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questions
1
vote
2
replies
435
views
Should centering and scaling be done on methylation beta values for principal component analysis (PCA)?
PCA
PCAtools
8 weeks ago by
Pratik
★ 1.0k
4
votes
3
replies
428
views
Is it possible to bulk-download gene expression + methylation data for a specific copy number loss on TCGA?
tcga
updated 9 weeks ago by
Zhenyu Zhang
★ 1.1k • written 9 weeks ago by
Pratik
★ 1.0k
4
votes
1
reply
604
views
When running salmon or star_salmon , are samples “independent” from one another during quantification (ie. to remove low quality samples after a mult…
salmon
pre-processing
star_salmon
rna-seq
updated 18 months ago by
ATpoint
81k • written 18 months ago by
Pratik
★ 1.0k
12
votes
3
replies
783
views
Conceptual questions regarding computational genome/annotation versions and their impact on the actual truth of sequencing?
wes
sequencing
wgs
rna-seq
updated 18 months ago by
benformatics
3.9k • written 18 months ago by
Pratik
★ 1.0k
3
votes
2
replies
815
views
Pros and Cons of DNA Mass Spectrometry versus WES/WGS?
spec
mass
wes
dna
wgs
19 months ago by
Pratik
★ 1.0k
12
votes
4
replies
14k
views
How to use FindSubCluster in Seurat?
seurat
R
single cell RNA-seq
updated 2.3 years ago by
torabian.p
• 0 • written 3.1 years ago by
Pratik
★ 1.0k
6
votes
10
replies
5.8k
views
What is a count matrix for input into Seurat supposed to look like?
R
RNA-Seq
Monocle3
Seurat
updated 22 months ago by
Ram
43k • written 3.6 years ago by
Pratik
★ 1.0k
1
vote
3
replies
2.4k
views
How to quickly find and filter coexpressed markers with one specific gene of interest in individual cells using scRNA-seq data?
scRNA-seq
Seurat
coexpression
updated 2.4 years ago by
jaro.slamecka
▴ 240 • written 2.4 years ago by
Pratik
★ 1.0k
6
votes
6
replies
2.6k
views
How to compare expression levels of specific genes between sample groups after generating DEG list?
RNA-seq
TMM
edgeR
2.4 years ago by
Pratik
★ 1.0k
2
votes
1
reply
755
views
Is a single dot on a UMAP or t-SNE for scRNA-seq - a single cell?
scRNA-seq
updated 2.4 years ago by
jared.andrews07
★ 16k • written 2.4 years ago by
Pratik
★ 1.0k
4
votes
3
replies
1.7k
views
How to rename the elements in columns(txdb)?
GenomicFeatures
GenomicRanges
GenomeInfoDb
2.5 years ago by
Pratik
★ 1.0k
4
votes
4
replies
1.7k
views
Good or bad idea to annotate with newer genome build?
array
methylation
beadchip
build
annotation
2.5 years ago by
Pratik
★ 1.0k
0
votes
0
replies
777
views
Why is there not a intronsBy() function in GenomicFeatures? only intronsByTranscript()?
GenomicRanges
GenomicFeatures
genic
introns
intronsbytranscript
2.6 years ago by
Pratik
★ 1.0k
5
votes
3
replies
1.3k
views
Is removing strand information when obtaining intergenic regions from GRanges necessary?
GenomicRanges
methylation
strand
intergenic
genic
updated 2.6 years ago by
Carlo Yague
8.6k • written 2.6 years ago by
Pratik
★ 1.0k
2
votes
3
replies
1.2k
views
How to plot/combine biological replicates on a genomic features plot for methylated array?
array
methylation
beadchip
plot
features
genomic
updated 2.7 years ago by
Papyrus
★ 2.9k • written 2.7 years ago by
Pratik
★ 1.0k
3
votes
2
replies
1.1k
views
What cut-offs to use for Genomic Features Pie Chart for Methylation Array Data?
beadchip
array
methylation
2.7 years ago by
Pratik
★ 1.0k
7
votes
3
replies
1.2k
views
How to normalize and transform RNA-seq data of different samples for PCA?
TMM
PCA
RNA-seq
edgeR
updated 2.7 years ago by
Kevin Blighe
87k • written 2.7 years ago by
Pratik
★ 1.0k
1
vote
1
reply
1.6k
views
What format should a dataframe be in to use the AddMetaData function in Seurat?
seurat
R
RNA-Seq
rna-seq
scRNA-seq
2.8 years ago by
Pratik
★ 1.0k
9
votes
5
replies
12k
views
How to read a dataframe into Seurat for AddMetaData properly?
seurat
rna-seq
RNA-Seq
R
2.8 years ago by
Pratik
★ 1.0k
33
votes
4
replies
12k
views
How do you generate TMM normalized counts using EdgeR?
R
RNA-seq
edgeR
updated 13 months ago by
Gordon Smyth
★ 6.9k • written 2.8 years ago by
Pratik
★ 1.0k
9
votes
13
replies
1.9k
views
mapped reads (m aligned) is higher for a subset sample?
salmon
fastqc
multiqc
RNA-seq
updated 2.8 years ago by
Kevin Blighe
87k • written 2.8 years ago by
Pratik
★ 1.0k
6
votes
4
replies
1.2k
views
Up to date bulk RNA-seq Quality Control tools?
QC
RNA-seq
2.8 years ago by
Pratik
★ 1.0k
10
votes
10
replies
2.2k
views
6 follow
How do I make a ComplexHeatmap from this dataframe?
scaling
scale
heatmap
2.8 years ago by
Pratik
★ 1.0k
7
votes
7
replies
5.2k
views
How to fix missing values error message after SCTransform (Seurat)?
Seurat
R
SCTransform
2.8 years ago by
Pratik
★ 1.0k
4
votes
4
replies
2.2k
views
How to interpret ScanPy scatter plots for QC filtering?
Python
jupyter-lab
ScanPy
RNA-Seq
scRNA-seq
2.8 years ago by
Pratik
★ 1.0k
0
votes
0
replies
502
views
Database for signalling pathway agonists and antagonists?
database
gene
3.1 years ago by
Pratik
★ 1.0k
4
votes
4
replies
3.0k
views
How do I use FindAllMarkers after making additional cluster assignments?
Seurat
R
single cell-RNA seq
scRNA-seq
3.1 years ago by
Pratik
★ 1.0k
1
vote
1
reply
1.7k
views
How to interpret highly variable genes plot in Scanpy?
python
single-cell RNA Seq
updated 14 months ago by
mt_pereira
• 0 • written 3.1 years ago by
Pratik
★ 1.0k
6
votes
7
replies
1.3k
views
How to record Seurat DE analysis efficiently?
R
RNA-Seq
rna-seq
3.1 years ago by
Pratik
★ 1.0k
2
votes
3
replies
1.5k
views
What is the difference between a heatmap-dendrogram of a gene-gene correlation matrix made from one cluster versus multiple clusters?
scRNA-Seq
Seurat
RNA-Seq
R
rna-seq
3.3 years ago by
Pratik
★ 1.0k
9
votes
9
replies
1.6k
views
Is there a way to use multiple processors (parallelize) to create a heatmap for a large dataset?
parallel processing
heatmap
scRNA-seq
3.3 years ago by
Pratik
★ 1.0k
3
votes
2
replies
8.4k
views
How do I subset a Seurat object using variable features?
seurat
RNA-Seq
scRNA-seq
R
updated 3.3 years ago by
bioinformatics2020
▴ 800 • written 3.3 years ago by
Pratik
★ 1.0k
18
votes
15
replies
35k
views
How to embed known cell information into Seurat object? AddMetaData?
next-gen
R
Seurat3
scRNA-seq
updated 22 months ago by
Hamid Ghaedi
3.2k • written 3.5 years ago by
Pratik
★ 1.0k
2
votes
5
replies
916
views
How would I input the count matrices per sample files into Monocle3?
RNA-Seq
next-gen
R
Monocle3
3.6 years ago by
Pratik
★ 1.0k
5
votes
9
replies
1.6k
views
Could I use the ExpressionSet generated from GEOquery for Monocle3 or does it have to be formatted differently?
RNA-Seq
R
monocle3
next-gen
updated 3.6 years ago by
Kevin Blighe
87k • written 3.6 years ago by
Pratik
★ 1.0k
0
votes
0
replies
796
views
Working Monocle 3 with series_matrix files?
RNA-Seq
rna-seq
3.6 years ago by
Pratik
★ 1.0k
36 results • Page
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