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21 results • Page
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Tera-scale metagenomic coassembly tool
co-assembly
Metagenomics
just now by
Moinuddin
• 0
0
votes
1
reply
27
views
Broad and Narrow peaks
ATAC
ChIP
seq
updated 1 hour ago by
ATpoint
82k • written 1 hour ago by
Jacek
▴ 20
1
vote
1
reply
105
views
RNAseq coverage vs depth for transcript isoform expression?
RNAseq
updated 20 minutes ago by
Gordon Smyth
★ 7.2k • written 15 hours ago by
marineandriot
• 0
0
votes
0
replies
50
views
How can i use ESM-1v ?
VEP
ESM-1v
11 hours ago by
Meto
• 0
0
votes
1
reply
133
views
Design for complex RNA-Seq experiment using Deseq2
Model.Matrix
RNA-Seq
Limma
DESeq2
edgeR
updated 15 hours ago by
swbarnes2
14k • written 19 hours ago by
Ezequiel
• 0
0
votes
0
replies
65
views
Cell type annotation mixed with other type cells
cell
annotation.
updated 15 hours ago by
GenoMax
142k • written 16 hours ago by
Long
• 0
0
votes
2
replies
164
views
Trimming tool
Trimmer
tool
updated 17 hours ago by
ntsopoul
▴ 60 • written 19 hours ago by
GeneC
• 0
0
votes
0
replies
67
views
sci-RNA-seq
cell
single
seurat
sci-rna-seq
counts
18 hours ago by
kilcdincer
▴ 10
0
votes
2
replies
154
views
GG Sankey plot
GO
sankey_plot
gglpot
updated 15 hours ago by
LauferVA
4.2k • written 20 hours ago by
ijarne
• 0
0
votes
0
replies
90
views
genomic region of transcription factor
search
HOMER
motif
20 hours ago by
qudrat.nii
▴ 10
1
vote
5
replies
299
views
Reconstruction of locus, order contigs
contigs
cluster
alignment
locus
updated 20 hours ago by
dthorbur
★ 2.0k • written 1 day ago by
BATMAN
• 0
0
votes
6
replies
268
views
ComplexHeatmap - How to change fontsize of rowAnnotation
ComplexHeatmap
16 hours ago by
hannes.bongartz
• 0
0
votes
4
replies
257
views
How to handle duplicated genes in TCGA data?
TCGA
GDC
mRNA
updated 4 hours ago by
txema.heredia
▴ 130 • written 1 day ago by
Ngrin
• 0
3
votes
4
replies
287
views
Would you bother re-mapping RNA-seq data from an old GRCh38 build to a newer version?
RNA-seq
patch
freeze
genome
updated 22 hours ago by
Jeremy Leipzig
22k • written 2 days ago by
Ali
• 0
0
votes
4
replies
261
views
how to treat the replicates while performing WGCNA
clustering
WGCNA
replicates
5 hours ago by
mavy
▴ 10
1
vote
15
replies
670
views
Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NULL > pointer.
blast
ncbi
8 hours ago by
hophuquy0944
• 0
0
votes
5
replies
254
views
calculating genomic coverage/ base overlap in R
genomics
updated 43 minutes ago by
1769mkc
★ 1.2k • written 3 days ago by
Xbox_27
• 0
1
vote
8
replies
430
views
Overlapping Ranges within Granges object
Genomicranges
IRanges
GRanges
updated 9 hours ago by
Alex Reynolds
35k • written 4 days ago by
ntsopoul
▴ 60
1
vote
4
replies
283
views
Help with Biopython for Beginner
Python
ORF
FASTA
Biopython
updated 2 hours ago by
Joe
21k • written 9 days ago by
cput
• 0
0
votes
7
replies
4.3k
views
B allele frequency (BAF)
snp
updated 9 hours ago by
aidangcruickshank
▴ 10 • written 3.7 years ago by
rthapa
▴ 90
38
votes
12
replies
31k
views
9 follow
How to systematically check if a bam file is truncated
Exomeseq
updated 21 hours ago by
alanh
▴ 170 • written 7.1 years ago by
jonessara770
▴ 240
21 results • Page
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Recent Votes
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
Answer: RNAseq coverage vs depth for transcript isoform expression?
Answer: ChatGPT optimized for bioinformatics questions
Comment: ChatGPT optimized for bioinformatics questions
C: How can I perform Differential expression analysis with just one control and one
C: How can I perform Differential expression analysis with just one control and one
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Popular Question
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mohammadhassanj
▴ 260
Scholar
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dsull
★ 6.0k
Popular Question
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finswimmer
16k
Popular Question
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Ezequiel
• 0
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alanh
▴ 170
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Peter
6.0k
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ashkan
▴ 160
Recent Replies
Comment: calculating genomic coverage/ base overlap in R
by
1769mkc
★ 1.2k
you can `dput(head(df)` for the both the data frame so that other can test for possible solutions
Comment: Broad and Narrow peaks
by
ATpoint
82k
What is your question? It's unclear.
Comment: Help with Biopython for Beginner
by
Joe
21k
One question before offering more solutions: are you trying to learn Python with this as an example problem, or are you trying to find the …
Answer: RNAseq coverage vs depth for transcript isoform expression?
by
Gordon Smyth
★ 7.2k
See the exploration of isoform precision vs read length and sequencing depth in our paper: https://doi.org/10.1093/nar/gkad1167. Table 1 o…
Comment: How to handle duplicated genes in TCGA data?
by
txema.heredia
▴ 130
Why does the tool require gene symbols and not ensembl ids? Is it retrieving information from somewhere else? If so, your best bet is to fi…
Comment: how to treat the replicates while performing WGCNA
by
mavy
▴ 10
Thank you so much for your response . Really appreciate it. I will try the way you mentioned and will get back if I have any query
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
hophuquy0944
• 0
i have the same error, i used high performance computer, here is my code to set memory. srun --nodes=1 --ntasks=1 --cpus-per-task=24 -…
Comment: Overlapping Ranges within Granges object
by
Alex Reynolds
35k
Yes, `bedmap` will perform operations on one or two BED files.
Comment: B allele frequency (BAF)
by
aidangcruickshank
▴ 10
Apologies for resurrecting this post, but any idea what that functions "regions" paramater takes? Would it be a GRanges object? The documen…
Comment: How to handle duplicated genes in TCGA data?
by
Ngrin
• 0
Thanks @txema.heredia.The tool I am going to use only accepts gene symbols. This is the reason. So I cannot use ENS IDs.
Answer: Design for complex RNA-Seq experiment using Deseq2
by
swbarnes2
14k
This is a rather small experiment, I don't know that you can establish a meaningful baseline for each patient with a single pre sample, and…
Comment: GG Sankey plot
by
LauferVA
4.2k
@bk11 i changed this comment to an answer. if you disagree please let me know. thanks for sharing your knowledge. VAL
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation
by
hannes.bongartz
• 0
Thanks for the input. Unfortunately, that didn't help either. I appreciate any other tips. Thank you
Answer: GG Sankey plot
by
bk11
★ 2.5k
You need to change your data table into a 'long' format. You can do something like this- GOs_childs_recursive <- GOs_childs_recursive …
Answer: Trimming tool
by
ntsopoul
▴ 60
I use Trim Galore which automatically recognizes adaptors. https://github.com/FelixKrueger/TrimGalore Here is the script I am using for…
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