Biostar

12,072 results • Page 1 of 242

Hello, I'm working with genomic coordinates derived from differentially accessible regions (DARs) in ATAC-seq data analysis. I aim to investigate whether any mutations within these regions are associated with various cancers. To accomplish this, I believe I need access to a cancer genome database that includes mutation information. Could anyone recommend databases or resources where I can f…

Genomics Bioinformatics ATACseq CancerResearch

updated 13 minutes ago • David

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 1 hour ago • Biostar

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...challenge lies in accurately annotating a draft genome assembly after its construction. In this course, we will delve into the essential processes and strategies require…

Genome-Assembly Genome-Annotation

updated 5 hours ago • carlopecoraro2

I have few peptide sequences which i want to validate using MS data. Anyone know how can i do it ? Thanks !!

Transcriptomics Mass Bioinformatics spectrometry Proteins

updated 7 hours ago • atharvakarkare14

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 10 hours ago • Ruqaiya

Trying to predict ncRNAs from RNA-seq data. Using [CPAT][1] tool i have obtained a csv file with multiple columns. What should be the threashold value for coding probability ? I am considering value < 0.5. ![Table][2] [1]: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3616698/ [2]: /media/images/7fcc8708-5af9-4e9c-b74e-3c50c3ca

Genomics Proteomics Bioinformatics

updated 2 days ago • atharvakarkare14

like there should be a simple enough solution to this question, but I can't seem to find anything online. Any help or direction would be greatly appreciated. Thank you

population-genetics phylogenetic

updated 2 days ago • SineWave

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 2 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 2 days ago • Guille

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...approaches for differential expression analysis The purpose of this intense one week summer course is to get a deep understanding in Next-Generation Seque…

DNA-seq variant-calling RNA-seq illumina transcriptomics

updated 3 days ago • David Langenberger

Dear all, you can now sharpen your research skills with this online course (May 13-16), which will equip you with modern Meta-analysis techniques in R (metafor & psychmeta). Learn to: * Pool...with R is helpful. For more information, please visit: https://www.physalia-courses.org/courses-workshops/metain-r

Meta-Analysis Statistics R

updated 3 days ago • carlopecoraro2

Dear all, Ready to level up your statistical modeling skills? This 5-day course offers a hands-on introduction to generalized linear models (GLMs) using R. ---------- Dates: 6-10 May (online) ---------- This course is aimed...and private sectors. ---------- Limited number of seats left: https://www.physalia-courses.org/courses-workshops/glm-in-r-1

Generalized-Linear-Models GLM R

updated 4 days ago • carlopecoraro2

herald

updated 5 days ago • Biostar

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 5 days ago • Estevão

Dear all, We have the last 4 seats left for our upcoming online course on Spatial Omics in R/Bioconductor, scheduled for May 20-22, 2024. For more details and registration, please visit...Dear all, We have the last 4 seats left for our upcoming online course on Spatial Omics in R/Bioconductor, scheduled for May 20-22, 2024. For more details and registration, please visit: https://www.physalia…

Bioconductor Spatial-Omics Spatial-Transcriptomics

updated 5 days ago • carlopecoraro2

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 6 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 6 days ago • sansan_96

Hi, I am working with a RNAseq deriving from fungus and at the moment I have used Salmon for quantification. However, I have noticed that between STAR and Salmon, the mapping rate has lowered consistently. In fact, in Salmon, the mapping rate is almost the half than the one in STAR. I could get higher mapping rate using `fmd` compared to `quasi`. Nevertheless, I think the percentage is still …

RNA-seq Salmon Quantification

updated 6 days ago • Patadu94

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 7 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 7 days ago • feather-W

Dear all, We are pleased to announce the upcoming online course on "DNA Methylation in Ecology and Evolution," taking place from September 16th to 20th. ---------- > Course website: https...www.physalia-courses.org/courses-workshops/dnamethylation/ ---------- This course will delve into various methodologies for obtaining and analyzing DNA methylation...inte…

Pacbio Nanopore DnaMethylation Evolution

updated 7 days ago • carlopecoraro2

researchers, data generators and user communities **You have** - A post-graduate degree in bioinformatics, biology, computer science or a related field or equivalent professional experience - At least four years...experience working in a production bioinformatics environment - A high degree of proficiency in at least one dynamic programming language e.g. Python or Perl...package to sup…

ebi embl genomics ensembl

updated 7 days ago • Ben_Ensembl

officers. - Coordination of training workshop delivery, liaising with international hosts and course collaborators to set up both standalone courses and Ensembl segments of longer courses. - Monitoring and recording...user perspective to discussions of future plans. **You have** - A PhD or equivalent experience in bioinformatics, molecular biology, genetics or a related discipline - Experie…

ebi embl genomics ensembl

updated 7 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 studio. I have difficulties

VIPER MARINA ARACNe

updated 7 days ago • Biostars2200

store: ---------- 1. **Generalised Linear Models in R** - Online, May 6th to May 10th - https://www.physalia-courses.org/courses-workshops/glm-in-r-1 2. **Meta-analysis in R** - Online, May 13th...to May 16th - https://www.physalia-courses.org/courses-workshops/metain-r/ 3. **Ecological Time Series Analysis and Forecasting in R** - Online, May 27th to May 31st - https://www.physalia...courses.o…

Statistics R Data-Analysis

updated 7 days ago • carlopecoraro2

thousands of variants. I want to separate the cancer related variants among these, is there any online platforms that I can compare my variants with? OR how to proceed with this data? Could someone please help? Thanks

variant-annotation

updated 7 days ago • sainavyav22

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 9 days ago • rebecca.calvo

Hi, I am a beginner in bioinformatics and I would like to learn the basic pipeline for quantifying expression of rna sequences from transcriptomic

differential-expression transcriptome

updated 10 days ago • siddharth.patel.153

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 10 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 10 days ago • BioQueen

Dear all, We're excited to announce our upcoming five-day course on Agent-Based Modelling Using NetLogo, happening from July 29th to August 2nd, 2024, at the Faculty of Biology and Environmental...Dear all, We're excited to announce our upcoming five-day course on Agent-Based Modelling Using NetLogo, happening from July 29th to August 2nd, 2024, at the Faculty of Biology and Environmental Prote…

Netlogo Individual-Based-Models Agent-Based-Models

updated 10 days ago • carlopecoraro2

Dear all, There are still a few seats available for the online course on Meta-analysis in R, happening in May (13-16). Course website: https://www.physalia-courses.org/courses-workshops...Dear all, There are still a few seats available for the online course on Meta-analysis in R, happening in May (13-16). Course website: https://www.physalia-courses.org/courses-workshops/metain-r/ This …

Meta-Analysis Statistics R

updated 10 days ago • carlopecoraro2

although there exists some debate. Quantile/Upper Quartile normalization is another option. Then of course is the issue of batch effects. An option to deal with that is `sva::ComBat()`, which "removes" batch effects and gives me a batch

gene-expression TPM RNA-Seq counts batch-effect

updated 11 days ago • Ram

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 11 days ago • dmj6ab

Hello, I am currently working on my master's thesis in bioinformatics (2 weeks in). My tutor has asked me to work with VCF files from ICGC database. Our goal use this data to training

bcftools SnpEff WGS VEP VCF

updated 12 days ago • Javier

Hi I have RNA-Seq data from patients and downloaded online RNA-Seq control datasets. What do you recommend me to correct batch effects. What quality controls can I perform during...my analyses? Also if the online data are FPKM and my data are raw counts, how should I approach that? Any thoughts would be appreciated

RNA-Seq batch-effect

updated 12 days ago • Victoria

I also have my own sequence that will need to be used as a reference. So far, I have found several online resources (tutorials/general workflows) for different types of analysis. I have no experience with doing this type

Sequencing RNA-seq DNA-Seq

updated 12 days ago • niruf

systems* **When?** May 27-29, 2024 **Where?** Online **Link?** [Website][1] **In a nutshell** - **Learn** the fundamental best-practices of bioinformatic pipeline development - **Understand...analysis pipelines using Nextflow! The purpose of the workshop is to introduce the concepts of bioinformatic pipeline development through the context of the open source Workflow Management System (WM…

workshop RNA-seq nextflow DNA-seq

updated 12 days ago • David Langenberger

Hi everyone, I am a student of Biotechonology and I want to learn Bioinformatics. I want to learn mainly the sequencing stuff and data analysis. I do know linux and python and R but I never used...no idea what am I doing. So, can anybody give me an idea or a workflow that I should follow to learn bioinformatics. If had a project I might have learned some but without prior knowledge no project ide…

Sequencing

updated 12 days ago • Adi

Hi, I'm new to bioinformatics and I'm analyzing some genomes I obtained from BGI. The average size of these reads is 100bp, but after trimming

Bwa-sampe BGI

updated 12 days ago • lorena9132

herald

updated 14 days ago • Biostar

I'm seeking guidance on how to get out of a situation I'm currently in. After reporting my former supervisor's spouse for discriminatory harassment, I've experienced multiple examples of retaliation (I say former supervisor, because I was recently given a new supervisor, but they only have a background in wet lab work). I'll refer to my former supervisor as Dr. Y and their spouse as Dr. X. They a…

Career advice

updated 14 days ago • swim35396

Dear all, Join us for an immersive online course on Network Analysis in R from 22nd-25th April. This course provides a comprehensive overview of network data...modelling, etc), as well as aptitude with the R coding language and the tidyverse. > - Course website: https://www.physalia-courses.org/courses-workshops/network-analysis-in-r

NetworkAnalyis R

updated 15 days ago • carlopecoraro2

Dear all, We're thrilled to share news of our upcoming online course, "Meta-Analysis in R," running from May 13 to 16, 2024. ---------- **Course Details**: - Website: *https://www.physalia-courses.org/courses...workshops/metain-r/* - Overview: This course offers a comprehensive introduction to contemporary meta-analysis methods. - Topics Covered: We'll explore the systematic...integral, focus…

Meta-Analysis R

updated 17 days ago • carlopecoraro2

focusing on the gene POLD1, utilizing data extracted from the Dependency Map (DepMap) portal. In the course of my investigation, I have encountered a perplexing discrepancy between the outcomes derived from small interfering

DepMap

updated 17 days ago • Shicheng Guo

The University of Pennsylvania Institute for Translational Medicine and Therapeutics Bioinformatics Group is offering a three year postdoctoral position, with the possibility to extend. Will work as part of...a team that performs a broad range of bioinformatics analyses, primarily with high throughput data. Will be developing pipelines for RNA-Seq analysis and performing...meetings. This position…

RNA-Seq genome

updated 17 days ago • ggrant543

submit an application can be found here: https://phd.health.au.dk/application/opencalls/phd-project-bioinformatics-phd-project Please contact me with any questions regarding the project or the application procedure. Best...Søren Besenbacher [1]: https://www.moma.dk/bioinformatics/computational-genomics

PhD Genomics Cancer

updated 17 days ago • besen

Registration is now open for our new online live course: **INTRODUCTION TO NETWORK ANALYSIS AND MODELLING**. Taught by **Dr. Virginia Dominguez-García**. Dates: **June 3rd...and registration: https://www.transmittingscience.com/courses/systems-biology/introduction-to-network-analysis-and-modelling/ **COURSE OVERVIEW** Networks are pervasive in various...systems using network theory. The cou…

Python Network-Analysis

updated 17 days ago • Transmitting Science communication

Registration is now open for our Online Live Course: **GENERALISED ADDITIVE MIXED MODELS (GAMM): MODELLING SPACE-TIME CORRELATION STRUCTURES**. Taught by **Antonio...Canepa**. Dates: **May 27th-31st, 2024**. Total course hours: 21. Places are limited to 18 participants and will be occupied by strict registration order. More information...and registration on the course webpage: https://www.tr…

GAMM Rlang Rstats Rproject

updated 17 days ago • Transmitting Science communication

Registration is now open for the new online live course: **INTRODUCTION TO MACHINE LEARNING IN R**. Taught by Dr. Nicolas Attalides. Dates: **September 6th-21st, 2024**. Total...and registration on the course website: https://www.transmittingscience.com/courses/statistics-and-bioinformatics/introduction-to-machine-learning...the results of machine learning algorithms on a daily basis, for exa…

Rstats TScourses Rlang Rproject

updated 17 days ago • Transmitting Science communication

12,072 results • Page 1 of 242

Recent Votes

Answer: High Malat-1 expression in single cell data

The Biostar Herald for Monday, April 29, 2024

A: Bam And Indexed Bam Files

High Malat-1 expression in single cell data

Segmentation fault using gemma

Produce PCA bi-plot for 1000 Genomes Phase III - Version 2

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