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28 results • Page
1 of 1
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0
votes
0
replies
32
views
How can i use ESM-1v ?
VEP
ESM-1v
3 hours ago by
Meto
• 0
0
votes
0
replies
54
views
RNAseq coverage vs depth for transcript isoform expression?
RNAseq
updated 7 hours ago by
GenoMax
142k • written 7 hours ago by
marineandriot
• 0
0
votes
1
reply
104
views
Design for complex RNA-Seq experiment using Deseq2
Model.Matrix
RNA-Seq
Limma
DESeq2
edgeR
updated 8 hours ago by
swbarnes2
14k • written 12 hours ago by
Ezequiel
• 0
0
votes
0
replies
54
views
Cell type annotation mixed with other type cells
cell
annotation.
updated 8 hours ago by
GenoMax
142k • written 8 hours ago by
Long
• 0
0
votes
2
replies
139
views
Trimming tool
Trimmer
tool
updated 10 hours ago by
ntsopoul
▴ 60 • written 12 hours ago by
GeneC
• 0
0
votes
0
replies
59
views
sci-RNA-seq
cell
single
seurat
sci-rna-seq
counts
11 hours ago by
kilcdincer
▴ 10
0
votes
2
replies
123
views
GG Sankey plot
GO
sankey_plot
gglpot
updated 8 hours ago by
LauferVA
4.2k • written 12 hours ago by
ijarne
• 0
0
votes
0
replies
82
views
genomic region of transcription factor
search
HOMER
motif
13 hours ago by
qudrat.nii
▴ 10
1
vote
5
replies
283
views
Reconstruction of locus, order contigs
contigs
cluster
alignment
locus
updated 12 hours ago by
dthorbur
★ 2.0k • written 1 day ago by
BATMAN
• 0
0
votes
6
replies
242
views
ComplexHeatmap - How to change fontsize of rowAnnotation
ComplexHeatmap
8 hours ago by
hannes.bongartz
• 0
0
votes
0
replies
67
views
Understanding behaviour of SCTransform in Seurat
Seurat
scRNASeq
normalization
updated 17 hours ago by
GenoMax
142k • written 17 hours ago by
yura.grabovska
▴ 90
4
votes
7
replies
449
views
In one PCA plot, can I calculate the percentage of different factors that contribute to the PCA?
PCA
R
VARIANCE
updated 17 hours ago by
marco.barr
▴ 130 • written 2 days ago by
diqixiaoyaoer
▴ 20
0
votes
0
replies
75
views
constructing pangenome through psvcp
psvcp
pangenome
20 hours ago by
analyst
▴ 50
0
votes
1
reply
110
views
What marks a De-Novo Genome assembly as FAILED?
nanopore
denovo
illumina
assembly
genome
updated 19 hours ago by
dthorbur
★ 2.0k • written 20 hours ago by
Umer
▴ 50
0
votes
3
replies
208
views
How to handle duplicated genes in TCGA data?
TCGA
GDC
mRNA
5 hours ago by
Ngrin
• 0
4
votes
9
replies
412
views
Faster Needleman-Wunsch rapid global alignment of two sequences?
Needleman-Wunsch
alignment
16 hours ago by
Gabriel R.
★ 2.9k
0
votes
2
replies
181
views
How to generate table_annovar from VCF input?
vcf
annovar
updated 22 hours ago by
Pierre Lindenbaum
161k • written 1 day ago by
melissachua90
▴ 70
0
votes
1
reply
220
views
solution-Transcriptome.cpp:18:Transcriptome: exiting because of *INPUT FILE* error: could not open input file /geneInfo.tab #2142
STAR
updated 19 hours ago by
GenoMax
142k • written 1 day ago by
huxiangyulove
• 0
0
votes
4
replies
268
views
Merge clusters in Seurat UMAP
seurat
umap
21 hours ago by
kilcdincer
▴ 10
6
votes
4
replies
284
views
Details on salmon index
Salmon
updated 16 hours ago by
Rob
6.6k • written 1 day ago by
Lorenzo
• 0
3
votes
4
replies
280
views
Would you bother re-mapping RNA-seq data from an old GRCh38 build to a newer version?
RNA-seq
patch
freeze
genome
updated 14 hours ago by
Jeremy Leipzig
22k • written 1 day ago by
Ali
• 0
2
votes
11
replies
663
views
DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts in whole blood: is it normal to always get NS?
rstudio
DEG
limma
22 hours ago by
egascon
• 0
0
votes
3
replies
242
views
Sam file Header problem
Sam
Header
problem
file
updated 22 hours ago by
Pierre Lindenbaum
161k • written 2 days ago by
saifulislam99121
• 0
0
votes
3
replies
217
views
how to treat the replicates while performing WGCNA
clustering
WGCNA
replicates
updated 13 hours ago by
andres.firrincieli
3.6k • written 2 days ago by
mavy
▴ 10
1
vote
15
replies
633
views
Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NULL > pointer.
blast
ncbi
28 minutes ago by
hophuquy0944
• 0
1
vote
8
replies
401
views
Overlapping Ranges within Granges object
Genomicranges
IRanges
GRanges
updated 1 hour ago by
Alex Reynolds
35k • written 4 days ago by
ntsopoul
▴ 60
0
votes
7
replies
4.2k
views
B allele frequency (BAF)
snp
updated 2 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 13 hours ago by
alanh
▴ 170 • written 7.1 years ago by
jonessara770
▴ 240
28 results • Page
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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…
Answer: Trimming tool
by
GenoMax
142k
There are plenty. `bbduk.sh` from BBMap suite (https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/bbduk-guide/ )…
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation
by
bk11
★ 2.5k
Please check out [in this link.][1] [1]: https://github.com/jokergoo/ComplexHeatmap/issues/349
Comment: Reconstruction of locus, order contigs
by
dthorbur
★ 2.0k
[Here](https://www.biostars.org/p/9544689/) is a forum post that may answer your question.
Comment: how to treat the replicates while performing WGCNA
by
andres.firrincieli
3.6k
> 1) I do not want to merge the MEs rather I asked about replicates, as > some replicates of same sample are showing different behavior for…
Comment: How to systematically check if a bam file is truncated
by
alanh
▴ 170
For more details about what `samtools quickcheck` actually checks for, add a few `-v`'s to the command line. $ samtools quickcheck -…
Comment: How to handle duplicated genes in TCGA data?
by
Zhenyu Zhang
★ 1.2k
Second what is said above, ensembl_id is the unique identifier. As a good bioinformatics habit, always use unique identifier for your anal…
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