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Recent Replies
Comment: How to interpret the nine-square plot from mageckFlute
by
ATpoint
66k
That having said, MAGeCK MLE (which FLUTE runs) calcualtes a "representative" β value for each gene as an aggregate of all shRNA/sgRNAs per…
Comment: Does this mean it is running? It has been like this for a while. I am using Trim
by
ATpoint
66k
Look, some general forum etiquette:
This is an open forum where **volunteers** try to help out each other. That means, if you post a quest…
Answer: Automated way to pull representative/RefSeq genome using full species name?
by
GenoMax
123k
Plenty of past threads: https://www.biostars.org/p/396415/ and https://www.biostars.org/p/468971/#468989
https://github.com/kblin/ncbi-…
Answer: How to interpret the nine-square plot from mageckFlute
by
jared.andrews07
★
14k
Light purple means unchanged in treatment samples and decreased in control samples. Dark purple means unchanged in treatment samples and in…
Comment: Meta-analysis of gene expression data versus individual dataset analysis
by
maryam_rashidifar
▴
10
No i just need it for part of my manuscript.
The Challenge is about some additional genes in meta-analysis that were not common in all t…
Comment: CPM or TPM in GSEA analysis
by
benformatics
3.3k
This is **incorrect** since GSEA uses the gene expression **ranks** so you should use the normalized counts (e.g. TPM).
Comment: How to convert abundance table to mean ranked abundance table in R
by
LChart
1.4k
That file is giving you the abundance estimates on a per-sample (per-input-bam-file) basis. "Mean abundance" describes mean of those values…
Comment: Splitting CRAM files
by
GenoMax
123k
Yes. You could do this on the fly.
$ samtools view new.bam | cut -f1 -d$'\t' | cut -f1-4 -d$':' | sort | uniq
NS500177:19:H2HLYAF…
Comment: Splitting CRAM files
by
langziv
▴
20
So I need to convert the CRAM files to FASTQ files in order to get that information?
Comment: ImportError: cannot import name 'transpose' from partially initialized module 't
by
Razi
•
0
Thanks! the problem is solved:
I was using transposer.py by default (it doesn't have an atrribute transpase), so we should rename transpose…
Comment: How to plot ROC curve using qRT-PCR data?
by
Mensur Dlakic
★
21k
If you are asking whether the ROC calculation will work with correlation values instead of `[0, 1]`, the answer is yes. I don't know whethe…
Comment: Gene Tracks from 10x Data
by
LChart
1.4k
IGV
right click reads -> Experiment Type -> RNA
this will split reads out by the "CB" tag for you.
This won't generate .wig files for yo…
Comment: Box plots with logFC values
by
LChart
1.4k
As in you would like to display the logFC as an annotation; or you would like to transform it so that every datapoint is shown not in its a…
Answer: Brain cell type deconvolution
by
LChart
1.4k
The PsychEncode consortium performed cell type deconvolution using non-negative least squares (https://www.science.org/doi/10.1126/science.…
Comment: Box plots with logFC values
by
swbarnes2
12k
How can you do a box plot of a single LogFC value?
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