User: Dataminer
Dataminer • 2.7k
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Posts by Dataminer
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2
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1
answer
144
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1
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... 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 ...
written 6 weeks ago by
Dataminer • 2.7k
• updated
5 weeks ago by
rpolicastro ♦ 3.2k
0
votes
1
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129
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1
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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
0
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1
answer
129
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1
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... 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)
...
written 6 weeks ago by
Dataminer • 2.7k
• updated
6 weeks ago by
Jean-Karim Heriche ♦ 24k
4
votes
1
answer
292
views
6 follow
1
answer
... 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 ...
written 7 months ago by
Dataminer • 2.7k
• updated
7 months ago by
Kevin Blighe ♦ 69k
0
votes
1
answer
242
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1
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... 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
2
votes
1
answer
242
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1
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... 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 ...
1
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0
answers
636
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0
answers
... 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 ...
0
votes
2
answers
2.1k
views
2
answers
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
8
votes
2
answers
2.1k
views
5 follow
2
answers
... 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 ...
written 23 months ago by
Dataminer • 2.7k
• updated
17 months ago by
gable_works • 40
1
vote
1
answer
997
views
1
answers
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
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For Confusion with High Confidence SNP Calls (Overlap B/w RNA-seq & WGBS calls) and Genome Assemblies Used for Alignment and Annotation
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For How to check if my SNPs are also present in 1000 genome project
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For Mapping Genes To Pathway
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For Tools to identify biologically relevant SNP calls from a vcf file
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For Extracting List Of Genes Associated With A Pathway In Kegg
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16 months ago,
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For Conversion Form Broad Peak Format Of Macs2 To Narrow Peak Format
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Prophet
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For Extracting List Of Genes Associated With A Pathway In Kegg
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16 months ago,
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For Extracting List Of Genes Associated With A Pathway In Kegg
Student
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For Extracting List Of Genes Associated With A Pathway In Kegg
Student
23 months ago,
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For Extracting List Of Genes Associated With A Pathway In Kegg
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created a question with more than 5,000 views.
For Statistical Measure Of Biological Significance For Overlapping Genomic Regions
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For How to check if my SNPs are also present in 1000 genome project
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For Nobel Prize And Bioinformatics
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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
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For Extracting List Of Genes Associated With A Pathway In Kegg
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