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182 results • Page
4 of 4
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86
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News:
New course: Manipulation of NGS Data for Genomic and Population Genetics Analyses
KeepLearning
TScourses
3 days ago by
Transmitting Science communication
▴ 70
0
votes
0
replies
94
views
ReactomeGSA
ReactomeGSA
3 days ago by
Shaimaa Gamal
▴ 10
0
votes
3
replies
165
views
Problem with Calling Variants from RNA-Seq data
vcf
gatk
benchmark
giab
rna-seq
2 days ago by
Esraa
• 0
0
votes
9
replies
607
views
Applying the metacell2 algorithm using python
python
single-cell
scanpy
metacell2
updated 2 days ago by
Wayne
★ 2.0k • written 11 days ago by
JACKY
▴ 140
0
votes
0
replies
110
views
Is it okay to assemble my 12 metatranscriptome samples with Trinity separately?
trinity
metatranscriptome
2 days ago by
jway
• 0
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
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
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
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
124
views
select set of intervals that cover a genomic region
GRanges
bed
2 days ago by
ntsopoul
▴ 60
0
votes
1
reply
571
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
351
views
Duplicated reads (IDs) from nanopore sequencing
bam
nanopore
sequencing
2 days ago by
njornet
▴ 20
0
votes
0
replies
110
views
qPCR gene expression data analysis
qPCR
geneexpression
anova
2 days ago by
ebertomeup
• 0
0
votes
0
replies
106
views
Blog:
The Current State and Future Prospects of Long-Read Sequencing
LRS
2 days ago by
Novogene
▴ 420
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
164
views
perseus software (version 1.5.5)
preseus
mass
spectrometry
data
updated 1 day ago by
DGTool
▴ 20 • written 3 days ago by
iqra
• 0
0
votes
1
reply
148
views
Seurat v5 and how to correctly integrate across multiple experiments
Seurat
scRNA
R
updated 1 day ago by
Papyrus
★ 2.9k • written 2 days ago by
yura.grabovska
▴ 90
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
246
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
104
views
cat-bgen fail
bgenix
updated 1 day ago by
Ram
43k • written 1 day ago by
lambard
• 0
0
votes
1
reply
155
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
0
replies
105
views
Error when running create-maf-vcf at convertGVCFToHVCFForChrom step - PHGv2
PHG
pangenome
PHG_v2
1 day ago by
Jsarria.EEAD
• 0
0
votes
0
replies
99
views
Use of ichor CNA
Dog
CNA
genome
1 day ago by
sainavyav22
• 0
0
votes
0
replies
95
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
1
reply
153
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
151
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
279
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
0
votes
0
replies
76
views
How do I quantify the non-coding transcripts that I have generated after using CPAT,PLEK, and BLAST altogether?
transcript
Quantify
non-coding
1 day ago by
Varsha
• 0
0
votes
3
replies
249
views
Sam file Header problem
Sam
Header
problem
file
updated 1 day ago by
Pierre Lindenbaum
161k • written 2 days ago by
saifulislam99121
• 0
0
votes
2
replies
185
views
How to generate table_annovar from VCF input?
vcf
annovar
updated 1 day ago by
Pierre Lindenbaum
161k • written 1 day ago by
melissachua90
▴ 70
182 results • Page
4 of 4
Recent Votes
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
C: How can I perform Differential expression analysis with just one control and one
How can I perform Differential expression analysis with just one control and one cancer sample?
Comment: scRNAseq Differential expression analysis
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★ 6.0k
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Recent Replies
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
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.
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