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509
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Answer: Answer: adding gene and CDS feature types in ensemble gtf annotation with transcript and
20 days ago by Pratik ★ 1.0k
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0
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224
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Answer: Answer: How to do DE between cells expressing specific gene in scanpy?
29 days ago by Pratik ★ 1.0k
1
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1
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395
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Answer: Answer: Get the gene functions specific for clusters (RNA seq)
3 months ago by Pratik ★ 1.0k
0
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0
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489
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Comment: Comment: Should centering and scaling be done on methylation beta values for principal co
3 months ago by Pratik ★ 1.0k
1
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2
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489
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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
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0
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468
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Comment: Comment: Is it possible to bulk-download gene expression + methylation data for a specifi
3 months ago by Pratik ★ 1.0k
4
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3
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468
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Is it possible to bulk-download gene expression + methylation data for a specific copy number loss on TCGA?
tcga
updated 3 months ago by ★ 1.2k • written 3 months ago by ★ 1.0k
0
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0
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7.8k
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Comment: Comment: How to find CpG island shore?
17 months ago by Pratik ★ 1.0k
0
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1
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7.8k
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Answer: Answer: How to find CpG island shore?
17 months ago by Pratik ★ 1.0k
4
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1
reply
629
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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 82k • written 19 months ago by ★ 1.0k
0
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0
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573
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Job: Research Technician – Computational Biology Core - (UConn CBC) - Connecticut
connecticut technician
updated 17 months ago by 43k • written 19 months ago by ★ 1.0k
12
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3
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831
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Conceptual questions regarding computational genome/annotation versions and their impact on the actual truth of sequencing?
wes sequencing wgs rna-seq
updated 19 months ago by 3.9k • written 19 months ago by ★ 1.0k
0
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0
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849
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Comment: Comment: Pros and Cons of DNA Mass Spectrometry versus WES/WGS?
20 months ago by Pratik ★ 1.0k
3
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2
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849
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Pros and Cons of DNA Mass Spectrometry versus WES/WGS?
spec mass wes dna wgs
20 months ago by Pratik ★ 1.0k
0
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1
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6.0k
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Comment: Comment: What is a count matrix for input into Seurat supposed to look like?
23 months ago by Pratik ★ 1.0k
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0
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36k
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Comment: Comment: How to embed known cell information into Seurat object? AddMetaData?
2.1 years ago by Pratik ★ 1.0k
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0
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1.7k
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Comment: Comment: Seurat subset cluster cell annotation
2.3 years ago by Pratik ★ 1.0k
3
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0
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1.4k
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Answer: Answer: scSeq millions of cells
2.3 years ago by Pratik ★ 1.0k
1
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1
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1.5k
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Comment: Comment: Forcing Seurat to include certain genes during integration
2.3 years ago by Pratik ★ 1.0k
0
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1
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1.8k
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Answer: Answer: scRNA seq differential gene expression analyses
2.4 years ago by Pratik ★ 1.0k
13
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4
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14k
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How to use FindSubCluster in Seurat?
seurat R single cell RNA-seq
updated 2.4 years ago by • 0 • written 3.2 years ago by ★ 1.0k
0
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0
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6.0k
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Comment: Comment: What is a count matrix for input into Seurat supposed to look like?
2.4 years ago by Pratik ★ 1.0k
6
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10
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6.0k
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What is a count matrix for input into Seurat supposed to look like?
R RNA-Seq Monocle3 Seurat
updated 23 months ago by 43k • written 3.7 years ago by ★ 1.0k
4
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1
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1.8k
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Answer: Answer: how to find each cluster in single-cell represent which cell type?
2.5 years ago by Pratik ★ 1.0k
3
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1
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1.2k
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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
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1
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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
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3
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2.5k
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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 ▴ 240 • written 2.5 years ago by ★ 1.0k
1
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0
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826
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Comment: Comment: PathFindR: Running Reactome for Mouse
2.5 years ago by Pratik ★ 1.0k
0
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0
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651
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Comment: Comment: Finding players and targets of expression-regulating pathways
2.4 years ago by Pratik ★ 1.0k
0
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0
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2.7k
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Comment: Comment: How to compare expression levels of specific genes between sample groups after g
2.5 years ago by Pratik ★ 1.0k
0
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2
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2.7k
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Comment: Comment: How to compare expression levels of specific genes between sample groups after g
2.5 years ago by Pratik ★ 1.0k
6
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6
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2.7k
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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
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1
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1.0k
views
Comment: Comment: How to create shiny app for deseq2 object creation
2.5 years ago by Pratik ★ 1.0k
0
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0
replies
1.0k
views
Answer: Answer: Entry level jobs
2.5 years ago by Pratik ★ 1.0k
7
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0
replies
1.2k
views
Answer: Answer: General question about clustering in scRNAseq
2.5 years ago by Pratik ★ 1.0k
2
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1
reply
773
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Is a single dot on a UMAP or t-SNE for scRNA-seq - a single cell?
scRNA-seq
updated 2.5 years ago by ★ 16k • written 2.5 years ago by ★ 1.0k
0
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0
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1.8k
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Answer: Answer: How to show relabel sub cluster on the original cluster in Seurat
2.6 years ago by Pratik ★ 1.0k
1
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0
replies
1.7k
views
Answer: Answer: Database for Enhancers with Coordinates
2.6 years ago by Pratik ★ 1.0k
1
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1
reply
880
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Answer: Answer: Pathogen-drug network
2.6 years ago by Pratik ★ 1.0k
0
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0
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1.0k
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Comment: Comment: Chromosome sizes downloading (in bp).
2.6 years ago by Pratik ★ 1.0k
0
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0
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1.7k
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Comment: Comment: How to rename the elements in columns(txdb)?
2.6 years ago by Pratik ★ 1.0k
4
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3
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1.7k
views
How to rename the elements in columns(txdb)?
GenomicFeatures GenomicRanges GenomeInfoDb
2.6 years ago by Pratik ★ 1.0k
0
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0
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1.7k
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Comment: Comment: How to rename the elements from columns(txdb)?
2.6 years ago by Pratik ★ 1.0k
0
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0
replies
5.9k
views
Answer: Answer: Extracting exons and transcripts from gff3/gtf
2.6 years ago by Pratik ★ 1.0k
0
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0
replies
1.8k
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Comment: Comment: Good or bad idea to annotate with newer genome build?
2.6 years ago by Pratik ★ 1.0k
1
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0
replies
1.8k
views
Comment: Comment: Good or bad idea to annotate with newer genome build?
2.6 years ago by Pratik ★ 1.0k
4
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4
replies
1.8k
views
Good or bad idea to annotate with newer genome build?
array methylation beadchip build annotation
2.6 years ago by Pratik ★ 1.0k
0
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0
replies
820
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
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1
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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
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0
replies
7.1k
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
171 results • Page 1 of 4
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