Biostar

34,946 results • Page 1 of 699

**Location** Department of Neurology, NeuroGenomics and Informatics Center, Washington University in St. Louis **Description** The Washington University School of Medicine, Department of Neurology, has an opening for a post- doctoral research associate to join the [Belloy lab][1] in the NeuroGenomics and Informatics Center (NGI). The successful candidate will be involved in projects to perform…

Genomics Alzheimer multiomics neuroimaging

updated 1 hour ago • belloy

if everything is correctly implemented. ``` # Calculate TPM for RNA-seq data having a vector of gene lengths x <- RNA_counts/geneLength norm_RNA_counts <- t(t(x) * 1e6 / colSums(x)) # Calculate TPM for miRNA-seq data library_sizes_miRNA

TCGA normalization TPM miRNA

updated 1 hour ago • Ngrin

of each step in the process. For instance, the first step, 'Exclude', assesses whether any genes in my AnnData object correlate with lateral genes, which, from my understanding, is undesirable. What should I do with...this information? The guidelines aren't clear, and I'm also unsure what qualifies as a lateral gene. Moreover, I'm confused about the differences between the 'Direct' step and the…

single-cell scanpy cells meta python

updated 3 hours ago • JACKY

items. I have the following variables: gender - male/female percentage x -low/high gene y - continuous (gene expression of gene y) I built the model with: coxph(formula=Surv(PFI.t,PFI.e)=gender + percentage:gene_y...0.05 '.' 0.1 ' ' 1 I have two questions: 1) Is my interpretation correct that with increasing gene expression of gene y the risk of dieing increases for the gro…

Cox

updated 6 hours ago • Bine

16 distinct clusters. Now, I need to label these clusters based on differentially expressed genes and determine their corresponding cell types using marker genes. My question is regarding the optimal number of marker...genes to consider. Should I focus on the top 4 genes, top 20 genes, or all significant genes? Additionally, if the markers exhibit

scRNAseq

updated 6 hours ago • MAPK2

and linkage disequilibrium, and annotated based on variant effects relative to the B73 RefGen_v5 gene annotations. submitted by: [Istvan Albert](https://www.biostars.org/u/2/) --- ### [PhyKIT: A Multitool for Phylogenomics[v1] | Preprints.org...biases in phylogenomic data sets, (iv) identifying radiation events or lack of resolution using gene support frequencies, and (v) conducting evolution…

herald

updated 8 hours ago • Biostar

gene-specific coverage from the BAM file def calculate_gene_coverage(gene_info, bam_file): gene_coverage = {} for gene_id, gene_name...bam_file = 'ILS_W_V_558_S2_R1_001_val.bam' # Parse GTF file to get gene information gene_info = parse_gtf(gtf_file) # Print gene information print("Gene Information:") for gene_id, gene_name in.…

linux WGS Bioinformatics SARS CoV2

updated 9 hours ago • Adyasha

In gene ontology if 2 genes are taking part in same biological process can they be considered homologs

gene-ontology

updated 9 hours ago • beshka194

Hello, I ran RGI tool and obtained AMR gene count data using MAGs (not reads) as shown below: rgi main -i sample1.fasta -o sample1 -a DIAMOND -n 24 --clean First question...Hello, I ran RGI tool and obtained AMR gene count data using MAGs (not reads) as shown below: rgi main -i sample1.fasta -o sample1 -a DIAMOND -n 24 --clean First question is

abundance RGI

updated 9 hours ago • arshad1292

Hi everyone, is the same as this post title. Our partners and I have established a bioinformatics algorithm competition to promote the attention and development of spatial transcriptomics and solicit new methods for multi-modal data and multi-omics data analysis. **[This is not a commercial. The entire contest is for public benefit.]** It names: **[2024 Mammoth International Contest On Omics Sc…

cell-clustering Spatial-transcriptomics

updated 9 hours ago • MICOS

there be a different way for looking at possible sample/condition-specific transcripts of known genes? </guide_gff

stringtie stringtie-merge

updated 1 day ago • DGTool

Hi I did gene expression analysis with dseq2 I'm trying to understand if positive logfoldchange mean mot expression in the mutant...countFiles[i]) counts <- read.table(countFilePath, header = FALSE, col.names = c("gene", sampleNames[i])) countDataList[[i]] <- counts } # Merge all count data into a single data frame by gene mergedCounts <- Reduce...function(x, y) merge(x…

DESEQ2 logfoldchange

updated 2 days ago • adi.gershon1

to filter cells with high Malat-1 expression? Or would it be better to regress out the Malat-1 gene during scaling

single-cell

updated 2 days ago • carolofharvest

Hi all, I am trying to visualize the result of gene set enrichment analysis. This is my plot and the code in R. Is there any way that I can change the code then the text (names...Hi all, I am trying to visualize the result of gene set enrichment analysis. This is my plot and the code in R. Is there any way that I can change the code then the text (names of...gene sets) to be sorted as the examp…

barplot RNA-seq GSEA enrichment

updated 2 days ago • Rob

Hi! I can't solve this problem. Here there is my code, can someone help me to find and solve the code? I am stuck because I can't normalise my data, as it says "DGEList function not found", but maybe there are other errors too. Thank you ```r if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("genefu") if (!require("BiocManager", quietly =…

DGEList R

updated 2 days ago • Natali

Hello, I´m new in NGS and I´m trying to run fastq screen but when I do it, it send me these message: "Aligner (--aligner) not specified. Did not find Bowtie/Bowtie2/BWA paths and/or index files Please check: you have provided the full path to the aligner INCLUDING the executable filename Please check: the specified genome indices comprises the full path AND the basename of the index files See doc…

BWA Bowtie2 FastqScreen

updated 2 days ago • Ximena

Hi, I'm working on a project where we aim to predict the immunogenicity of neoantigens from patients with pancreatic cancer cohorts from the ICGC. We only have access to the VCF files of the patients, from which I extracted the SNV and indel variants for each patient, filtering them to retain only the variants affecting protein-coding genes (I have retained the unfiltered ones as well). Curren…

formats vcf fastaq HLA_imputation HLA_typing

updated 3 days ago • Javier

I am trying to find raw counts for differential gene expression analysis using stringtie but it is getting me error as below. i have used featurecounts software for the...I am trying to find raw counts for differential gene expression analysis using stringtie but it is getting me error as below. i have used featurecounts software for the same

stringtie RNA-seq

updated 3 days ago • ahmad.sajad4541

1], there are different columns in the file. However, as these MAF files only contains mutated genes (IND, DEL, SNP...), I am not sure how I can identify WT genes for each patient. The resulting data frame I would like to have is a matrix...of WT, and MUT with patient ID as row index and gene names as column names. [1]: https://docs.gdc.cancer.gov/Encyclopedia/pages/Mutation_Annotation_F…

TCGA maf mutation

updated 3 days ago • Yuju

![enter image description here][1]to know the type of variant and know if ATM has a genetic predisposition to melanoma [1]: /media/images/9e7ad951-22dc-409a-b6dc-177b75e6

genetic Variant predisposition

updated 3 days ago • mikemakaveli1

![enter image description here][1] [1]: /media/images/5b236885-bbd9-43b9-bd3c-e21835af

IGV variant gene

updated 3 days ago • mikemakaveli1

used to determine deletions and duplications on mtDNA. The original script did not include the gene names. Therefore, I would like to add the gene names along the gray axis, and for this, I have a bed file with the coordinates

plot mtDNA R

updated 3 days ago • marco.barr

I request you for small help with Augustus gene prediction tool. I am using Augustus for annotation of a *de novo* assembled genome of a plant species. Reading the Augustus...is available [here][1] I would like to know how I can make use of this data for a more accurate gene prediction. Any input is highly appreciated. [1]: https://docs.google.com/spreadsheets/d/1jXWUXEyUeQ4AYklN4-iheNW5zmO…

augustus annotation assembly genome

updated 3 days ago • Vijith

MNP, ... annotation) My problem is clustering result is not clear. Clusters have same markers are located in different space at UMAP. And some cell clusters don't have any marker genes. I changed PCA dims(high dims) and harmony

Seurat scRNA-seq Harmony DoubletFinder Merge

updated 3 days ago • Jeyong

Hi, I'm analyzing my chipseq data and am encountering some issues. I'm new to chipseq so any help is appreciated. Here is my pipeline: I have triplicates for my treatment and triplicates for control. 1. Align filtered & trimmed Illumina fastq (paired end) to ref genome using bowtie. 2. Convert SAM file to sorted BAM file using samtools. 3. Use MACS2 to call peaks. This was done on Gala…

MACS2 DiffBind ChIP-seq

updated 4 days ago • yvonneh

I'm new to working with TCGA, but I'd like to look at RNAseq expression of a certain gene between responders and non-responders of a given treatment. My understanding is there are a number of tools for accessing

TCGA RNA-seq

updated 4 days ago • Qroid

Hi, everyone! I have a question about why does gene length effect the normalisation. I understand that the sequencing depth influence the normalisation, so we need to...Hi, everyone! I have a question about why does gene length effect the normalisation. I understand that the sequencing depth influence the normalisation, so we need to remove...the influence of sequencing depth. Many tutorials have…

RNA-seq CPM sequencing

updated 4 days ago • Chen

which RNA:DNA hybrids (R-loops) regulation exerts its influence on biological systems in terms of gene regulation and genome stability. We are looking for a highly motivated postdoctoral researcher, who will develop computational

NGS Genomics Post-doc R-loops

updated 4 days ago • 4r-rtg

Hello everyone! I'm comparing the expression of sets of miRNA data in order to identify what are the miRNAs that have significant similarity in their expression in two different samples. I have conducted DGEs using NOISeq, and was succeeded in identifying significant differential expressed genes. By filtering out those that are not significantly different, I don't think that it is correct to a…

Gene-Expression RNA NOISeq DGE

updated 4 days ago • alifafiq1

type and mutant samples. I normalized using DESeq2 and obtained a list of differentially expressed genes. However, some of the differentially expressed genes have raw counts with differences of over 200-fold between biological

RNA-seq TPM Normalization DESeq2

updated 4 days ago • JH

I'll call these two reciprocal crosses C1 and C2. The main question I am interested in is how gene expression in the hybrids differs from the two parents, to identify transgressively expressed genes. We can ask that...to decide for which genes we can pool the reciprocal crosses, and for which genes they should be considered separately. The benefit of being able...to pool them together for some…

edgeR

updated 4 days ago • Rhiannon

Hi, can you help me with this: I have a gene of interest, i.e, AhR. I want to download its eQTL data for all tissues from GTEx. I find I cannot do it from GTEx Portal: https

eQTL GTEx

updated 4 days ago • Jeol

TE repeats? 2. What are the subsequent downstream processes that I can go for; as of now, I assume gene prediction using Augustus is a better move. Any other suggestions

sequence annotation repeatmasker illumina assembly

updated 4 days ago • Vijith

are looking for is the relationship between the different stages and the unique patterns that these genes show, of course we have 13 but while I deduce it I wanted to know a good suggestion or things that I should take previously...2 replicates except for the 2nd plot, which has 4. Subsequently, a filtering of 10% variability in gene expression was done, basically making an average, then the stan…

RNA-seq ontology GO

updated 5 days ago • Oscar

typed them but I feel that this is not discriminatory enough. I have seen papers make a core-plasmid gene analysis using Roary and generate a phylogenetic tree on this basis (the plasmids were all from the same family and similar

bacteria plasmid wgs hybridassembly sequencing

updated 5 days ago • nicole.kavanagh

Dr. Michael Love Dear Sir, Sir I have a Dataset of which I did mapping, and filtered out the genes, and then put it as an expression data in DESeq2, these are some problems I would like to address. when I put in the dataset...am not able to run it for DEG analysis because system asks me to remove the first column which is of gene names, and the even if I run it, it gives me only the number …

deseq2 R

updated 5 days ago • jagdish7921

object. After selecting specific terms, cneplot is black and white without any nodes. only showing gene and terms names and lines between them. nodes are not showing up. These are package details and codes I used. ```r library(RColorBrewer...1] [1]: /media/images/6c5488cc-ab70-44f1-a8b7-a9d93f8a As you can see there is no color for genes and terms and even nodes are not appearing. Please …

cneplot

updated 5 days ago • Dr Huma Naz

m trying to calculate adjusted pvalue in R. Let's say I have pvalues of spearman correlation from 5 genes and 2 metabolites (10 tests were happened). I can make the outcome into matrix below: ``` Metabolite1 Metabolite2 Gene1 0.1539985

statistics R p-value

updated 6 days ago • Jonathan Yoou

I am trying to extract all the genes that are present in a particular GO term in Arabidopsis. I was able to do so with this code, ```r go.trial <- getBM(attributes

r RNA-seq

updated 6 days ago • Sudip

FeatureCounts tool on the BAM file using the GTF file, I am unable to find any variability in the gene counts. Instead, I am only getting '0' values for each gene count. Could you please suggest the possible reasons behind this...could provide some guidance on how I can troubleshoot and resolve this problem to obtain meaningful gene expression results from the reference-based mapping

featureCounts

updated 6 days ago • Ravita

Hello everyone! Is there a way to introduce specific SNPs on the fasta sequence of a gene? I am working on a Pharmacogenetics project and I want to simulate reads for specific haplotypes of PGX genes. Therefore...I want to introduce in the FASTA of a specific gene (e.g., CYP3A4), the specific variants that would define a specific haplotype (e.g., rs 27371759 that defines haplotype CYP3A4

simulation snps haplotypes pharmacogenetics

updated 6 days ago • Riccardo

the command I run for linkage pruning: plink2 \ --vcf ${FILE}.vcf \ --allow-extra-chr \ --set-all-var-ids @:# \ --indep-pairwise 50 10 0.3 \ --make-bed \ --out ${FILE}_pruningFact.0.3 Here the error I'm getting: Error: chrX is present

PLINK2

updated 6 days ago • 8armed

method can be used to integrate these datasets. Second, the transcriptomics data has over 20,000 gene information, and the proteomics has about 1,000 gene information. I'm curious about the potential issues that might arise

OMICS

updated 6 days ago • 이민경[학생](대학원 융합의과학과)

analysis using a Tomato genome downloaded from [this page][1], I would like to perform a Gene Enrichment analysis on the differentially expressed genes. However, I have never used a GOterm.txt (from [here][2]) as a reference

RNA-Seq GO

updated 6 days ago • Hamtaro

I'm a beginner in bioinformatics and I have some question about cmap, precisely, regarding Landmark gene selection. I am grateful for all of your responses. here are a few questions. It's a question about paper "A Next Generation...Profiles. Subramanian A, Narayan R et al 1. I want to learn about the Affymetrix HGU133A microarray gene expression dataset that was exactly used when choosing the 97…

L1000 landmark-gene cmap

updated 7 days ago • kim

checkv for quality assessment. Checkv is not properly working . It continuously shuts down in the gene-calling step. Can anyone assist in rectifying this issue? $ checkv end_to_end "/mnt/d/metagenomic works _project/New_analysis_work...contamination [1/8] Reading database info... [2/8] Reading genome info... [3/8] Calling genes with prodigal-gv... Error: 8 prodigal-gv …

viromics metagenomics

updated 7 days ago • Petchimuthu

2] The "columns" on these p-values are weird, and do not seem related to any particular biology (gene, promoter, or region). I saw that in [a tutorial from here][1] the m-values are used instead of beta, but they use also a chip-based

EM-seq methylation

updated 7 days ago • Lluís R.

with the row /locus tag? The reason is that in CLC it's useful to have the information about the gene product in the first /element, so that i can read the product name when i pass my pointer on the first element. That is, from

gbkformat

updated 7 days ago • alenew.am

ID names gpl <- getGEO('GPL570', destdir=".") probe.gene <- Table(gpl)[,c("ID","Gene Symbol")] colnames(probe.gene) <- c("ID","Symbol") probe.gene <- subset(probe.gene, Symbol != '') ids <- probe.gene ids$Symbol <- data.frame

limma ArrayExpress DifferentialExpression GEOquery

updated 7 days ago • SSSJec

Istvan Albert](https://www.biostars.org/u/2/) --- ### [Exploring the Genetic Basis of Variation in Gene Predictions with a Synthetic Association Study | PLOS ONE](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0011645

herald

updated 7 days ago • Biostar

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