Tag: ATTR
R: MA-Plot
R: MA-Plot plotMA {limma} R Documentation MA-Plot Description Creates an MA-plot with color coding for control spots. Usage plotMA(MA, array=1, xlab=”A”, ylab=”M”, main=colnames(MA)[array], xlim=NULL, ylim=NULL, status, values, pch, col, cex, legend=TRUE, zero.weights=FALSE, …) Arguments MA an RGList, MAList or MArrayLM object, or any list with components M containing log-ratios and…
Bioconductor Package Installation
When I try to install the gtf for hg38 BiocManager::install(“TxDb.Hsapiens.UCSC.hg38.knownGene”) I get the following error: ‘getOption(“repos”)’ replaces Bioconductor standard repositories, see ‘?repositories’ for details replacement repositories: CRAN: cran.rstudio.com/ Bioconductor version 3.14 (BiocManager 1.30.16), R 4.1.2 (2021-11-01) Installing package(s) ‘TxDb.Hsapiens.UCSC.hg38.knownGene’ Error in readRDS(dest) : error reading from connection Per stackoverflow.com/questions/67455984/getoptionrepos-replaces-bioconductor-standard-repositories-see-reposito I…
Loop through columns to generate PCA from DESeq2 data
I’d like to generate a PCA of my bulk RNAseq data, coloured by each of my variables in the DESeq2 object “vsd”. My current code looks like this (to generate a single plot): pcaData <- plotPCA(vsd, intgroup=c(“Age”, “BlastRate”), returnData=TRUE) percentVar <- round(100 * attr(pcaData, “percentVar”)) ggplot(pcaData, aes(PC1, PC2, color=Age, shape=BlastRate))…
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…
Intellia gets upgrade at Brookline amid ‘unchanged’ patent risk on CRISPR/Cas9 technology
Andy/iStock via Getty Images Intellia Therapeutics (NTLA -3.1%) was upgraded by Brookline Capital Management to Buy from Hold with a $91 price target. Brookline analyst Leah Cann said the patent risk is unchanged, but the valuation has become attractive. In February, the U.S. Patent and Trademark Office backed the Broad…
use tcgabiolinks package to download TCGA data
TCGA Data download in terms of ease of use ,RTCGA The bag should be better , And because it’s already downloaded data , The use is relatively stable . But also because of the downloaded data , There is no guarantee that the data is new .TCGAbiolinks The package is…
Estimating prediction accuracy of a Cox survival model using sbrier (R)
You can use the pec package, instead. Example: library(pec) set.seed(18713) library(prodlim) library(survival) dat=SimSurv(100) pmodel=coxph(Surv(time,status)~X1+X2,data=dat) perror=pec(list(Cox=pmodel),Hist(time,status)~1,data=dat) ## cumulative prediction error crps(perror) # between min time and 1 ## same thing: ibs(perror) library(survival) library(ipred) data(“DLBCL”, package = “ipred”) smod <- Surv(DLBCL$time, DLBCL$cens) coxmod <- coxph(smod ~ IPI, data = DLBCL) coxmod Call:…
Bug#1004869: python-xarray: autopkgtest regression on i386
Source: python-xarray Version: 0.21.0-1 X-Debbugs-CC: debi…@lists.debian.org Severity: serious User: debi…@lists.debian.org Usertags: regression Hi Maintainer python-xarray’s autopkgtests are failing on the i386 architecture [1]. I’ve copied what I hope is the relevant part of the log below. Regards Graham [1] ci.debian.net/packages/p/python-xarray/unstable/i386/ =================================== FAILURES =================================== ___________________ test_interpolate_chunk_advanced[linear] ____________________ method = ‘linear’ @requires_scipy @requires_dask @pytest.mark.parametrize(“method”, [“linear”, “nearest”]) @pytest.mark.filterwarnings(“ignore:Increasing number…
clusterProfiler won’t read gene list
clusterProfiler won’t read gene list 0 So I have a list of DE genes that I would like to analyse for enriched GO and KEGG terms. I was going to use clusterProfiler for this, but I can’t seem to get past constructing the gene list. I have followed the vignette…
Intellia Therapeutics Set to Enter Clinic with First Solo Ex Vivo Candidate
Courtesy Intellia Therapeutics Intellia Therapeutics is celebrating another first today as the U.S. Food and Drug Administration (FDA) has accepted the Investigational New Drug (IND) application for NTLA-5001, its first wholly-owned ex vivo CRISPR genome editing candidate. NTLA-5001 is being developed for the treatment of acute myeloid leukemia (AML). Intellia…
Tools for Normalizing and Comparing ChIP-seq Samples
data(H3K27Ac, package = “MAnorm2”) attr(H3K27Ac, “metaInfo”) ## Make a comparison between GM12891 and GM12892 cell lines and create an MA ## plot on the comparison results. # Perform MA normalization and construct bioConds to represent the two cell # lines. norm <- normalize(H3K27Ac, 5:6, 10:11) norm <- normalize(norm, 7:8, 12:13)…
Breakout “CRISPR platform” company Mammoth Biosciences is officially a unicorn
The CRISPR-based biotech startup Mammoth Biosciences is officially a unicorn, the company says. The billion dollar valuation comes on the back of a $150 million series D round led by Redmile Group, with participation from Foresite Capital, Senator Investment Group, Sixth Street, Greenspring Associates, Mayfield, Decheng Capital, Plum Alley and…
Biotech Company Driven by Cutting Edge Science and Patients, Not Ego
Photo courtesy of Intellia Therapeutics Sports fans know that nothing is better for the chemistry of a team than winning, and on the CRISPR field, Intellia Therapeutics is on a winning streak. On June 26, Intellia set the biotech world on fire, announcing the first-ever clinical data supporting the safety…
DESeq2 analysis example, opinions?
Hello everyone, Purpose of the analysis: In there a difference between TOV21G-PacR and TOV21G-cont, and between the PacR and cont? My question is if this analysis makes sense for you? I am analyzing this particular gene set (GSE172016). Within the data there are two cell lines (“OVCAR3” and “TOV21G”) and…
Extract multiple times a fasta sequence from a list by name
Hi everybody! I have uploaded on R a list of 9K fasta sequences, on which 40K SNPs map to – which means, some sequence host 1+ SNP. I have a R object (and a vcf as well) with the fasta sequences names and the SNP positions and I want to…
Therapeutic Advances Using In Vivo CRISPR Genome Editing
Broadcast Date: September 16, 2021Time: 8 am PT, 11 am ET, 17:00 CET When CRISPR-Cas9 gene-editing technology exploded onto the life science stage almost a decade ago, it was widely touted as a potentially curative therapy for many genetic diseases, using various ex vivo and in vivo delivery methods. That promise is…
haplotype network analysis with Pegas package in R
Hi all, I am very new in haplotype analysis and have faced with some problems that I do not know how to solve. I want to generate haplotype networks for sodium channel (DKr gene) in anopheles species. I have converted my vcf into fast file, produced multiple alignment with ClustalW…
spots not filling the whole tissue image
Issue with Seurat SpatialPlot: spots not filling the whole tissue image 0 In Seurat, SpatialPlot generates a plot with an enlarged/expanded image of tissue section as compared to the original spot image. This seems to happen on the relatively small image with a number of spots around 500. I ‘d…
Another Milestone for CRISPR-Cas9 Technology: First Trial Data for Treatment Delivered Intravenously
Unlike most other CRISPR/Cas-9 therapies that are ex vivo treatments in which cells are modified outside the body, this study was successful with an in vivo treatment Use of CRISPR-Cas9 gene editing technology for therapeutic purposes can be a boon for clinical laboratories. Not only is this application a step…
Converting an S4 object into a dataframe in R
I have an S4 object named ‘res’ which I got while using an R package called RDAVIDWebService. I can’t seem to find a way to convert this object into a dataframe in R. I tried using the function ‘as.data.frame(res)’ but it throws this error: > as.data.frame(res) Error in as.data.frame.default(res) :…
