Markdown: Output Plots within For Loop

I am using child Rmd files in markdown, also works in sweave. in Rmd use following snippet: “`{r run-numeric-md, include=FALSE} out = NULL for (i in c(1:num_vars)) { out = c(out, knit_child(‘da-numeric.Rmd’)) } “` da-numeric.Rmd looks like: Variabele `r num_var_names[i]` ———————————— Missing : `r sum(is.na(data[[num_var_names[i]]]))` Minimum value : `r min(na.omit(data[[num_var_names[i]]]))`…

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how to make 2d rendering on directx 11 more faster – Graphics and GPU Programming

I make an editor for own game engine and I used for 2d rendering Direct2D but I wanted to render a directx texture on window in editor, I didn’t find convenient way to convert directx texture to direct2d bitmap. I decided to make own 2d render on directx 11 and…

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Heatmap deseq2

I’m using deseq2 for DEA but when I create a heatmap with only DEGs, it looks very strange: I’m not sure whether there are only overexpressed genes or whether the dataset is not normalized properly. I probably made a mistake somewhere in my coding but I don’t know where to…

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Immune-related Prognostic Genes of ccRCC

Introduction Kidney cancer is one of the most commonly diagnosed tumors around the globe.1 According to the statistics from the World Health Organization, annually, there are more than 140,000 RCC-related deaths.2 ccRCC is the most typical subtype of kidney cancer and contributes to the majority of kidney cancer-related deaths.3,4 Until…

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Figure.03

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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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Comparative de novo transcriptome analysis identifies salinity stress responsive genes and metabolic pathways in sugarcane and its wild relative Erianthus arundinaceus [Retzius] Jeswiet

1. Singh, A. et al. Phytochemical profile of sugarcane and its potential health aspects. Pharmacogn. Rev. 9, 45–54 (2015). CAS  PubMed  PubMed Central  Google Scholar  2. Eggleston, G. Positive aspects of cane sugar and sugar cane derived products in food and nutrition. J. Agric. Food Chem. 66, 4007–4012 (2018). CAS …

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Monocle3 differential expression failed when active.assay is not “RNA”

after run estimate_size_factors, data with active.assay = ‘integrated’ works too, but no deg in the result. > [email protected] = ‘integrated’ > cds_raw <- as.cell_data_set(seurat_object) Warning: Monocle 3 trajectories require cluster partitions, which Seurat does not calculate. Please run ‘cluster_cells’ on your cell_data_set object > cds <- cluster_cells(cds_raw) > pr_graph_test_res <-…

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python – NameError: name ‘Seq’ is not defined

I want to fill null value with Average. data2 = data.na.drop(Seq(“code”)).select(avg(col(“code”))) data2.display() This error I got: ————————————————————————— NameError Traceback (most recent call last) <command-1060196488305723> in <module> —-> 1 data2 = data.na.drop(Seq(“code”)).select(avg(col(“code”))) 2 data2.display() NameError: name ‘Seq’ is not defined Read more here: Source link

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Change log2FoldChange range – plotMA

You can use base R graphics to make these plots. The data is sitting there in columns of the res object, so you can filter it directly, and use boolean vectors to pick out the things you need: # make sure there are no NA values sum(is.na(res$log2FoldChange)) # choose some…

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[forlilab/Meeko] PDBQT tree error

[x] I believe this to be a bug with Meeko resulting from OpenBabel issue #2433. I report it here because Meeko has the same error. Environment Information Operating system and version: Centos 7.4 Expected Behavior Example 1. C1(NC2=NC(C3=CN=CC=C3)=CC=N2)=CC=CC=C1 As for example 1 molecule, obabel give a PDBQT file with 2…

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GeneTonic: an R/Bioconductor package for streamlining the interpretation of RNA-seq data | BMC Bioinformatics

1. Van den Berge K, Hembach KM, Soneson C, Tiberi S, Clement L, Love MI, Patro R, Robinson MD. RNA sequencing data: Hitchhikers guide to expression analysis. Annu Rev Biomed Data Sci. 2019;2(1):139–73. doi.org/10.1146/annurev-biodatasci-072018-021255. Article  Google Scholar  2. Conesa A, Madrigal P, Tarazona S, Gomez-Cabrero D, Cervera A, McPherson A,…

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R ggtree: How to label single tree tip with ggtree similar to labeling nodes with geom_cladelabel

I’m having trouble with labeling single tips in my tree with ggtree. I’m trying to highlight and label nodes from a tree with geom_hilight and geom_cladelabel. This seems to work fine with nodes that have more than 1 tree tip, but when I try to label a single tip, I…

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ggplot2 – R ggplot – ploting multiple variables with sub-categories in the same plot with two axes

I have this data: date area people_tested positive_cases positive 2021-12-09 Total 76282.0 402.0000 0.005300000 2021-12-10 Total 84023.0 389.0000 0.004600000 2021-12-09 Total_3da NA 382.3333 0.004900000 2021-12-10 Total_3da NA 377.6667 0.004933333 2021-12-09 Paris_3da 75257.4 NA NA 2021-12-10 Paris_3da 71553.6 NA NA and I would like to create a plot with a line…

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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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Microarray analysis and functional prediction of differentially expressed circular RNAs in acquired middle ear cholesteatoma | BioMedical Engineering OnLine

1. Castle JT. Cholesteatoma pearls: practical points and update. Head Neck Pathol. 2018;12(3):419–29. Article  Google Scholar  2. Xie S, Wang X, Ren J, Liu W. The role of bone resorption in the etiopathogenesis of acquired middle ear cholesteatoma. Eur Arch Otorhinolaryngol. 2017;274(5):2071–8. Article  Google Scholar  3. Bhutta MF, Williamson IG,…

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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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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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r – How to draw boxplot by multiple groups using ggplot2?

I try to get a boxplot with the following specifications for the following variables: assets, liability. My data is firms financial statement and firms are classified big and small firms (categorical variable lbg30). Time (years) is also categorized by two period pre-crisis and post-crisis (categorical variable postcrisis). So I want…

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ggplot: remove lines at ribbon edges

You can remove the border using the colour argument: ggplot(d, aes(Time, y, color = Object, fill = Object)) + geom_line(size = 2) + geom_ribbon(aes(ymin = lower, ymax = upper), alpha = .3, colour = NA) geom_ribbon understands linetype aesthetic. If you want to map linetype to a variable include it…

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python – How to get the Cumulative Distribution Function with PyMC3?

I am trying to recreate the models in John Kruschke’s ‘Doing Bayesian Data Analysis‘ and am currently trying to model ordinal data (chapter 23 in the book. This is the JAGS model that I’m trying to recreate: total = length(y) #Threshold 1 and nYlevels-1 are fixed; other thresholds are estimated….

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r – How to avoid too much space around polar chart in ggplot

This is my dataframe: my_df <-structure(list(Statistic = c(“Shots on target %”, “Shots on target %”, “% of dribblers tackled”, “% of dribblers tackled”, “Ground passes”, “Ground passes”, “Passes Completed”, “Passes Completed”, “Live-ball passes”, “Live-ball passes”, “Passes Attempted (Right)”, “Passes Attempted (Right)”, “Passes Attempted”, “Passes Attempted”, “Successful Pressure %”, “Successful Pressure…

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shade alternate days with POSIXct timestamp data

I can plot a line of a variable vs timestamp (plot p1 below). However, I’d like to shade the plot for alternate days. The data has an entry once an hour for two days. dat <-structure(list(TIMESTAMP = structure(c(2L, 3L, 14L, 19L, 20L, 21L, 22L, 23L, 24L, 25L, 4L, 5L, 6L,…

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Merge and Perfectly Align Histogram and Boxplot using ggplot2

since yesterday I am reading answers and websites in order to combine and align in one plot an histogram and a boxplot generated using ggplot2 package. This question differs from others because the boxplot chart needs to be reduced in height and aligned to the left outer margin of the…

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r – ggplot2 vertical colorbar title right centered

Here is a solution, inspired in this SO post.Note that in the question you have fill = guide_colourbar(.) when it should be colour = guide_colourbar(.). library(ggplot2) ggplot(df, aes(x=img_type, y=metric),show.legend = FALSE) + geom_point(aes(size = abs_corr, colour=corr))+ scale_size(range =c(-0.1,20) )+ scale_colour_gradient2( low = “#7e1952”, high = “#2f7a9a”, space = “Lab”, na.value…

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[Solved] Having two RStudio instances running GRASS simultaneously

for (roads_r in rasters){ # roads_r is a rasterized lines object, value 1 where roads, rest is NA # built a random name (I’m aware I could use tempdir(), but explored this to have files at hand tmp_custom <- paste0(“tmp”, paste0(sample(1:9, 1), sample(1:9, 1), sample(1:9, 1), sample(1:9, 1))) tempDir <-…

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Generating multiple heatmaps with heatmap3 and lapply

Generating multiple heatmaps with heatmap3 and lapply 1 Hey everybody I have a series of .csv files from RNA-seq data stored in a list and I am trying to produce a heatmap for each of them by using heatmap3 function combined with lapply in R, after first converting each of…

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Frontiers | The cGAS-STING Pathway: A Promising Immunotherapy Target

Introduction Invaded by exogenous or endogenous pathogens, the host immune system will be activated accordingly to resist harm and maintain homeostasis, which includes innate immunity and adaptive immunity. As the first line of host immune defense, innate immunity plays a critical role in recognizing extracellular and intracellular pathogens (1, 2)….

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raster – Explicit temp files in rgrass7 / fasterRaster to avoid interferences when running simultaneous R sessions

I’m finding errors using the function fasterRastDistance() in the fasterRaster R library when running the same script in several simultaneous RStudio instances. The error looks like this: ERROR: You must select the PERMANENT mapset before updating the current location’s projection (current mapset is <<UNKNOWN>>) access: Invalid argument ERROR: LOCATION <C:/Users/JavierF/AppData/Local/Temp/RtmpqoyKjm<UNKNOWN>>…

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NA values for mitochondrial gene percentage

NA values for mitochondrial gene percentage 0 I am running Seurat on publicly available dataset of ~400k cells. More than 80% of the cells are returned as NA when I use percentageFeatureSet(object, pattern = “^MT-“). How should I interpret these result? Does this mean the 80% of cells are of…

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Tanzania Independence Day 2021: Google Doodle celebrates Tanzanian Republic Day

Google Doodle observes Tanzania Independence Day, which is additionally now and then alluded to as ” Republic Day,” on December 9, 2021. This public holiday is always celebrated on December 9th. The day celebrates the finish of British rule in Tanganyika in 1961. It was on this day in 1961…

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r – Position Trend line regression equation in ggplot

i am trying to plot trend lines equation with R square for three variable (SA,SA1,SA2) using ggplot geom_smooth(). While plotting three variables i get overlapping equation. I tried to adjust the y lab position using stat_regline_equation(label.y = c(1.78e15,3.9e17,2.5e15)) but miserably failed in doing so. DATA LINK (Requirement: 3 trend lines…

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AYUSH_MALAKAR_HW6.doc – Course IST 687 Assignment HW 6 Name Ayush Malakar Date library’ggplot2#including package#Step-1 AQ_dataset

################################################ Course: IST 687# Assignment: HW 6# Name: Ayush Malakar# Date: 08/17/2021# ###############################################library(‘ggplot2’) #including package#Step-1AQ_dataset<- airquality #loading the dataset into a new variable#Step-2AQ<- na.omit(AQ_dataset) #removing NA’s from the dataset#Step-3 (1)#1x <- ggplot(AQ, aes(x=Ozone)) #defining plot and aestheticsx<- x+geom_histogram(bins =5, colour=’black’, fill=’white’) # defining the shape and structure of the histogramx…

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AYUSH_MALAKAR_HW9.doc – Course IST 687 Assignment HW 9 Name Ayush Malakar Date#library library”kernlab library”ggplot2 library”e1071

############################################### # Course: IST 687 # Assignment: HW 9 # Name: Ayush Malakar # Date: 09/09/2021 # ############################################### #library library(“kernlab”) library(“ggplot2”) library(“e1071”) library(“gridExtra”) #Step 1: Load the data airquality #replacing NA’s with mean values airquality$Ozone[is.na(airquality$Ozone)] <- round(mean(airquality$Ozone, na.rm = TRUE)) airquality$Solar.R[is.na(airquality$Solar.R)] <- round(mean(airquality$Solar.R, na.rm = TRUE)) airquality #Step 2: Create…

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Error while converting Gene ID to Ensembl IDs

I have a DEGs data frame with Gene IDs. Pic for reference below I am trying to convert the Gene_IDs into Ensembl IDs. I have tried the following methods library(“AnnotationDbi”) library(“org.Hs.eg.db”) res3$ensid = mapIds(org.Hs.eg.db, keys=res3$Gene_ID, column=”ENSEMBL”, keytype = “SYMBOL”, multiVals = “first”) The above code converted most of the gene…

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R how to correct for multiple comparisons in ggplot correlations?

I have the following dataset: structure(list(Age_group = structure(c(4L, 2L, 2L, 2L, 4L, 2L, 2L, 4L, 3L, 1L, 2L, 1L, 1L, 4L, 1L, 2L, 1L, 4L, 3L, 4L, 4L, 1L, 2L, 2L, 1L, 2L, 1L, 3L, 3L, 2L, 2L, 3L, 4L, 3L, 2L, 4L, 2L, 2L, 3L, 4L, 4L, 4L, 1L,…

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r – ggplot: multiple time periods on same plot by month

I am trying to plot multiple time-periods on the same time-series graph by month. This is my data: pastebin.com/458t2YLg. I was trying to avoid dput() example but I think it would have caused confusion to reduce the sample and still keep the structure of the original data. Here is basically…

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Probe annotation file for microarray platform MoGene-1_0-st-v1

Hi, I would use the pre-built Bioconductor annotation databases / packages for this array (I have used this array a few times over the years): mogene10sttranscriptcluster.db mogene10stprobeset.db Most likely mogene10sttranscriptcluster.db is what you want: require(mogene10sttranscriptcluster.db) columns(mogene10sttranscriptcluster.db) [6] “ENTREZID” “ENZYME” “EVIDENCE” “EVIDENCEALL” “GENENAME” [11] “GO” “GOALL” “IPI” “MGI” “ONTOLOGY” [16] “ONTOLOGYALL”…

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Google

Google uporablja piškotke in podatke zaradi: zagotavljanja in vzdrževanja storitev, kot sta spremljanje izpadov delovanja ter zaščita proti neželeni vsebini, goljufijam in zlorabam; merjenja dejavnosti ciljnih skupin in statističnih podatkov glede spletnih mest zaradi razumevanja, kako se uporabljajo naše storitve. Če se strinjate, bomo piškotke in podatke uporabili tudi zaradi:…

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WHAT IS NA12878?

WHAT IS NA12878? 1 WHAT? Who? is NA12878? Why did NA12878 become representative? I want to know NA12878 for information! plz~ explain NA12878.!! thank u ! NA12878 • 91 views Login before adding your answer. Traffic: 2185 users visited in the last hour Read more here: Source link

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‘Deprecated’ Error with ngs.plot.r after sys admin update Bioconductor

Loading R libraries…..Done Configuring variables… Using database: /home/yensin/software/ngsplot/database/hg19/hg19.ensembl.genebody.protein_coding.RData Done Analyze bam files and calculate coverageWarning message: ‘isNotPrimaryRead’ is deprecated. Use ‘isSecondaryAlignment’ instead. See help(“Deprecated”) ………………………………………………………………………………………………………………………………………………………………………………….Done Plotting figures…Error in seq.default(min.e, max.e, length.out = ncolor + 1) : ‘from’ cannot be NA, NaN or infinite Calls: plotheat -> ColorBreaks -> seq ->…

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How to extract genomic upstream region of a protein identified by its NCBI accession number?

How to extract genomic upstream region of a protein identified by its NCBI accession number? 1 I have a list of NCBI protein accession numbers. I would like to extract out the upstream genomic region of the corresponding gene’s nucleotide sequence. I will be thankful to you if you can…

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iCOMIC: a graphical interface-driven bioinformatics pipeline for analyzing cancer omics data

Abstract Despite the tremendous increase in omics data generated by modern sequencing technologies, their analysis can be tricky and often requires substantial expertise in bioinformatics. To address this concern, we have developed a user-friendly pipeline to analyze (cancer) genomic data that takes in raw sequencing data (FASTQ format) as input…

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IRE combined with toripalimab versus IRE alone for LAPC

Introduction Pancreatic ductal adenocarcinoma (PDAC) is a lethal gastrointestinal disease with increasing morbidity, which also has a growing impact on cancer-specific mortality worldwide.1 Nearly 40% of all PDAC cases are localized to the pancreas and characterized with the involvement of major vascular structures, leading to unresectable disease without metastases detected…

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Gromacs Contact Map | Contact Information Finder

Listing Results Gromacs Contact Map Contact maps using Gromacs ResearchGate Just Now Researchgate.net View All Contact maps using Gromacs ? I used gmx mdmat in gromacs to create contact maps, but it seems that the mdmat gives the minimum average distance rather than the average centre-of-mass distance. Estimated Reading Time:…

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extract p-value from Tukey test and put in a Table.

Hi, I need to get in a list the values of p adj of multiple comparisons from Tukey test. I report the part of the script that gives me problems: for (i in 1:1293) { p_adjs = rep(NA, 1293) p_adjs = matrix(p_adjs, nrow=1293, ncol=6) if (sum(is.na(matrixDataLog[i,]))<3) { tukey = TukeyHSD(anova)…

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protti source: R/fetch_alphafold_prediction.R

#’ Fetch AlphaFold prediction #’ #’ Fetches atom level data for AlphaFold predictions either for selected proteins or whole #’ organisms. #’ #’ @param uniprot_ids optional, a character vector of UniProt identifiers for which predictions #’ should be fetched. This argument is mutually exclusive to the code{organism_name} argument. #’ @param…

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pandas – DataFrame to CSV save error on Kaggle Python. How to solve?

I’m trying to save a dataframe containing 20 million rows to a CSV format, with this: df_merge.to_csv(‘processed.csv’) After executing the code, I got this error message: OSError: [Errno 30] Read-only file system: ‘processed.csv’ What is this and how can I handle it? NOTE: The code is run on kaggle. Complete…

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Bottom-Up Proteomics and LiP-MS Quality Control and Data Analysis Tools

Peptides are mapped onto PDB structures or AlphaFold prediction based on their positions. This is accomplished by replacing the B-factor information in the structure file with values that allow highlighting of peptides, protein regions or amino acids when the structure is coloured by B-factor. In addition to simply highlighting peptides,…

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