Biostar

16,505 results • Page 1 of 331

and deep learning molecular generation. Currently, I am looking for opportunities in the fields of bioinformatics or drug design, either as a job or a postdoctoral position. I am also open to collaboration with like-minded

search job

updated 3 hours ago • tulip

Dear all, there are only 4 seats left for the upcoming online course "BIOINFORMATIC ANALYSIS OF TRANSPOSABLE ELEMENTS ". Dates: June, 3th-7th ---------- > Course website: https://www.physalia-courses.org...Dear all, there are only 4 seats left for the upcoming online course "BIOINFORMATIC ANALYSIS OF TRANSPOSABLE ELEMENTS ". Dates: June, 3th-7th ----------…

GenomeAssembly Transcriptomics TransposableElements ManualCuration

updated 3 hours ago • carlopecoraro2

for allele specific PCR I designed the forward primers for amplification of normal allele and for mutant allele and reverse allele but what I did was I designed the primers in such a manner that the forward primer began like from the beginning of the reverse strand and the reverse primer began somewhere in the middle of the sequence and not at the end of the sequence. My question is will this cau…

PCR laboratory molecularbiology genetics bioinformatics

updated 22 hours ago • beshka194

i],col="gray40") radialtext(mt.axis$name[i], center=c(400,400),deg=mt.axis$deg.axis[i],start=416,nice=T,col="gray30") } with(dat[order(dat$value),],draw.arc(400,400,radius,deg1=deg1,deg2=deg2, lwd=lwd.arc,col=col)) dev.off

plot mtDNA R

updated 2 days ago • marco.barr

489201 # maximum duplicate fragments in control = 1 # Redundant rate in control: 0.14 # d = 210 chr start end length abs_summit pileup -log10(pvalue) fold_enrichment -log10(qvalue) name NC_014034.1 513165 513418 254 513402

MACS2 DiffBind ChIP-seq

updated 2 days ago • yvonneh

completed scientific university degree - A doctorate (PhD) in a field relevant to the position (eg. Bioinformatics or related field) - Strong programming skills and knowledge of statistical methods - Familiarity with Linux

NGS Genomics Post-doc R-loops

updated 3 days ago • 4r-rtg

Hi there, Apologies if this is a silly question but my bioinformatic experience is quite limited and unfortunately entirely self-taught (I am a PhD student). I was hoping for some

bacteria plasmid wgs hybridassembly sequencing

updated 3 days ago • nicole.kavanagh

to NumPy. However, operations on non-numeric data were slow – the reason why many of the widely used Bioinformatics tools were written in low-level languages. **What is not so great about Bioinformatic tools written in low-level...language as a tool that serves the purpose and needs is useful. I’ve been a user of many popular bioinformatics tools written in low-level languages and I’ve only gre…

BioNumPy Python NumPy

updated 5 days ago • Chakri

second_sample_id} \ --normal-sample !{third_sample_id} \ --max-reads-per-alignment-start 90000 \ --bam-output "result/!{tumor_sample_id}${PREFIX_FOR_OUTPUT}${part_prefix}.realigned.bam" \ --bam-writer-type CALLED_HAPLOTYPES...third_sample_bam} \ --tumor-sample !{tumor_sample} \ --max-reads-per-alignment-start 90000 \ --bam-output "result/!{t…

cancer mutect variant-calling GATK somatic-variants

updated 5 days ago • Alexandros

www.ecseq.com/summer-school][1] In a nutshell: - **Learn** the essential computing skills for NGS bioinformatics - **Understand** NGS analysis algorithms (e.g. read alignment) and data formats - **Use** bioinformatics tools for handling...course is to get a deep understanding in Next-Generation Sequencing (NGS) with a special focus on bioinformatics issues. Advantages and disadvantages of cu…

DNA-seq variant-calling RNA-seq illumina transcriptomics

updated 5 days ago • David Langenberger

Hello, I'm a student new to bioinformatics. First, we have transcriptomics data with three replicates and proteomics data with two replicates. I would

OMICS

updated 5 days ago • 이민경[학생](대학원 융합의과학과)

Hello, I'm a beginner in bioinformatics and I have some question about cmap, precisely, regarding Landmark gene selection. I am grateful for all of

L1000 landmark-gene cmap

updated 5 days ago • kim

The **Biostar Herald** publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed. You...The **Biostar Herald** publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed. You too can submit [links here](/herald/). Thi…

herald

updated 6 days ago • Biostar

Dear all, There are still 4 seats available for the onlineccourse on Genome Annotation, which will run from the 13th to the 16th of May. ---------- Course website: https://www.physalia-courses.org/courses-workshops/genome-annotation/ Recent technological advancements in long-read DNA sequencing, coupled with a significant reduction in costs, have rendered the generation of genome assemblies f…

Genome-Assembly Genome-Annotation

updated 6 days ago • carlopecoraro2

am not a bioinformatician by training but am currently learning and trying to develop this skillset starting with the assembly of a new genome, so I appreciate all the help in advance. I am using the VGP genome assembly pipeline...Hi-C data from pooled, unrelated individuals. I am now trying to use this data for scaffolding, starting with pre-processing the Hi-C data by mapping with BWA-MEM2 a…

GenomeAssembly BWA-MEM2 Hi-C

updated 6 days ago • Winter

Hello, I am new to bioinformatics and I have a microbiology background. I am trying to reproduce this same data from the paper [Whole-genome...Hello, I am new to bioinformatics and I have a microbiology background. I am trying to reproduce this same data from the paper [Whole-genome sequencing

WGS Bacterial-Genomics

updated 6 days ago • Ruqaiya

of floating point numbers. I have followed the typical limma-voom workflow (https://ucdavis-bioinformatics-training.github.io/2018-June-RNA-Seq-Workshop/thursday/DE.html) up to the point where it is time to fit the

limma voom R

updated 8 days ago • pairedttest

Hello, I'm doing my masters on Bioinformatics and, as expected, I've hit a sort of roadblock of which I'm unsure how to proceed (my PI isn't very well versed on...bioinformatics). We are researching different treatments for a DSS-induced colitis model in mice. We usually go about this

RNA-Seq edgeR

updated 8 days ago • Guille

in a post title was tricky, so I apologize if the title is unclear. I'll explain in detail below. To start, I have two bed files, one with non-overlapping regions of varying sizes, and one with SNP positions: $ cat A.bed chr1 65564...bed file, and only print these combinations to a new bed file if the SNP is +/- 250,000 bp from the start of the region in A.bed. So, the third bed file, C.…

SNPs BED eqtl bedtools

updated 9 days ago • J

1. Take the genomic VCF file (pf7K covering ~20K genomes). 2. Subset it using gene coordinates (start and end coordinates) and only considering Variants with "PASS,." filter using bcftools 3. Running ka_ks.py on the resulting

dnds kaks VCF

updated 9 days ago • rohitsatyam102

I am using bat (rhinolophus sinicus) snRNA-seq brain samples located [here][1]. The associated paper is located [here][2]. The samples were prepped with the MGI DNBelab C4 scRNA Preparation Kit and were sequenced on the BGI DNBSEQTM technology platform. I downloaded all the bat brain tissue samples with parallel-fastq-dump. Below is an example of downloading a single sample. parallel-fastq-…

STARSolo scRNA-seq STAR snRNA-seq MGI

updated 11 days ago • atowns21

with n_obs × n_vars = 14872 × 36601 obs: 'batch', 'cluster' var: 'Accession', 'Chromosome', 'End', 'Start', 'Strand' obsm: 'X_umap' layers: 'matrix', 'ambiguous', 'spliced', 'unspliced' I generated this object by combining loom files and

loomfile scvelo scipy annData numpy

updated 11 days ago • Kash

herald

updated 11 days ago • Biostar

I created a Seurat object for each one and then merged those 2 Seurat objects together... I just started with scRNA-seq analysis and not sure if this is the correct way to go about it... # Integrate the datasets merged.Seurat

clustering subclustering scRNAseq

updated 11 days ago • alphaflylizard

I am new to the field of bioinformatics and would like to buy a computer for my lab that allows the analysis of several single cell samples, probably

updated 11 days ago • Estevão

I have a large data of virus genome sequences from NCBI but they have internal stop/start codons warning in codonw software due to which i'm not able to analyse them. Since then I've tried using EMBOSS explorer

rscu codonw

updated 12 days ago • SHREYA

I've compiled a table containing DMRs with annotations, including columns such as seqnames start end width strand pvalue qvalue meth.diff annotation geneChr geneStart geneEnd geneLength geneStrand geneId distanceToTSS

rrbs methylkit

updated 12 days ago • Srinka

I need some advice for the new task I have to process. I am new to Bioinformatics and I have to perform QC of the bulk RNAseq data. I have successfully ran Fastqc and multiqc and after seeing

RNA-seq QC Trimmomatic

updated 12 days ago • dxj294

Hello, I am looking for recommendations for bioinformatics tools to perform gene family analysis. I'm currently reviewing CAFE: Computational Analysis of gene Family

Genome gene-family

updated 12 days ago • sansan_96

Hello all, This is probably not a bioinformatics question directly but I am a bioinformatician who has gotten involved with immunology/virology recently...for conferences/ do you have any recommendations for conferences which would also be open for some bioinformatics-based data? So far, I have found: [ECI-2024][1] (I unfortunately missed their submission deadline) and [18th Vaccine

virology conferences immunology

updated 13 days ago • manaswwm

bulk RNA-seq data of tumor samples and matched normal samples. I want to know if there are any bioinformatic tools to detect the somatic variation of tumor samples based on RNA-seq data? Can GATK do this task? Thanks in

RNA-seq variation somatic

updated 13 days ago • feather-W

UK Contract Duration: 2 years (Project based contract) Grading: Grade 6 (Monthly salary starting at £3,456 after tax) + Other paid benefits and allowances based on circumstances Closing Date: 19 May 2024 Reference...researchers, data generators and user communities **You have** - A post-graduate degree in bioinformatics, biology, computer science or a related field or equivalen…

ebi embl genomics ensembl

updated 13 days ago • Ben_Ensembl

Location: EMBL-EBI, Hinxton near Cambridge, UK Contract Duration: 3 years (Grant based contract) Grading: Grade 7 (monthly salary starting at £3,934 after tax) + other paid benefits based on personal circumstances Closing Date: 5 May 2024 Reference Number: EBI02236 [Apply now][1] Ensembl is seeking an enthusiastic Project Leader to join our Outreach team. Ensembl develops free, comprehensi…

ebi embl genomics ensembl

updated 13 days ago • Ben_Ensembl

Hello, I've newly started learning bioinformatics. I wonder how to infer regulons from an expression matrix (row=genes, columns=samples) in R

VIPER MARINA ARACNe

updated 13 days ago • Biostars2200

Hi there I recently start working with some archaic samples (aDNA), specifically two high coverage samples of Neanderthal and Denisova. The latter

samtools bam

updated 14 days ago • Matteo Ungaro

the assembly. I filtered a list of transcripts for primer design, but most of the transcripts do not start with start or stop codons. What factors should I consider for designing primers for those transcripts without start

Primers TRINITY

updated 15 days ago • mathavanbioinfo

Note: I am very new to bioinformatics! I am on a Windows 11 machine using BLAST+ 2.15.0 to run blastp queries against a custom database of shotgun

shotgun metagenomics blastp taxonomy

updated 15 days ago • rebecca.calvo

most the final products have somewhat similar scRNA profile, however I do see variability in the starting material profile. What is the best way to determine the homogeneity and heterogeneity based on cluster frequency...Statistical method to show that the final product is homogeneous irrespective of heterogenous starting material, PCA or cluster frequency. How can I determine the inter and in…

CV PCA scRNA Cluster-Frequency

updated 15 days ago • Nitin

opt/R/4.2.3/bin/R # tell Rstudio which version to use from terminal rstudio # now starting RStudio from the terminal runs R version 4.2.3 (clicking on the desktop icon will still use the default R version

R Ubuntu Linux Bioconductor Rstudio

updated 15 days ago • BioinfGuru

using karyoploteR. My dataset looks like this (with made up examples below): - chromosome number - start: denotes start position of copy number variation - end: denotes the end position of the variation on the chromosome - ploidy...log2_ratio chromosome start end ploidy 1 58865614 58865899 3.512352 2 …

Copy-number-variation genomics

updated 16 days ago • Emmi

of mitochondrial genes compared to other cells after thresholding (10%). Low expression of genes starting with Rmrp, Mrpl, and Mrps. Low expression of ribosomal genes (genes starting with Rpl or Rps). Very high expression of

single-cell

updated 16 days ago • Kazo

I think I run in something of a non-concordant result and I wanted to check out here for some advice. Starting at the SNP calling with ANGSD, I used the following script (notice I changed file names): ``` #!/bin/bash #SBATCH --account my_account...100 \ --min_maf 0.05 \ --n_threads 40 \ --out $OUTDIR/ANGSD_SNPcalls.ld ``` And here is where I start to doubt the process. The output is enormous, p…

lcwgs ngsTools ANGSD genomics

updated 16 days ago • DanielEB_fisk

Hi, I am a beginner in bioinformatics and I would like to learn the basic pipeline for quantifying expression of rna sequences from transcriptomic...gi|126697566|ref|NC_009089.1|:1-1320 0 1320 7904 Basically it tells me the location(start 0, end 1320) and the count (7904). How do I take this data and figure out which exact genes they relate to? I want to get the read

differential-expression transcriptome

updated 16 days ago • siddharth.patel.153

test this model on a different dataset. Ideally I should remove the study specific effects before I start. But if you put the new data, together with the old data into `removeBatchEffects` my intution is that the data from study

limma machine-learning batch-effect

updated 16 days ago • i.sudbery

Update**: Our manuscript has been published in Bioinformatics -- https://doi.org/10.1093/bioinformatics/btx635. **Abstract**: We propose a data-adaptive, non-parametric, and non

RNA-Seq scRNA-Seq R Batch-Effect

updated 16 days ago • Ar

Hi! I'm new at bioinformatics and I'm working with a project where I combine several datasets from GEO. I retrieve the data from GREIN(GEO

Batch-effect transcriptomics

updated 16 days ago • BioQueen

12_* **But it gave error;** *-bash-4.2$ ./generate_index.sh Apr 17 10:17:17 ..... started STAR run Apr 17 10:17:17 ... starting to generate Genome files Apr 17 10:21:17 ..... processing annotations GTF Apr 17 10:21:48 ... starting

align RNA-Seq linux STAR

updated 17 days ago • n_navy

Hi there, I am wondering how to remove batch effect on segmented_scna data downloading from TCGA PANCANA project. The demo of data format is as following: ``` Sample Chromosome Start End Num_Probes Segment_Mean TCGA-KL-8323-11A-01D-2308-01 1 3218610 104558357 58272 0.0026 TCGA-KL-8323-11A-01D-2308-01...from TCGA PANCANA project. The demo of data format is as following: ``` Sample Chromosome St…

Combat CNA Batch-Effect

updated 17 days ago • sugus

Hello there, hope all of you are fine. I do hope you are enjoying this weekend. In my little experience, I always had to deal with samples coming from different batches (i.e. coming from different hospitals or experiments done in different days). One postdoc in my lab showed me how to deal with batch effect by using **SVA package.** I guess it is a brilliant idea to work with that, but if I don'…

RNA-Seq deseq2 batch-effect

updated 17 days ago • Mozart

may be due to the overall experimental design. So for an overall background, I was brought on as a bioinformatics analyst after the experiment was ordered and sequenced. From what I know so far there were four experimental

ChIP-Seq batch-effect sequencing

updated 17 days ago • dmj6ab

16,505 results • Page 1 of 331

Recent Votes

Comment: agilent human all exon sureselct v7 bed file

Answer: install package

Comment: Overlap File for RACON Genome Polisher

Overlap File for RACON Genome Polisher

Answer: LD-prune variants while maintaining a list of SNPs

Comment: TaxID mapping file

Answer: LD-prune variants while maintaining a list of SNPs

Recent Locations • All