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19 results • Page
1 of 1
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Views
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4
votes
6
replies
3.8k
views
How to interpret DEXseq results in therms of significance
DEXseq
RNA-Seq
exon
updated 5 hours ago by
Sara
▴ 30 • written 6.7 years ago by
Lila M
★ 1.2k
2
votes
8
replies
438
views
How to access TCGA samples that were treated with a specific drug?
TCGA
RNA-seq
39 minutes ago by
Qroid
▴ 40
0
votes
4
replies
266
views
Question regarding WGCNA
WGCNA
Network-construction
updated 2 hours ago by
andres.firrincieli
3.6k • written 2 days ago by
deepak
• 0
0
votes
4
replies
248
views
Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA2 - where to go from here?
nf-core
16S
amplicon
dada2
ampliseq
10 minutes ago by
sovrappensiero
▴ 90
0
votes
1
reply
229
views
creating batch colum for batch correction
batch-correction
combat
9 hours ago by
Expert
▴ 10
0
votes
1
reply
178
views
Help with DGEList function
DGEList
R
updated 21 hours ago by
marco.barr
▴ 90 • written 2 days ago by
Natali
• 0
2
votes
2
replies
175
views
Gene Specific coverage from WGS data
linux
WGS
Bioinformatics
SARS
CoV2
updated 7 hours ago by
GenoMax
142k • written 6 days ago by
Adyasha
• 0
1
vote
0
replies
142
views
.lgen file has 3+ different alleles
PLINK
lgen
ped
updated 11 hours ago by
zx8754
11k • written 3 days ago by
Emilie
▴ 10
0
votes
0
replies
68
views
How to implement an IGV to streamlit app?
python
streamlit
igv
11 hours ago by
avigail.shnaider
• 0
0
votes
1
reply
66
views
16S rRNA microbiome differential abundance analysis with DESeq2 finds same microbial Genus in both groups.
microbiome
16S
DESeq2
updated 2 hours ago by
andres.firrincieli
3.6k • written 6 hours ago by
Antonio
• 0
0
votes
0
replies
54
views
Error while loading model of Spatial data deconvolution using cell2location
Python
cell2location
updated 7 hours ago by
Ram
43k • written 7 hours ago by
sidrah.maryam
▴ 50
0
votes
0
replies
51
views
Help with VG Toolkit: VCF Output is Empty
vg
updated 10 hours ago by
Pierre Lindenbaum
161k • written 10 hours ago by
sarumonsus
• 0
0
votes
0
replies
44
views
Normalizing AMR gene count data
abundance
RGI
updated 7 hours ago by
Ram
43k • written 7 hours ago by
arshad1292
▴ 100
0
votes
0
replies
41
views
vdjtools
vdjtools
5 hours ago by
yueli7
▴ 250
0
votes
0
replies
39
views
Cox Model with interaction item interpretation
Cox
4 hours ago by
Bine
▴ 60
0
votes
0
replies
37
views
What is the proper way to identify the cell types of scRNAseq cluster?
scRNAseq
4 hours ago by
MAPK2
▴ 40
0
votes
0
replies
32
views
how to downlad slices of CRAM fro ICGC ARGO
icgc
samtools
cram
4 hours ago by
Javier
• 0
0
votes
0
replies
20
views
Applying the metacell2 algorithm using python
single-cell
scanpy
cells
meta
python
1 hour ago by
JACKY
▴ 140
0
votes
0
replies
10
views
How to compute TPM normalized values for TCGA miRNA data?
TCGA
miRNA
TPM
normalization
20 minutes ago by
Ngrin
• 0
19 results • Page
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Recent Votes
Answer: Gene ontology and homologs
Comment: anRichment is missing
Comment: Gene Specific coverage from WGS data
Comment: Gene Specific coverage from WGS data
Comment: High Malat-1 expression in single cell data
A: Meme-Tools: Bit score
Meme-Tools: Bit score
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Recent Replies
Comment: Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA
by
sovrappensiero
▴ 90
Ah, yes this makes sense! I knew this was an issue with, say, using kraken2 on shotgun metagenomic reads, but I don't have a lot of experi…
Comment: How to access TCGA samples that were treated with a specific drug?
by
Qroid
▴ 40
Thank you. Maybe it's best to confirm with the authors about how they're getting responder/non-responder labels. I'll do that now.
Comment: Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA
by
Chris Dean
▴ 390
If you sequenced a short hypervariable region, most of your sequence reads will not be able to be assigned to the species level. One possi…
Comment: anRichment is missing
by
GenoMax
142k
Consider emailing Dr. Horvath about this. Until enough people make him aware of this issue WGCNA "problem" is unlikely to get fixed.
Comment: anRichment is missing
by
Tatyana
• 0
Unfortunately, there are only tutorials and codes for tutorials for WGCNA, not installation files for any their packages... :(
Comment: anRichment is missing
by
GenoMax
142k
See this link for the WGCNA documentation and code from Peter Langfelder : https://bioinformatics.stackexchange.com/questions/21885/where-t…
Comment: anRichment is missing
by
Tatyana
• 0
The problem is back, Horwath's lab web is down again. Is it possible to get anRichment istallation file somewhere? (The greater problem is …
Comment: 16S rRNA microbiome differential abundance analysis with DESeq2 finds same micro
by
andres.firrincieli
3.6k
1. Maribaculaceae is a family not a genus 2. Who said that ASV with the same taxonomic classification must have the same behaviour? 3. With…
Comment: Question regarding WGCNA
by
andres.firrincieli
3.6k
the within-group variability is so small that these look like technical replicates rather than independent biological replicates
Answer: Gene ontology and homologs
by
geneontologyhelp
▴ 400
No. Homology is defined as shared common ancestry. Two genes that take part in the same biological process may not have the same functio…
Answer: error in R code
by
Matthias Zepper
4.6k
I quickly googled [the source code of that function][1], and the error is triggered by this condition: if(length(wn) < 1 || !is.whol…
Comment: Clarification regarding SAM flags "mate reverse strand" (flag 16/0x10) and "read
by
kalavattam
▴ 190
Thanks for the explanation. I noticed and corrected a typo in which "*read* reverse strand" initially read as "*mate* reverse strand" in t…
Comment: Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA
by
sovrappensiero
▴ 90
It's a commercial product, a *Staphylococcus hominis* genome. This species is not found in the DADA2 results, so I guess DADA2 is not ident…
Comment: Question regarding WGCNA
by
Ram
43k
Plots are incomplete without legends. Please share the complete plot with mappings for shape and color.
Comment: Quetion regarding WGCNA
by
deepak
• 0
Thank you for your reply andres.firrincieli. I have attached the PCA plot of the expression data used in the WGCNA. ![enter imag…
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