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758 results • Page
2 of 16
Sort: Rank
Rank
Views
Votes
Replies
1
vote
5
replies
798
views
Converting IGV to Figure using Illustrator (or other tools)
Illustrator
IGV
written 6 months ago by
Daniel
▴ 30
0
votes
0
replies
111
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
202
views
Genotyping sites with N in reference genome
GATK
UnifiedGenotyper
updated 2 days ago by
Zhenyu Zhang
★ 1.2k • written 2 days ago by
shpak.max
▴ 50
2
votes
4
replies
269
views
Can 5' and 3' scRNAseq be processed with the same pipeline?
singlecell
seurat
10XGenomics
scRNAseq
updated 2 days ago by
yura.grabovska
▴ 90 • written 2 days ago by
ev97
▴ 20
1
vote
14
replies
618
views
Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NULL > pointer.
blast
ncbi
18 hours ago by
hophuquy0944
• 0
0
votes
4
replies
239
views
Sequencing Depth (Read Depth) Calculations
depth
1 day ago by
LucisTheFather
• 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
110
views
Is it okay to assemble my 12 metatranscriptome samples with Trinity separately?
trinity
metatranscriptome
2 days ago by
jway
• 0
2
votes
2
replies
184
views
Cannot install bwa-mem2 via conda
conda
mamba
python
updated 1 day ago by
Ram
43k • written 2 days ago by
jsmith120f
• 0
2
votes
2
replies
196
views
genome finishing
finishing
genome
updated 2 days ago by
nd48
▴ 20 • written 2 days ago by
trezini
• 0
1
vote
5
replies
215
views
Circos Plot to Visualize Chromatin Accessibility Changes from ATAC-seq Data
circos
atacseq
updated 2 days ago by
Pierre Lindenbaum
161k • written 2 days ago by
biology_inform
▴ 50
1
vote
4
replies
285
views
Add stats to boxplot in R
stats
R
2 days ago by
Ghada
• 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
149
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
244
views
calculating genomic coverage/ base overlap in R
genomics
updated 1 day ago by
Ram
43k • written 2 days ago by
Xbox_27
• 0
1
vote
5
replies
260
views
Annotating file using bcftools
annotation
plink
bcftools
1 day ago by
kl
▴ 10
0
votes
9
replies
347
views
Duplicated reads (IDs) from nanopore sequencing
bam
nanopore
sequencing
1 day ago by
njornet
▴ 20
0
votes
3
replies
162
views
Problem with Calling Variants from RNA-Seq data
vcf
gatk
benchmark
giab
rna-seq
2 days ago by
Esraa
• 0
3
votes
3
replies
224
views
Getting differential ChIP-seq peaks between conditions after calling consensus peaks
MAnorm
ChIP-seq
consensus
peaks
updated 1 day ago by
ATpoint
82k • written 2 days ago by
Alexandra
• 0
1
vote
1
reply
221
views
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
limma
updated 2 days ago by
dariober
14k • written 3 days ago by
Holly
▴ 10
1
vote
4
replies
282
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
2 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
2 days ago by
Transmitting Science communication
▴ 70
0
votes
5
replies
281
views
bbmerge (bbmap) ~ error with insert size file output
bbtools
bbmerge
bbmap
updated 1 day ago by
GenoMax
142k • written 2 days ago by
chrisk
• 0
0
votes
1
reply
164
views
perseus software (version 1.5.5)
preseus
mass
spectrometry
data
updated 1 day ago by
DGTool
▴ 20 • written 2 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 2 days ago by
GenoMax
142k • written 2 days ago by
Dude
• 0
0
votes
0
replies
96
views
NEURON, Brian2, NEST, or PyNN
NEST
NEURON
PyNN
Brian2
2 days ago by
brunofelicianodeomena
• 0
1
vote
2
replies
207
views
Alphafold 3 pLDDT coloring scheme in chimerax?
ChimeraX
Alphaphold
Alphaphold3
updated 2 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
2 days ago by
sansan_96
▴ 90
1
vote
2
replies
217
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
203
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
213
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
278
views
Using ggplotly in R
ggplot
ggplotly
updated 2 days ago by
jared.andrews07
★ 16k • written 3 days ago by
jen
▴ 10
1
vote
2
replies
225
views
Why does assigning genes with biomart give me different values than using a transcripts_to_genes.txt file?
biomart
RNAseq
kallisto
1 day ago by
bioinfo
▴ 150
0
votes
3
replies
260
views
RNAseq RNA content
mRNA
Linux
rRNA
RNA-seq
RNA
updated 3 days ago by
noodle
▴ 580 • written 3 days ago by
doramora
▴ 10
0
votes
1
reply
145
views
Post-imputation QC for input into GWAS analyses
gwas
prs
updated 3 days ago by
LauferVA
4.2k • written 3 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
2 days ago by
melissa.joubert
• 0
4
votes
1
reply
202
views
Extracting only 4-fold degenerate sites from gene sequences/alignments?
alignments
3 days ago by
J.
▴ 40
0
votes
0
replies
110
views
Is there a real ground truth for CNV data?
CNV
3 days ago by
jennyp0706
• 0
0
votes
3
replies
211
views
Biomart issue, why so few 3'utrs?
utr
biomart
updated 3 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 3 days ago by
kilcdincer
▴ 10
4
votes
4
replies
3.0k
views
CNVkit for somatic copy number detection
cnv
cnvkit
exome
WES
updated 3 days ago by
Anitha
• 0 • written 5.1 years ago by
stephaniem
• 0
1
vote
7
replies
389
views
Overlapping Ranges within Granges object
Genomicranges
IRanges
GRanges
2 days ago by
ntsopoul
▴ 60
0
votes
3
replies
203
views
How to access GWAVA software of data
GWAVA
updated 3 days ago by
GenoMax
142k • written 3 days ago by
nonaddldy
▴ 10
0
votes
2
replies
221
views
Inquiry about deseq2 transformation
RNA-seq
deseq2
2 days ago by
Chen
• 0
1
vote
1
reply
172
views
The total expressed genes in RNA-Seq data
RNA-SEQ
updated 3 days ago by
ATpoint
82k • written 3 days ago by
Pegasus
▴ 100
0
votes
1
reply
131
views
What is the bin size for Bamcompare?
chip-seq
deeptools
bamcompare
updated 3 days ago by
Ram
43k • written 3 days ago by
Emily
▴ 20
1
vote
3
replies
271
views
Is there any way to modify this pie chart ?
pie
ggplot
R
chart
updated 1 day ago by
GenoMax
142k • written 4 days ago by
ohtang7
▴ 40
0
votes
0
replies
94
views
In what situations is 'outer' typically used when using anndata.concat()?
concat
anndata
scanpy
3 days ago by
Spring
• 0
0
votes
2
replies
178
views
Is it necessary to do genotype quality filteration after snp calling with GATK
snp
filteration
genotype
quality
GATK
3 days ago by
IdaHao0921
• 0
758 results • Page
2 of 16
Recent Votes
A: Peaks And Nearby Genes
Answer: How to download dbSNP153 vcf files in hg19/GRCH37 version
Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
Answer: TFs and Gene databases
A: Is there a software that can compare phylogenetic trees to each othe (face to fa
Comment: Differentially Expressed Genes between two conditions (scRNA, single GEO dataset
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Recent Replies
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…
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation
by
hannes.bongartz
• 0
It doesn't work. The annotation labels are still in a default fontsize. I cant find a way to set the fontsize.
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation
by
Ram
43k
Yes. The solution to most things with ComplexHeatmap is to play around with parameters.
Comment: Reconstruction of locus, order contigs
by
BATMAN
• 0
I do not want to re-annotate the genome. I ask if there is a way to extract the region aligned with the mauve, in .gbk format.
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation
by
hannes.bongartz
• 0
Thank you. What exactly do you mean? Changing `ha = rowAnnotation(text = anno_mark(at = mark_at, labels = gene_names_interesting_in_cluster…
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