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12 results • Page
1 of 1
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0
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45
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How to add Ensembl ids after Pseudobulk analysis by DESeq2
Seurat
Pseudobulk
single-cell
DESeq2
scRNA
analysis
6 hours ago by
Sara
▴ 30
0
votes
0
replies
60
views
How to decrease the motif score?
scores
Motif
11 hours ago by
Hadia
• 0
0
votes
0
replies
54
views
immuCell Abundance infiltrate
ImmuCell
Abundance
infiltrate
updated 11 hours ago by
Pierre Lindenbaum
162k • written 11 hours ago by
elbakri.fatimazahrae
• 0
0
votes
1
reply
101
views
Setting a threshold on gene expression for subsetting (scRNA-seq)
scRNA-seq
updated 14 hours ago by
ATpoint
82k • written 17 hours ago by
carolofharvest
▴ 40
0
votes
0
replies
54
views
MaxEntScan for rMATS results
MaxEntScan
rMATS
15 hours ago by
adi.gershon1
• 0
0
votes
0
replies
116
views
ERROR with Maker annotation: The assumed RepeatMasker installation directory /opt/home/sony/miniconda3/envs/MAKER2/share/RepeatMasker does not ap…
RepeatMasker.
MAKER.
annotation.
21 hours ago by
Sony
▴ 10
0
votes
0
replies
70
views
Trouble with PLINK's logistic regression analysis and covariatesTrouble with PLINK's logistic regression analysis and covariates
PLINK
GWAS
SNP
22 hours ago by
F110152169
• 0
4
votes
2
replies
152
views
Number of non-ATCG nucleotides replaced by Salmon
rna-seq
stringtie
indexing
salmon
updated 23 hours ago by
Rob
6.6k • written 23 hours ago by
Tonya S.
▴ 10
2
votes
4
replies
252
views
Harmony integration group.by.var parameter
single-cell
harmony
13 hours ago by
Picasa
▴ 640
1
vote
3
replies
213
views
How to calculate cell type frequency between two groups in single cell data
Seurat
single-cell
sc-RNA
cell-type
updated 13 hours ago by
Bastien Hervé
5.3k • written 1 day ago by
Sara
▴ 30
1
vote
2
replies
296
views
Error when i use EVidenceModeler to do the genome annotation
EVidenceModeler
annotation
genome
15 hours ago by
peanut
• 0
1
vote
10
replies
3.5k
views
Merging multiple samples in Seurat
scRNA-seq
snRNA-seq
RNA-seq
Seurat
updated 5 hours ago by
Picasa
▴ 640 • written 7 months ago by
AFP3
• 0
12 results • Page
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Recent Votes
Low DESeq2 Sensivity on scRNA Pseudobulk Samples
DESEQ2: How can I convert ensembl gene id's to HGNC gene names.
Problem with Ensembl version identifiers after running DESeq2
Issues with adding gene name and entrez ID to DESeq2 result having Ensembl ID.
A: Looking for differential gene expression between treatment, within a specific cl
How to compare cell-type ratios in sc-RNA seq data?
How to calculate cell type frequency between two groups in single cell data
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Recent Replies
Comment: Merging multiple samples in Seurat
by
Picasa
▴ 640
did you split by sample or donor ?
Comment: Harmony integration group.by.var parameter
by
Picasa
▴ 640
For downstream analysis, after integration, my plan is to annotate each cluster/cell type and then perform a DGE analysis of KO versus WT f…
Comment: How to calculate cell type frequency between two groups in single cell data
by
Bastien Hervé
5.3k
That is correct
Answer: Setting a threshold on gene expression for subsetting (scRNA-seq)
by
ATpoint
82k
That depends on the data and the marker. Generally I would plot violins per cluster for the marker(s) and see whether one robustly overexpr…
Comment: Error when i use EVidenceModeler to do the genome annotation
by
peanut
• 0
thank you so much ,i get it
Comment: Number of non-ATCG nucleotides replaced by Salmon
by
Tonya S.
▴ 10
Oops, yes, that must be where they are coming from. For some reason, I was thinking the genome was just soft-masked. How embarrassing! Than…
Answer: Number of non-ATCG nucleotides replaced by Salmon
by
Rob
6.6k
If there are no other signs that anything is awry, I probably wouldn't worry about this. Is it possible that these non-canonical nucleotid…
Comment: Introducing NovaDemux, a Sequence Demultiplexer that Increases Yield and Salvage
by
Brian Bushnell
20k
I examined nine 10B runs and five 25B runs (we just started getting 25B flowcells a few months ago). I did not pay close attention but it …
Comment: Introducing NovaDemux, a Sequence Demultiplexer that Increases Yield and Salvage
by
GenoMax
142k
> I don't know how widespread these issues are outside of JGI. Very few small/medium sequencing centers likely have NovaSeq X. This is the…
Comment: Introducing NovaDemux, a Sequence Demultiplexer that Increases Yield and Salvage
by
Brian Bushnell
20k
Supporting figures, taken from some slides I prepared for internal use. HDist 0, 1, and 2 correspond to 0, 1, and 2 mismatches allowed in …
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation
by
hannes.bongartz
• 0
This works. Thank you so so much!
Comment: Harmony integration group.by.var parameter
by
jared.andrews07
★ 17k
>I am not sure, but using "Sample_ID" might remove the differences between the conditions right ? More than likely, it'd at least impact t…
Comment: Harmony integration group.by.var parameter
by
Picasa
▴ 640
Thanks jared.andrews07 for your answer. So, you are suggesting to use only "Donor" in the integration? ```r RunHarmony(seu_obj, group.by.…
Comment: Single cell analysis: Unable to subset cells in seurat object using desired nFea
by
sc_analysis
• 0
I am not sure what should be the cut off. Looking at the vlnplot before subsetting i thought most of the cells are falling under 7500 nfeat…
Comment: How to calculate cell type frequency between two groups in single cell data
by
Sara
▴ 30
Thank you for your comment and sorry if this question might be so basic. How can I normalize the number of cells? If I am not wrong the i…
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