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User: Dataminer

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Dataminer • 2.7k
Reputation:
2,690
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Location:
Netherlands
Last seen:
1 month, 1 week ago
Joined:
9 years, 10 months ago
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Posts by Dataminer

<prev • 321 results • page 1 of 33 • next >
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to consider only intronic reads in cell ranger pipeline
... Hello community, I am processing some single nuclei RNA seq data and unfortunately while performing the experiment there was high leakage of mRNA and that leads to ambient RNA all over. I thought may be considering only intronic reads while mapping would circumvent this problem, but I am not sur ...
cell ranger snrna written 6 weeks ago by Dataminer • 2.7k • updated 5 weeks ago by rpolicastro ♦ 3.2k
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Comment: C: Shiny board with seurat object
... Hi, My seurat works fine and I get all the images and analysis done. It is when I try to put the seurat object into R shiny, it throws up this error. ...
written 6 weeks ago by Dataminer • 2.7k
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Shiny board with seurat object
... Dear community, I am trying to make a shiny app by reading in seurat object. Unfortunately, it doesn't work. I have deployed the following code: library(shiny) library(shinythemes) library(Seurat) library(ggplot2) library(gridExtra) library(egg) library(RColorBrewer) ...
shiny seurat written 6 weeks ago by Dataminer • 2.7k • updated 6 weeks ago by Jean-Karim Heriche ♦ 24k
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6 follow
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Mismatch in probe ids
... Dear members, I am using "An end to end workflow for differential gene expression using Affymetrix microarrays" as described [here][1] at one of the step it requires to map probe ids to gene names and symbols. The methods uses anno_palmieri <- AnnotationDbi::select(hugene10sttranscriptcl ...
microarray affymetrix written 7 months ago by Dataminer • 2.7k • updated 7 months ago by Kevin Blighe ♦ 69k
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Comment: C: Processing bulk RNA-seq TMM matrix to get DEGs
... Thank you for your reply. I concur, that raw reads are more useful than these normalised read counts. I was hoping for a work around but it seems that there isn't any. ...
written 9 months ago by Dataminer • 2.7k
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Processing bulk RNA-seq TMM matrix to get DEGs
... Dear Community, I am using a publicly available RNA-seq datasets that were processed as follows: "Gene expression normalizations were performed using the TMM method (PMID: 20196867), and further normalization was applied by adjusting the expression to gene length. In addition, only the genes and t ...
rna-seq written 9 months ago by Dataminer • 2.7k • updated 9 months ago by ATpoint ♦ 44k
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Your favourite workflow for Hi-C data analysis (Plant Genome)
... Dear Community, A lot of tools are present for Hi-C data analysis, some these include HiCCUPs, diffHiC. Fit-HiC, mHiC, hicexplorer, HiPPIE etc. My question is regarding Hi-C data analysis associated with plant genomes. In plant genomes we encounter polyploidy and repeats. This also results in hand ...
hi-c written 22 months ago by Dataminer • 2.7k • updated 20 months ago by Biostar ♦♦ 20
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Comment: C: Paired end peak callers
... Hi Fredrieke, Thank's for the Genrich. I am not after any specific functionality, in general I have found that MACS2 doesn't work quite well with H3K9me3 or H3K27me3 marks (might be more). I don't know what the issue is and how it can be fixed. On the other hand PeakRanger (CCAT) works quite well w ...
written 23 months ago by Dataminer • 2.7k
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Paired end peak callers
... Hi, Are their any peak callers other than macs that can be used for paired end data ? If yes, please describe your experience with them. Thank you ...
chip-seq written 23 months ago by Dataminer • 2.7k • updated 17 months ago by gable_works • 40
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Comment: C: Hi-C data alignment with star
... Hi, I was using exactly the same bwa mem -A1 -B4 -E50 -L0 -t 12 ref.fa file1.fastq Btw I have plant genome polyploidy ...
written 24 months ago by Dataminer • 2.7k

Latest awards to Dataminer

Popular Question 6 months ago, created a question with more than 1,000 views. For Confusion with High Confidence SNP Calls (Overlap B/w RNA-seq & WGBS calls) and Genome Assemblies Used for Alignment and Annotation
Popular Question 6 months ago, created a question with more than 1,000 views. For How to check if my SNPs are also present in 1000 genome project
Epic Question 6 months ago, created a question with more than 10,000 views. For Mapping Genes To Pathway
Popular Question 6 months ago, created a question with more than 1,000 views. For Tools to identify biologically relevant SNP calls from a vcf file
Epic Question 6 months ago, created a question with more than 10,000 views. For Best Database Of Transcription Factor Binding Sites
Student 6 months ago, asked a question with at least 3 up-votes. For Biological Pathways And Drug Designing
Great Question 6 months ago, created a question with more than 5,000 views. For Peaks And Nearby Genes
Great Question 8 months ago, created a question with more than 5,000 views. For Peaks And Nearby Genes
Epic Question 8 months ago, created a question with more than 10,000 views. For Extracting List Of Genes Associated With A Pathway In Kegg
Great Question 16 months ago, created a question with more than 5,000 views. For Conversion Form Broad Peak Format Of Macs2 To Narrow Peak Format
Popular Question 16 months ago, created a question with more than 1,000 views. For Tools to identify biologically relevant SNP calls from a vcf file
Prophet 16 months ago, created a post with more than 20 followers. For Extracting List Of Genes Associated With A Pathway In Kegg
Great Question 16 months ago, created a question with more than 5,000 views. For Peaks And Nearby Genes
Great Question 20 months ago, created a question with more than 5,000 views. For Extracting List Of Genes Associated With A Pathway In Kegg
Student 21 months ago, asked a question with at least 3 up-votes. For Extracting List Of Genes Associated With A Pathway In Kegg
Student 23 months ago, asked a question with at least 3 up-votes. For Extracting List Of Genes Associated With A Pathway In Kegg
Great Question 2.5 years ago, created a question with more than 5,000 views. For Statistical Measure Of Biological Significance For Overlapping Genomic Regions
Popular Question 2.5 years ago, created a question with more than 1,000 views. For How to check if my SNPs are also present in 1000 genome project
Great Question 2.5 years ago, created a question with more than 5,000 views. For Nobel Prize And Bioinformatics
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Tools to identify biologically relevant SNP calls from a vcf file
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Confusion with High Confidence SNP Calls (Overlap B/w RNA-seq & WGBS calls) and Genome Assemblies Used for Alignment and Annotation
Great Question 2.5 years ago, created a question with more than 5,000 views. For Nobel Prize And Bioinformatics
Great Question 2.9 years ago, created a question with more than 5,000 views. For Nobel Prize And Bioinformatics
Great Question 2.9 years ago, created a question with more than 5,000 views. For Chip Seq Data Analysis
Great Question 2.9 years ago, created a question with more than 5,000 views. For Extracting List Of Genes Associated With A Pathway In Kegg
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