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ipa gene-set-enrichment statistics

updated 12 months ago by Ram 43k • written 3.4 years ago by Aspire ▴ 330

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Popular Question to ashkan ▴ 160

Supporter to Umer ▴ 50

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Answer: RNAseq coverage vs depth for transcript isoform expression? by Gordon Smyth ★ 7.2k

See the exploration of isoform precision vs read length and sequencing depth in our paper: https://doi.org/10.1093/nar/gkad1167. Our resul…

Comment: How to handle duplicated genes in TCGA data? by txema.heredia ▴ 130

Why does the tool require gene symbols and not ensembl ids? Is it retrieving information from somewhere else? If so, your best bet is to fi…

Comment: how to treat the replicates while performing WGCNA by mavy ▴ 10

Thank you so much for your response . Really appreciate it. I will try the way you mentioned and will get back if I have any query

Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU by hophuquy0944 • 0

i have the same error, i used high performance computer, here is my code to set memory. srun --nodes=1 --ntasks=1 --cpus-per-task=24 -…

Comment: Overlapping Ranges within Granges object by Alex Reynolds 35k

Yes, `bedmap` will perform operations on one or two BED files.

Comment: B allele frequency (BAF) by aidangcruickshank ▴ 10

Apologies for resurrecting this post, but any idea what that functions "regions" paramater takes? Would it be a GRanges object? The documen…

Comment: How to handle duplicated genes in TCGA data? by Ngrin • 0

Thanks @txema.heredia.The tool I am going to use only accepts gene symbols. This is the reason. So I cannot use ENS IDs.

Answer: Design for complex RNA-Seq experiment using Deseq2 by swbarnes2 14k

This is a rather small experiment, I don't know that you can establish a meaningful baseline for each patient with a single pre sample, and…

Comment: GG Sankey plot by LauferVA 4.2k

@bk11 i changed this comment to an answer. if you disagree please let me know. thanks for sharing your knowledge. VAL

Comment: ComplexHeatmap - How to change fontsize of rowAnnotation by hannes.bongartz • 0

Thanks for the input. Unfortunately, that didn't help either. I appreciate any other tips. Thank you

Answer: GG Sankey plot by bk11 ★ 2.5k

You need to change your data table into a 'long' format. You can do something like this- GOs_childs_recursive <- GOs_childs_recursive …

Answer: Trimming tool by ntsopoul ▴ 60

I use Trim Galore which automatically recognizes adaptors. https://github.com/FelixKrueger/TrimGalore Here is the script I am using for…

Answer: Trimming tool by GenoMax 142k

There are plenty. `bbduk.sh` from BBMap suite (https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/bbduk-guide/ )…

Comment: ComplexHeatmap - How to change fontsize of rowAnnotation by bk11 ★ 2.5k

Please check out [in this link.][1] [1]: https://github.com/jokergoo/ComplexHeatmap/issues/349

Comment: Reconstruction of locus, order contigs by dthorbur ★ 2.0k

[Here](https://www.biostars.org/p/9544689/) is a forum post that may answer your question.

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