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18 results • Page
1 of 1
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Views
Votes
Replies
2
votes
11
replies
660
views
Data preparation for a ML model
machine-learning
RNA-Seq
R
python
biomarkers
18 hours ago by
sil_bioinfo
▴ 30
3
votes
4
replies
289
views
scRNA-seq: Consistent low number of cells and low fraction reads across the samples
scRNA-seq
cells
mRNA
expression
gene
updated 4 hours ago by
GenoMax
136k • written 1 day ago by
newbee
▴ 40
0
votes
2
replies
250
views
Can FPKM be used to create bar graphs for DEGs?
RNA-seq
15 hours ago by
junli1988
• 0
0
votes
2
replies
210
views
Cellcyclescoring did not work in Seurat V5
singlecell
updated 23 hours ago by
fracarb8
★ 1.3k • written 1 day ago by
synat.keam
▴ 80
2
votes
2
replies
182
views
R script in docker
R
Visual_studio_code
Docker
19 hours ago by
mrashad
▴ 70
0
votes
3
replies
182
views
In what case there are RR reads but no LL reads when detect inversions using IGV?
IGV
inversion
updated 16 hours ago by
Istvan Albert
99k • written 21 hours ago by
Jingfang
• 0
0
votes
1
reply
141
views
How to check for incorporation of plasmid DNA into human genomic DNA (ChIP-seq)?
plasmid
chipseq
updated 23 hours ago by
Nitin Narwade
★ 1.5k • written 1 day ago by
tss243
• 0
0
votes
1
reply
124
views
PAML Troubleshooting Help
PAML
codeml
updated 18 hours ago by
dthorbur
▴ 880 • written 1 day ago by
sebabiokr
▴ 10
0
votes
1
reply
86
views
How to get multiple protein domain database domain name from id's
annotations
blast2go
domain
domains
proteins
updated 6 hours ago by
GenoMax
136k • written 13 hours ago by
Nicolas
• 0
0
votes
0
replies
72
views
Extract upstream and downstream 50bp nontemplated sequences from a position
search
sequences
nontemplated
motif
11 hours ago by
Ty
• 0
0
votes
0
replies
69
views
How to do KEGG pathway analysis when I have a gene with multiple entrez IDs?
biomart
kegg
deseq2
15 hours ago by
bioinfo
▴ 140
0
votes
0
replies
65
views
How to estimate -g genome-size for Flye for de novo genome or for --meta mode when using Metaflye?
assembly
fasta
genomics
nanopore
pacbio
10 hours ago by
O.rka
▴ 710
0
votes
0
replies
64
views
GO categorization
Ontology
Gene
12 hours ago by
m.habib
• 0
0
votes
0
replies
62
views
Annotate Unplaced Scaffold with Chromosome Information
assembly
annotation
scaffold
Chromosome
15 hours ago by
Trevor
• 0
0
votes
0
replies
53
views
how to download the VCF/MAF files from cBioportal genie site
cBioportal
mutation
VCF
TMB
13 hours ago by
luckyday1661
• 0
0
votes
0
replies
35
views
Osmotic permeability of water transport in aquaporins
permeability
Osmotic
transport
Water
3 hours ago by
Peerzada
• 0
0
votes
0
replies
29
views
doubt about usage of megahit
trinity
megahit
2 hours ago by
meera
• 0
0
votes
0
replies
9
views
An incomprehensible error with R package gggenes
R
gggenes
visualize
21 minutes ago by
alice005201314
• 0
18 results • Page
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Recent Votes
Answer: bcftools mpileup --max depth : What would be a reasonable setting for this optio
Answer: bcftools mpileup --max depth : What would be a reasonable setting for this optio
Answer: What type of cancer did they study in this paper?
Answer: How to filter .fasta file based on conditional statement
A: The RNA-Seq data input for WGCNA in terms of gene co-expression network construc
Answer: Can someone explain PLINK allele REF/ALT management strategy?
Comment: Generate Read counts from bam file
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Recent Awards •
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Commentator
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ATpoint
78k
Popular Question
to
Peerzada
• 0
Popular Question
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luffy
▴ 110
Popular Question
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mohammedtoufiq91
▴ 230
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Mariah.Hoffman
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wiscoyogi
▴ 40
Recent Replies
Answer: Should I scale all genes in single cell Seurat?
by
antonioggsousa
3.0k
Hi, Scaling all features might be useful to plot genes that are not among the 2k HVG in a heatmap. Otherwise than that, I never encounter…
Comment: How to filter .fasta file based on conditional statement
by
rob_DNA
▴ 20
Oh wow that was a bit stupid.. I downloaded 39.06 but I accidentally used 39.01... anyway, thank you very much for your help!! I now used t…
Comment: How can I map coordinates between two strains of yeast?
by
Jimmy
▴ 10
Yes (S. cerevisiae)
Comment: scRNA-seq: Consistent low number of cells and low fraction reads across the samp
by
GenoMax
136k
> less than 100 for some samples Hmm. That is surprising but then in light of that fact ~20% recovery of cells does not sound bad.
Comment: scRNA-seq: Consistent low number of cells and low fraction reads across the samp
by
newbee
▴ 40
Thanks for raising these valid points. I do not have the answer right now. Lately, I heard from the PI that they started with a small numbe…
Comment: How to get multiple protein domain database domain name from id's
by
GenoMax
136k
A list of InterPro domains is available: https://ftp.ebi.ac.uk/pub/databases/interpro/current_release/entry.list
Answer: DIAMOND tutorial
by
GenoMax
136k
`DIAMOND` has a wiki page: https://github.com/bbuchfink/diamond/wiki Links for DIAMOND papers are here: https://github.com/bbuchfink/diamo…
Comment: How to do simple pathway analysis?
by
AK
★ 2.2k
Hi [he1k](https://www.biostars.org/u/139817/), Please use the following script which downloads and parses the keg data on the fly: [keg_hi…
Comment: Is there a need to batch correct FPKM or TPM values for within sample comparison
by
CTLong
▴ 20
That's what I would assume, because we are not taking into account cross sample differences here. Thanks
Comment: Is there a need to batch correct FPKM or TPM values for within sample comparison
by
CTLong
▴ 20
That's a good point. So its probably safest to not batch correct for within sample comparisons I guess?
Answer: Generating count matrix from Chromium Fixed RNA Profiling (FRP) data outside Cel
by
MohammadAlkadi
▴ 70
What is the purpose of doing so? I tried to do that by using the bam file generated by CellRanger. One **important detail** if you are work…
Comment: Guidance on Crucial Parameters for Bioinformatic Analysis of Metabolomic Data
by
Kevin Blighe
86k
Thank you - appreciate the translation.
Answer: Guidance on Crucial Parameters for Bioinformatic Analysis of Metabolomic Data
by
Kevin Blighe
86k
Em geral, uma taxa de descoberta falsa de 5% (p ajustado<0,05 ) deve ser usada para qualquer teste estatístico em que múltiplas hipóteses i…
Answer: WGCNA tutorial docs needed: Horvath Lab site down
by
ATpoint
78k
See link here from the developer: https://bioinformatics.stackexchange.com/a/21886/16676
Comment: WGCNA tutorial docs needed: Horvath Lab site down
by
Katie
• 0
I would also appreciate the PDFs if anyone has them please
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