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Alexander
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Matteo Schiavinato
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Michael Love
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Recent Replies
Comment: Frustrated with DEA results
by
Jeremy Leipzig
21k
If the FDR is killing your results, it's ok to filter out genes that are not informative
https://www.bioconductor.org/help/course-materials…
Comment: Github access with token headache
by
Begonia_pavonina
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110
I will post it in StackOverflow, should I delete this thread?
Comment: How to convert data in r?
by
bk11
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1.2k
Hope OP will add biological context to this query and answering-
data <- c(
"A \t 2212 \t 2267 \t 2299",
" \t 2015 \t 2068…
Comment: Github access with token headache
by
Ram
40k
This post does not fit the theme of this forum. Just because you're trying to upload a bioinformatics pipeline does not mean this needs bio…
Comment: Frustrated with DEA results
by
colindaven
5.5k
There are good answers here already which I would follow, but I also would expect to see differences (at least confounders like age, gender…
Comment: How to subset large BAM files specifically/ extract specific subsets?
by
GenoMax
134k
You may be able to do this by using the tool `reformat.sh` from BBTools without remapping.
Can you try:
reformat.sh in=your.bam out=f…
Comment: How to convert data in r?
by
Ram
40k
This post does not fit the theme of this forum. It's a simple R question. Please add more biological context or the question will be delete…
Comment: Number of accessible regions included by DESeq2 to generate the PCA plot with th
by
Michael Love
★
2.5k
Correct, by default.
I just changed in devel branch that it will print this argument to the console when plotPCA() is called.
Comment: CollectRnaSeqMetrics (Picard) output to convert FeatureCounts into TPM
by
Ram
40k
What is your end goal? TPM is only valid for comparing expression in the same sample or a very narrow use case where intra-sample compariso…
Comment: Chip-Seq and correlation of bam file
by
jared.andrews07
★
15k
Yes, which are also output to file by the function. Please read their example.
Comment: How to convert data in r?
by
biofalconch
★
1.0k
A good start would be looking into `stringr`'s `str_split`. Not the complete output but with some effort you can achieve the final result :…
Comment: How to subset large BAM files specifically/ extract specific subsets?
by
ella
•
0
Okay, I understand. I was also not able to succeed with the BED file. I will now reduce the headers in my reference to the IDs (e.g. "Pp3c1…
Comment: Allele frequency calculation for genotype dosage value
by
Sebastian
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Yes, you right. I didn't put it for make the post shorter. Do you know a source where i can confirm my formula? the package gwasurvivr uses…
Comment: How to subset large BAM files specifically/ extract specific subsets?
by
GenoMax
134k
Result file will still contain the original headers. Issue appears to be that you are unable to use those long names with spaces.
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