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12,590 results • Page
2 of 252
Sort: Rank
Rank
Views
Votes
Replies
0
votes
4
replies
267
views
how to treat the replicates while performing WGCNA
clustering
WGCNA
replicates
8 hours ago by
mavy
▴ 10
1
vote
1
reply
247
views
Calculate allelic frequency from VEP output vcf file
VEP
variant
2 days ago by
ramiro.barrantes
• 0
2
votes
6
replies
1.9k
views
How can you *consistently* download BioProject IDs from NCBI's BioSample database using Entrez Direct?
XML
ncbi
entrez-direct
updated 2 days ago by
Ram
43k • written 3.9 years ago by
millere
• 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
154
views
Add line under stat test
stats
R
updated 1 day ago by
Nyksubuz
▴ 20 • written 2 days ago by
Ghada
• 0
1
vote
5
replies
800
views
Converting IGV to Figure using Illustrator (or other tools)
Illustrator
IGV
written 6 months ago by
Daniel
▴ 30
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
1
vote
3
replies
207
views
Genotyping sites with N in reference genome
GATK
UnifiedGenotyper
updated 2 days ago by
Zhenyu Zhang
★ 1.2k • written 3 days ago by
shpak.max
▴ 50
2
votes
4
replies
271
views
Can 5' and 3' scRNAseq be processed with the same pipeline?
singlecell
seurat
10XGenomics
scRNAseq
updated 3 days ago by
yura.grabovska
▴ 90 • written 3 days ago by
ev97
▴ 20
1
vote
16
replies
696
views
Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NULL > pointer.
blast
ncbi
updated 2 hours ago by
GenoMax
142k • written 3 days ago by
hophuquy0944
• 0
0
votes
4
replies
241
views
Sequencing Depth (Read Depth) Calculations
depth
2 days ago by
LucisTheFather
• 0
0
votes
1
reply
140
views
Wrong ZYGOSITY by ensembl vep on DeepVariant vcf file
annotation
vcf
vep
zygosity
deepvariant
3 days ago by
asalimih
▴ 60
0
votes
0
replies
110
views
Is it okay to assemble my 12 metatranscriptome samples with Trinity separately?
trinity
metatranscriptome
3 days ago by
jway
• 0
2
votes
2
replies
185
views
Cannot install bwa-mem2 via conda
conda
mamba
python
updated 2 days ago by
Ram
43k • written 3 days ago by
jsmith120f
• 0
2
votes
2
replies
197
views
genome finishing
finishing
genome
updated 3 days ago by
nd48
▴ 20 • written 3 days ago by
trezini
• 0
1
vote
5
replies
219
views
Circos Plot to Visualize Chromatin Accessibility Changes from ATAC-seq Data
circos
atacseq
updated 3 days ago by
Pierre Lindenbaum
161k • written 3 days ago by
biology_inform
▴ 50
1
vote
4
replies
290
views
Add stats to boxplot in R
stats
R
2 days ago by
Ghada
• 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 3 days ago by
yura.grabovska
▴ 90
0
votes
1
reply
151
views
Difference in number of reads when using duplex and simplex base calling with Dorado
base
calling
nanopore
simplex
dorado
duplex
updated 2 days ago by
GenoMax
142k • written 3 days ago by
Lélé
▴ 10
0
votes
5
replies
274
views
calculating genomic coverage/ base overlap in R
genomics
updated 4 hours ago by
1769mkc
★ 1.2k • written 3 days ago by
Xbox_27
• 0
1
vote
5
replies
265
views
Annotating file using bcftools
annotation
plink
bcftools
2 days ago by
kl
▴ 10
0
votes
9
replies
352
views
Duplicated reads (IDs) from nanopore sequencing
bam
nanopore
sequencing
2 days ago by
njornet
▴ 20
0
votes
3
replies
165
views
Problem with Calling Variants from RNA-Seq data
vcf
gatk
benchmark
giab
rna-seq
3 days ago by
Esraa
• 0
3
votes
3
replies
229
views
Getting differential ChIP-seq peaks between conditions after calling consensus peaks
MAnorm
ChIP-seq
consensus
peaks
updated 2 days ago by
ATpoint
82k • written 3 days ago by
Alexandra
• 0
3
votes
1
reply
240
views
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
limma
updated 3 days ago by
dariober
14k • written 4 days ago by
Holly
▴ 30
1
vote
4
replies
284
views
Filtering VCF files based on VAF giving incorrect results
bcftools
GATK
Bioinformatics
picard
VCF
2 days ago by
Arton
▴ 10
0
votes
0
replies
94
views
ReactomeGSA
ReactomeGSA
3 days ago by
Shaimaa Gamal
▴ 10
0
votes
0
replies
86
views
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
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
1
reply
169
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
0
replies
99
views
Why the shape of RCS is contradictory to the p value for nonlinearity.
RCS
ggplot2
ggplot
R
updated 3 days ago by
GenoMax
142k • written 3 days ago by
Dude
• 0
0
votes
0
replies
96
views
NEURON, Brian2, NEST, or PyNN
NEST
NEURON
PyNN
Brian2
3 days ago by
brunofelicianodeomena
• 0
1
vote
2
replies
210
views
Alphafold 3 pLDDT coloring scheme in chimerax?
ChimeraX
Alphaphold
Alphaphold3
updated 3 days ago by
colindaven
6.4k • written 3 days ago by
mbrav005
• 0
0
votes
1
reply
146
views
Polish a large genome with Pilon
Pilon
Pacbio
Polish
Illumina
3 days ago by
sansan_96
▴ 90
1
vote
2
replies
224
views
Doubt about the process of annotation, detection, identification and classification of transposable elements
annotation
TransposableElements
2 days ago by
MarcosCosta
• 0
2
votes
2
replies
205
views
Genome Visualization Tools
bacterial
genome
updated 3 days ago by
GenoMax
142k • written 3 days ago by
dlera.lozano
▴ 10
2
votes
3
replies
215
views
RSeQC : infer_experiment.py Error: Could not retrieve index file
RSeQC
RNA-Seq
updated 3 days ago by
Ram
43k • written 3 days ago by
Prawesh
• 0
1
vote
3
replies
283
views
Using ggplotly in R
ggplot
ggplotly
updated 3 days ago by
jared.andrews07
★ 16k • written 3 days ago by
jen
▴ 10
1
vote
2
replies
228
views
Why does assigning genes with biomart give me different values than using a transcripts_to_genes.txt file?
biomart
RNAseq
kallisto
2 days ago by
bioinfo
▴ 150
0
votes
3
replies
264
views
RNAseq RNA content
mRNA
Linux
rRNA
RNA-seq
RNA
updated 3 days ago by
noodle
▴ 580 • written 4 days ago by
doramora
▴ 10
0
votes
1
reply
146
views
Post-imputation QC for input into GWAS analyses
gwas
prs
updated 3 days ago by
LauferVA
4.2k • written 4 days ago by
graeme.thorn
▴ 100
0
votes
2
replies
189
views
Using Cutadapt to trim adapters from paired-end small RNA sequence data
trimming
adapters
cutadapt
sRNA-seq
smallRNA
3 days ago by
melissa.joubert
• 0
4
votes
1
reply
204
views
Extracting only 4-fold degenerate sites from gene sequences/alignments?
alignments
4 days ago by
J.
▴ 40
0
votes
0
replies
110
views
Is there a real ground truth for CNV data?
CNV
4 days ago by
jennyp0706
• 0
0
votes
3
replies
213
views
Biomart issue, why so few 3'utrs?
utr
biomart
updated 4 days ago by
GenoMax
142k • written 4 days ago by
RNAseqer
▴ 270
1
vote
1
reply
147
views
sci-RNA-seq
Seurat
sci-RNA-seq
updated 3 days ago by
Ram
43k • written 4 days ago by
kilcdincer
▴ 10
4
votes
4
replies
3.0k
views
CNVkit for somatic copy number detection
cnv
cnvkit
exome
WES
updated 4 days ago by
Anitha
• 0 • written 5.1 years ago by
stephaniem
• 0
1
vote
8
replies
433
views
Overlapping Ranges within Granges object
Genomicranges
IRanges
GRanges
updated 12 hours ago by
Alex Reynolds
35k • written 4 days ago by
ntsopoul
▴ 60
0
votes
3
replies
204
views
How to access GWAVA software of data
GWAVA
updated 4 days ago by
GenoMax
142k • written 4 days ago by
nonaddldy
▴ 10
0
votes
2
replies
223
views
Inquiry about deseq2 transformation
RNA-seq
deseq2
2 days ago by
Chen
• 0
12,590 results • Page
2 of 252
Recent Votes
constructing pangenome through psvcp
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
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Recent Replies
Comment: constructing pangenome through psvcp
by
analyst
▴ 50
Fixed the issue by updating nucmer version.
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
GenoMax
142k
Can you create a small test database (`makeblastdb`) from your query file and try to run the search against the same file and see if that w…
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
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