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pathway database subjective

updated 4 months ago by Peter Karp ▴ 30 • written 13.1 years ago by Shigeta ▴ 470

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Popular Question to Info.shi ▴ 30

Supporter to el24 ▴ 40

Commentator to JACKY ▴ 120

Appreciated to Jon Binkley ▴ 160

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Comment: CHIPSEQ : Cut AND Run , DiffBind Parameters by DINESHR • 0

Regarding Diffbind, How does diffbind calculate common peaks with the samples. I'm observing that certain peaks identified as common using …

Comment: scRNA-seq: Consistent low number of cells and low fraction reads across the samp by rpolicastro 12k

Assuming Cell Ranger was ran correctly it's unlikely that the sample is useable. It looks like most droplets were probably empty.

Comment: bwa mem hangs after a few thousand reads by cee28 ▴ 30

Here is the output with the "-v 4" flag (not showing all the @SQ comments) : > @SQ SN:chrUn_GL000214v1 LN:137718 @SQ SN:chrUn_KI270742v1 L…

Answer: Where is the index command? by Michael 53k

There is a ready-made package for samtools, simply do apt install samtools Also, your screenshot shows you are using the root account…

Comment: bwa mem hangs after a few thousand reads by tshtatland ▴ 180

Use option `-v` with value of 4 or above to help diagnose the issue: `-v INT` Control the verbose level of the output. This option has not…

Comment: bwa mem hangs after a few thousand reads by tshtatland ▴ 180

Cross-posted here: [sequence alignment - bwa mem hangs after a few thousand reads - Bioinformatics Stack Exchange](https://bioinformatics.s…

Comment: Best practices for differential expression analysis with low-yield Nanopore/ONT by tw_140 • 0

Thank you, I really appreciate your insight! I will look into the dropouts I have.

Comment: Generate Read counts from bam file by NextGenSeek • 0

Are you analysing RNA or DNA heteroplasmy levels?

Comment: What type of cancer did they study in this paper? by GenoMax 136k

Perhaps the exact cancer type is not what is important. Looks like they are [**all solid tumors**][1] with a baseline sample and one after …

Comment: p-value combination methods by i.sudbery 18k

edgeR *is* an NB-GLM. The input to NB-GLMs, including edgeR and DESeq is read counts from each sample.

Answer: What type of cancer did they study in this paper? by jared.andrews07 ★ 16k

Cutaneous or ocular melanoma. It's from [this paper](https://aacrjournals.org/cancerimmunolres/article/10/2/162/678013/NKG7-Is-a-T-cell-Int…

Comment: p-value combination methods by sehriban.buyukkilic • 0

its output of edgeR. I'm asking for input of NB-GLM? what should be input of it?

Comment: How do I download a list of genes involved in cellular metabolism (in humans) ba by el24 ▴ 40

Hi @pratik, Thanks for the helpful solution above. I'm working on a similar task in Mouse species and noticed the CTD database is human-spe…

Comment: Match variants for allele frequency, LD score, and other features by Jautis ▴ 520

Trying to bump this

Comment: p-value combination methods by i.sudbery 18k

The parameters you have here are the *output* of an NB-GLM, not the input to an NB-GLM (most likely edgeR?)

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