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1
vote
0
replies
537
views
Answer:
Answer: adding gene and CDS feature types in ensemble gtf annotation with transcript and
5 weeks ago by
Pratik
★ 1.0k
0
votes
0
replies
255
views
Answer:
Answer: How to do DE between cells expressing specific gene in scanpy?
6 weeks ago by
Pratik
★ 1.0k
1
vote
1
reply
411
views
Answer:
Answer: Get the gene functions specific for clusters (RNA seq)
3 months ago by
Pratik
★ 1.0k
0
votes
0
replies
507
views
Comment:
Comment: Should centering and scaling be done on methylation beta values for principal co
3 months ago by
Pratik
★ 1.0k
1
vote
2
replies
507
views
Should centering and scaling be done on methylation beta values for principal component analysis (PCA)?
PCA
PCAtools
3 months ago by
Pratik
★ 1.0k
0
votes
0
replies
487
views
Comment:
Comment: Is it possible to bulk-download gene expression + methylation data for a specifi
4 months ago by
Pratik
★ 1.0k
4
votes
3
replies
487
views
Is it possible to bulk-download gene expression + methylation data for a specific copy number loss on TCGA?
tcga
updated 3 months ago by
Zhenyu Zhang
★ 1.2k • written 4 months ago by
Pratik
★ 1.0k
0
votes
0
replies
7.9k
views
Comment:
Comment: How to find CpG island shore?
18 months ago by
Pratik
★ 1.0k
0
votes
1
reply
7.9k
views
Answer:
Answer: How to find CpG island shore?
18 months ago by
Pratik
★ 1.0k
4
votes
1
reply
634
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 19 months ago by
ATpoint
82k • written 19 months ago by
Pratik
★ 1.0k
0
votes
0
replies
580
views
Job:
Research Technician – Computational Biology Core - (UConn CBC) - Connecticut
connecticut
technician
updated 17 months ago by
Ram
44k • written 20 months ago by
Pratik
★ 1.0k
12
votes
3
replies
851
views
Conceptual questions regarding computational genome/annotation versions and their impact on the actual truth of sequencing?
wes
sequencing
wgs
rna-seq
updated 20 months ago by
benformatics
3.9k • written 20 months ago by
Pratik
★ 1.0k
0
votes
0
replies
866
views
Comment:
Comment: Pros and Cons of DNA Mass Spectrometry versus WES/WGS?
21 months ago by
Pratik
★ 1.0k
3
votes
2
replies
866
views
Pros and Cons of DNA Mass Spectrometry versus WES/WGS?
spec
mass
wes
dna
wgs
21 months ago by
Pratik
★ 1.0k
0
votes
1
reply
6.1k
views
Comment:
Comment: What is a count matrix for input into Seurat supposed to look like?
2.0 years ago by
Pratik
★ 1.0k
0
votes
0
replies
37k
views
Comment:
Comment: How to embed known cell information into Seurat object? AddMetaData?
2.1 years ago by
Pratik
★ 1.0k
0
votes
0
replies
1.7k
views
Comment:
Comment: Seurat subset cluster cell annotation
2.3 years ago by
Pratik
★ 1.0k
3
votes
0
replies
1.4k
views
Answer:
Answer: scSeq millions of cells
2.3 years ago by
Pratik
★ 1.0k
1
vote
1
reply
1.5k
views
Comment:
Comment: Forcing Seurat to include certain genes during integration
2.4 years ago by
Pratik
★ 1.0k
0
votes
1
reply
1.8k
views
Answer:
Answer: scRNA seq differential gene expression analyses
2.4 years ago by
Pratik
★ 1.0k
13
votes
4
replies
15k
views
How to use FindSubCluster in Seurat?
seurat
R
single cell RNA-seq
updated 2.4 years ago by
torabian.p
• 0 • written 3.2 years ago by
Pratik
★ 1.0k
0
votes
0
replies
6.1k
views
Comment:
Comment: What is a count matrix for input into Seurat supposed to look like?
2.5 years ago by
Pratik
★ 1.0k
6
votes
10
replies
6.1k
views
What is a count matrix for input into Seurat supposed to look like?
R
RNA-Seq
Monocle3
Seurat
updated 2.0 years ago by
Ram
44k • written 3.7 years ago by
Pratik
★ 1.0k
4
votes
1
reply
1.9k
views
Answer:
Answer: how to find each cluster in single-cell represent which cell type?
2.5 years ago by
Pratik
★ 1.0k
3
votes
1
reply
1.2k
views
Answer:
Answer: How do I download a list of genes involved in cellular metabolism (in humans) ba
2.5 years ago by
Pratik
★ 1.0k
0
votes
1
reply
2.5k
views
Comment:
Comment: How to quickly find and filter coexpressed markers with one specific gene of int
2.5 years ago by
Pratik
★ 1.0k
1
vote
3
replies
2.5k
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 2.5 years ago by
jaro.slamecka
▴ 240 • written 2.5 years ago by
Pratik
★ 1.0k
1
vote
0
replies
834
views
Comment:
Comment: PathFindR: Running Reactome for Mouse
2.5 years ago by
Pratik
★ 1.0k
0
votes
0
replies
657
views
Comment:
Comment: Finding players and targets of expression-regulating pathways
2.4 years ago by
Pratik
★ 1.0k
0
votes
0
replies
2.7k
views
Comment:
Comment: How to compare expression levels of specific genes between sample groups after g
2.5 years ago by
Pratik
★ 1.0k
0
votes
2
replies
2.7k
views
Comment:
Comment: How to compare expression levels of specific genes between sample groups after g
2.5 years ago by
Pratik
★ 1.0k
6
votes
6
replies
2.7k
views
How to compare expression levels of specific genes between sample groups after generating DEG list?
RNA-seq
TMM
edgeR
2.5 years ago by
Pratik
★ 1.0k
0
votes
1
reply
1.1k
views
Comment:
Comment: How to create shiny app for deseq2 object creation
2.5 years ago by
Pratik
★ 1.0k
0
votes
0
replies
1.0k
views
Answer:
Answer: Entry level jobs
2.5 years ago by
Pratik
★ 1.0k
7
votes
0
replies
1.2k
views
Answer:
Answer: General question about clustering in scRNAseq
2.6 years ago by
Pratik
★ 1.0k
2
votes
1
reply
777
views
Is a single dot on a UMAP or t-SNE for scRNA-seq - a single cell?
scRNA-seq
updated 2.6 years ago by
jared.andrews07
★ 17k • written 2.6 years ago by
Pratik
★ 1.0k
0
votes
0
replies
1.9k
views
Answer:
Answer: How to show relabel sub cluster on the original cluster in Seurat
2.6 years ago by
Pratik
★ 1.0k
1
vote
0
replies
1.7k
views
Answer:
Answer: Database for Enhancers with Coordinates
2.7 years ago by
Pratik
★ 1.0k
1
vote
1
reply
887
views
Answer:
Answer: Pathogen-drug network
2.7 years ago by
Pratik
★ 1.0k
0
votes
0
replies
1.1k
views
Comment:
Comment: Chromosome sizes downloading (in bp).
2.7 years ago by
Pratik
★ 1.0k
0
votes
0
replies
1.8k
views
Comment:
Comment: How to rename the elements in columns(txdb)?
2.7 years ago by
Pratik
★ 1.0k
4
votes
3
replies
1.8k
views
How to rename the elements in columns(txdb)?
GenomicFeatures
GenomicRanges
GenomeInfoDb
2.7 years ago by
Pratik
★ 1.0k
0
votes
0
replies
1.8k
views
Comment:
Comment: How to rename the elements from columns(txdb)?
2.7 years ago by
Pratik
★ 1.0k
0
votes
0
replies
6.0k
views
Answer:
Answer: Extracting exons and transcripts from gff3/gtf
2.7 years ago by
Pratik
★ 1.0k
0
votes
0
replies
1.8k
views
Comment:
Comment: Good or bad idea to annotate with newer genome build?
2.7 years ago by
Pratik
★ 1.0k
1
vote
0
replies
1.8k
views
Comment:
Comment: Good or bad idea to annotate with newer genome build?
2.7 years ago by
Pratik
★ 1.0k
4
votes
4
replies
1.8k
views
Good or bad idea to annotate with newer genome build?
array
methylation
beadchip
build
annotation
2.7 years ago by
Pratik
★ 1.0k
0
votes
0
replies
832
views
Why is there not a intronsBy() function in GenomicFeatures? only intronsByTranscript()?
GenomicRanges
GenomicFeatures
genic
introns
intronsbytranscript
2.7 years ago by
Pratik
★ 1.0k
1
vote
1
reply
1.3k
views
Comment:
Comment: Is removing strand information when obtaining intergenic regions from GRanges ne
2.7 years ago by
Pratik
★ 1.0k
1
vote
0
replies
7.3k
views
Comment:
Comment: How to transform the deg gene list from seurat to a gene list input to clusterPr
2.7 years ago by
Pratik
★ 1.0k
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