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Comment: Convert SAM to BAM
A: How Can I Get The Human Chromosome Centromere Position And Chromosome Length In
Comment: Differences in GTF files hg19 and hg38
Answer: plyranges:: summarise() not recognizing previous summarized column (counts)
NM_transcript ID gene identification
Converting Genome Coordinates From One Genome Version To Another (Ucsc Liftover, Ncbi Remap, Ensembl Api)
Converting Genome Coordinates From One Genome Version To Another (Ucsc Liftover, Ncbi Remap, Ensembl Api)
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Comment: Limma returned only positive logFC values
by
Gordon Smyth
★ 6.1k
No, the updated code is no more correct than your original code. Before you undertake any differential expression analysis, you need to ha…
Comment: Differences in GTF files hg19 and hg38
by
heureuse
• 0
Thank you. Noted
Answer: Adjusting for batch effect and covariates with ComBat
by
zahra.elahi
• 0
For your first question that is "Shouldn't PCA analysis of combat_tpm look more homogenous than the original dataset?", NO, because you inc…
Answer: plyranges:: summarise() not recognizing previous summarized column (counts)
by
Alewa
▴ 120
solved, thanks! ``` #calculate the proportions of cpgs per chrom counts_cpgr <- cpgr %>% group_by(seqnames) %>% summarise(cnts = n()) count…
Comment: Limma returned only positive logFC values
by
melissachua90
▴ 40
Thank you for your comments. I've updated my code: group <- factor(type, levels=c("1a", "1b", "1c", "2a", "2b", "2c")) design <- m…
Comment: Creating a local version of Clustered NR database
by
GenoMax
130k
> One idea is to provide just the representative sequences as a first > pass. This seems reasonable since it should capture significant pa…
Comment: pal2nal -nogap -nomismatch options not working
by
Marie
• 0
Hi, did you end up solving this? I am running into the same issue. Marie
Comment: How to get information about promoter from bulk-RNAseq?
by
camillab.
▴ 130
and what about enhancer? is it possible to do it from a bulk-RNAseq?
Comment: How to get information about promoter from bulk-RNAseq?
by
camillab.
▴ 130
yes! clearly the terminology on my side needs to improved!
Comment: How to get information about promoter from bulk-RNAseq?
by
rpolicastro
12k
Generally speaking, most promoters only initiate transcription for a single gene, with a single gene potentially having multiple promoters …
Answer: How to get information about promoter from bulk-RNAseq?
by
Trivas
★ 1.2k
I'd probably select the genes of interest from your bulk RNA-seq results then use the UCSC table browser to get the sequence upstream of th…
Comment: How to add annotation columns with specific colors to the heatmap?
by
Ram
39k
Show us your exact code - it is quite easy to tweak colors in ComplexHeatmap with the `col=` argument.
Comment: VCF file CSQ flag
by
Ram
39k
True, but it's not technically impossible to annotate GVCFs, which is why I did not address that point.
Comment: Creating a local version of Clustered NR database
by
PeterC_NCBI
▴ 260
@genomax Sorry for the delay in reply. We're still working out the details of what exactly to provide. One idea is to provide just the rep…
Comment: Shannon's Entropy by Sliding Window in R
by
rohitsatyam102
▴ 690
Hi Were u able to achieve this?
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