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Limit : this week
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181 results • Page
3 of 4
Sort: Votes
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Views
Votes
Replies
0
votes
1
reply
139
views
Wrong ZYGOSITY by ensembl vep on DeepVariant vcf file
annotation
vcf
vep
zygosity
deepvariant
2 days ago by
asalimih
▴ 60
0
votes
0
replies
104
views
Reference panel of normals for ensembl named refgenome
Mutect2
5 days ago by
gernophil
▴ 80
0
votes
0
replies
76
views
Understanding behaviour of SCTransform in Seurat
Seurat
scRNASeq
normalization
updated 23 hours ago by
GenoMax
142k • written 23 hours ago by
yura.grabovska
▴ 90
0
votes
1
reply
244
views
Nomalization - TCGA, RNA-seq and Microarray
TCGA
RNA-seq
Nomalization
Microarray
updated 5 days ago by
Zhenyu Zhang
★ 1.2k • written 8 days ago by
jain72744
▴ 10
0
votes
11
replies
545
views
In IGV is this a heterogeneous mutation or false call?
mutations
IGV
heterogeneous
5 days ago by
Tuck898
• 0
0
votes
0
replies
113
views
DOCK6 installation on MacOS M1
installation
troubleshooting
DOCK6
updated 2 days ago by
GenoMax
142k • written 2 days ago by
Rodolfo Adrián
• 0
0
votes
0
replies
129
views
News:
Online course: An Introduction to Nanopore Direct RNA Sequencing
Nanopore
RNAseq
6 days ago by
carlopecoraro2
★ 2.5k
0
votes
1
reply
234
views
input file in rmats
rmats
updated 6 days ago by
Mathew
▴ 140 • written 8 days ago by
Lambodarswain316
• 0
0
votes
2
replies
210
views
Output file of samtools flagstat empty
samtools-flagstat
updated 5 days ago by
colindaven
6.4k • written 5 days ago by
ramendra.sarma
• 0
0
votes
9
replies
601
views
Using VEP annotation output as the input for a second VEP annotation
Annotation
VEP
VCF
2 days ago by
Arton
▴ 10
0
votes
0
replies
89
views
genomic region of transcription factor
search
HOMER
motif
19 hours ago by
qudrat.nii
▴ 10
0
votes
2
replies
223
views
Inquiry about deseq2 transformation
RNA-seq
deseq2
2 days ago by
Chen
• 0
0
votes
5
replies
285
views
bbmerge (bbmap) ~ error with insert size file output
bbtools
bbmerge
bbmap
updated 2 days ago by
GenoMax
142k • written 3 days ago by
chrisk
• 0
0
votes
4
replies
241
views
Sequencing Depth (Read Depth) Calculations
depth
2 days ago by
LucisTheFather
• 0
0
votes
0
replies
127
views
select set of intervals that cover a genomic region
GRanges
bed
2 days ago by
ntsopoul
▴ 60
0
votes
1
reply
574
views
scRNAseq quality control weird double curve in nFeature vs nCount plot
scRNA-seq
QC
single
cell
BDRhapsody
analysis
updated 2 days ago by
valdirbarth
▴ 20 • written 12 months ago by
Salomé
• 0
0
votes
9
replies
352
views
Duplicated reads (IDs) from nanopore sequencing
bam
nanopore
sequencing
2 days ago by
njornet
▴ 20
0
votes
0
replies
113
views
qPCR gene expression data analysis
qPCR
geneexpression
anova
2 days ago by
ebertomeup
• 0
0
votes
0
replies
109
views
Blog:
The Current State and Future Prospects of Long-Read Sequencing
LRS
2 days ago by
Novogene
▴ 420
0
votes
1
reply
157
views
Manual Assembly and Protein Translation, HELP, assignment revision
sequence
university
assembly
protein
genomics
updated 5 days ago by
Philipp Bayer
8.5k • written 5 days ago by
samRayne
• 0
0
votes
1
reply
173
views
What's next after GATK variant calling pipeline?
GATK
pipeline
figures
DNA-seq
updated 2 days ago by
Michael
54k • written 2 days ago by
mgranada3
▴ 30
0
votes
1
reply
168
views
perseus software (version 1.5.5)
preseus
mass
spectrometry
data
updated 2 days ago by
DGTool
▴ 20 • written 3 days ago by
iqra
• 0
0
votes
1
reply
149
views
Seurat v5 and how to correctly integrate across multiple experiments
Seurat
scRNA
R
updated 2 days ago by
Papyrus
★ 2.9k • written 2 days ago by
yura.grabovska
▴ 90
0
votes
7
replies
445
views
RNAseq one control two conditions, shared and exclusive genes
conditions
RNAseq
multiple
Rstudio
updated 5 days ago by
Mohamed Abderrahmane
▴ 20 • written 19 days ago by
matteo.levorato
• 0
0
votes
4
replies
252
views
how to treat the replicates while performing WGCNA
clustering
WGCNA
replicates
3 hours ago by
mavy
▴ 10
0
votes
1
reply
150
views
Difference in number of reads when using duplex and simplex base calling with Dorado
base
calling
nanopore
simplex
dorado
duplex
updated 1 day ago by
GenoMax
142k • written 2 days ago by
Lélé
▴ 10
0
votes
4
replies
407
views
Adata.raw.X in LIANA, something wrong with conversion from Seurat to adata in python.
k
5 days ago by
beginner123
• 0
0
votes
2
replies
232
views
java.nio.bufferunderflowexception haplotypecaller error for bqsr reads
deducplicated
java.nio.bufferunderflowexception
haplotypecaller
bqsr
5 days ago by
analyst
▴ 50
0
votes
4
replies
247
views
calculating genomic coverage/ base overlap in R
genomics
updated 1 day ago by
Ram
43k • written 2 days ago by
Xbox_27
• 0
0
votes
0
replies
106
views
cat-bgen fail
bgenix
updated 1 day ago by
Ram
43k • written 1 day ago by
lambard
• 0
0
votes
0
replies
66
views
sci-RNA-seq
cell
single
seurat
sci-rna-seq
counts
17 hours ago by
kilcdincer
▴ 10
0
votes
1
reply
157
views
How can I calculate the OS of each patient?
overall-survival
updated 1 day ago by
ATpoint
82k • written 1 day ago by
Pedro
• 0
0
votes
2
replies
159
views
Trimming tool
Trimmer
tool
updated 16 hours ago by
ntsopoul
▴ 60 • written 18 hours ago by
GeneC
• 0
0
votes
0
replies
108
views
Error when running create-maf-vcf at convertGVCFToHVCFForChrom step - PHGv2
PHG
pangenome
PHG_v2
1 day ago by
Jsarria.EEAD
• 0
0
votes
6
replies
263
views
ComplexHeatmap - How to change fontsize of rowAnnotation
ComplexHeatmap
14 hours ago by
hannes.bongartz
• 0
0
votes
0
replies
103
views
Use of ichor CNA
Dog
CNA
genome
1 day ago by
sainavyav22
• 0
0
votes
2
replies
149
views
GG Sankey plot
GO
sankey_plot
gglpot
updated 14 hours ago by
LauferVA
4.2k • written 19 hours ago by
ijarne
• 0
0
votes
0
replies
63
views
Cell type annotation mixed with other type cells
cell
annotation.
updated 14 hours ago by
GenoMax
142k • written 14 hours ago by
Long
• 0
0
votes
1
reply
196
views
Generating .bed file and .map file for polyploid vcf file through plink
bed
polyploid
map
plink
updated 5 days ago by
chrchang523
10k • written 10 days ago by
analyst
▴ 50
0
votes
1
reply
123
views
Design for complex RNA-Seq experiment using Deseq2
Model.Matrix
RNA-Seq
Limma
DESeq2
edgeR
updated 14 hours ago by
swbarnes2
14k • written 18 hours ago by
Ezequiel
• 0
0
votes
0
replies
49
views
How can i use ESM-1v ?
VEP
ESM-1v
9 hours ago by
Meto
• 0
0
votes
7
replies
4.3k
views
B allele frequency (BAF)
snp
updated 7 hours ago by
aidangcruickshank
▴ 10 • written 3.7 years ago by
rthapa
▴ 90
0
votes
4
replies
243
views
How to handle duplicated genes in TCGA data?
TCGA
GDC
mRNA
updated 2 hours ago by
txema.heredia
▴ 130 • written 1 day ago by
Ngrin
• 0
0
votes
0
replies
112
views
lncRNA
tcga
lncrna
5 days ago by
jain72744
▴ 10
0
votes
5
replies
335
views
How to convert normalized BigWig file to count matrix?
count-matrix
BigWig
5 days ago by
feather-W
• 0
0
votes
0
replies
97
views
Help interpreting KEGG module definitions for converting to NetworkX graph
definition
kegg
module
database
genomics
1 day ago by
O.rka
▴ 720
0
votes
0
replies
1
view
Broad and Narrow peaks
ATAC
ChIP
seq
just now by
Jacek
▴ 20
0
votes
1
reply
154
views
Add line under stat test
stats
R
updated 1 day ago by
Nyksubuz
▴ 20 • written 2 days ago by
Ghada
• 0
0
votes
1
reply
154
views
BiomartException: Query ERROR for existing dataset in BioMart
biomart
ensembl
wheat
python
pybiomart
updated 1 day ago by
Nyksubuz
▴ 20 • written 2 days ago by
Luqman
• 0
0
votes
4
replies
281
views
How to extract cells of different species after mapping with combined genome?
snRNA-seq
scRNA-seq
updated 1 day ago by
Tony
• 0 • written 2 days ago by
vk
▴ 10
181 results • Page
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Recent Votes
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Answer: ChatGPT optimized for bioinformatics questions
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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. Our resul…
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…
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
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