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49 results • Page
1 of 1
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0
votes
2
replies
94
views
How to extract cells of different species after mapping with combined genome?
snrnaseq
scrnaseq
updated just now by
Tony
• 0 • written 12 hours ago by
vk
▴ 10
0
votes
0
replies
14
views
Can I perform a correlation test with 3 biological replicates per condition?
deseq2
RNA-Seq
correlation
gene
replicate
23 minutes ago by
manuelmourato25
• 0
1
vote
1
reply
136
views
finding evidence(s) of a peptide translated from an "Upstream Open Reading Frame (uORF)"
UTR
peptide
masspec
uORF
updated 11 minutes ago by
Michael
54k • written 34 minutes ago by
Pierre Lindenbaum
161k
0
votes
1
reply
21
views
Details on salmon index
Salmon
updated 50 minutes ago by
ATpoint
82k • written 56 minutes ago by
Lorenzo
• 0
1
vote
6
replies
286
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
updated 23 minutes ago by
ATpoint
82k • written 23 hours ago by
egascon
• 0
0
votes
0
replies
17
views
API kegg - IndexError: list index out of range
kegg
API
Error
1 hour ago by
mirwa.zidi93
• 0
0
votes
0
replies
25
views
Blog:
The Current State and Future Prospects of Long-Read Sequencing
LRS
2 hours ago by
Novogene
▴ 420
0
votes
0
replies
32
views
Would you bother re-mapping RNA-seq data from an old GRCh38 build to a newer version?
RNA-seq
build
genome
2 hours ago by
Ali
• 0
0
votes
0
replies
30
views
qPCR gene expression data analysis
qPCR
geneexpression
anova
3 hours ago by
ebertomeup
• 0
0
votes
1
reply
54
views
Sam file Header problem
Sam
Header
problem
file
updated 3 hours ago by
Pierre Lindenbaum
161k • written 4 hours ago by
saifulislam99121
• 0
0
votes
4
replies
153
views
Tool:
Converting Degree Minutes (DM) to Decimal Degrees (DD) using python script
Minutes
Decimal
Degrees
python
Degree
offtopic
4 hours ago by
kuttibiotech2009
▴ 30
0
votes
1
reply
495
views
scRNAseq quality control weird double curve in nFeature vs nCount plot
scRNA-seq
QC
single
cell
BDRhapsody
analysis
updated 5 hours ago by
valdirbarth
▴ 20 • written 12 months ago by
Salomé
• 0
0
votes
0
replies
41
views
select set of intervals that cover a genomic region
GRanges
bed
6 hours ago by
ntsopoul
▴ 60
1
vote
0
replies
51
views
Tool:
Collect dispersed executable files and run them by using bingo.
bingo
6 hours ago by
dwpeng
▴ 10
0
votes
0
replies
42
views
BiomartException: Query ERROR for existing dataset in BioMart
biomart
ensembl
wheat
python
pybiomart
8 hours ago by
Luqman
• 0
1
vote
3
replies
110
views
ggrepel function: geom_text_repel()
ggrepel
ggplo2
R
1 hour ago by
sooni
▴ 20
0
votes
2
replies
105
views
how to treat the replicates while performing WGCNA
clustering
WGCNA
replicates
3 hours ago by
mavy
▴ 10
1
vote
1
reply
167
views
Calculate allelic frequency from VEP output vcf file
VEP
variant
13 hours ago by
ramiro.barrantes
• 0
1
vote
2
replies
138
views
In one PCA plot, can I calculate the percentage of different factors that contribute to the PCA?
PCA
R
VARIANCE
10 minutes ago by
diqixiaoyaoer
▴ 10
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 13 hours ago by
Ram
43k • written 3.9 years ago by
millere
• 0
0
votes
1
reply
82
views
What's next after GATK variant calling pipeline?
GATK
pipeline
figures
DNA-seq
updated 1 hour ago by
Michael
54k • written 14 hours ago by
mgranada3
▴ 30
0
votes
0
replies
64
views
Add line under stat test
stats
R
14 hours ago by
Ghada
• 0
1
vote
5
replies
752
views
Converting IGV to Figure using Illustrator (or other tools)
Illustrator
IGV
written 6 months ago by
Daniel
▴ 30
0
votes
0
replies
64
views
DOCK6 installation on MacOS M1
installation
troubleshooting
DOCK6
updated 16 hours ago by
GenoMax
142k • written 16 hours ago by
Rodolfo Adrián
• 0
1
vote
3
replies
151
views
Genotyping sites with N in reference genome
GATK
UnifiedGenotyper
updated 16 hours ago by
Zhenyu Zhang
★ 1.2k • written 17 hours ago by
shpak.max
▴ 50
0
votes
1
reply
110
views
Can 5' and 3' scRNAseq be processed with the same pipeline?
singlecell
seurat
10XGenomics
scRNAseq
updated 17 hours ago by
yura.grabovska
▴ 70 • written 17 hours ago by
ev97
▴ 20
0
votes
6
replies
214
views
Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NULL > pointer.
blast
meta
how-to
ncbi
forum
2 hours ago by
hophuquy0944
• 0
0
votes
4
replies
184
views
Sequencing Depth (Read Depth) Calculations
depth
7 hours ago by
LucisTheFather
• 0
0
votes
1
reply
98
views
Wrong ZYGOSITY by ensembl vep on DeepVariant vcf file
annotation
vcf
vep
zygosity
deepvariant
17 hours ago by
asalimih
▴ 60
0
votes
0
replies
72
views
Is it okay to assemble my 12 metatranscriptome samples with Trinity separately?
trinity
metatranscriptome
18 hours ago by
jway
• 0
2
votes
2
replies
136
views
Cannot install bwa-mem2 via conda
conda
mamba
python
code
updated 18 hours ago by
Istvan Albert
100k • written 19 hours ago by
jsmith120f
• 0
2
votes
2
replies
159
views
genome finishing
finishing
genome
updated 19 hours ago by
nd48
▴ 20 • written 23 hours ago by
trezini
• 0
1
vote
5
replies
177
views
Circos Plot to Visualize Chromatin Accessibility Changes from ATAC-seq Data
circos
atacseq
updated 19 hours ago by
Pierre Lindenbaum
161k • written 20 hours ago by
biology_inform
▴ 50
1
vote
4
replies
244
views
Add stats to boxplot in R
stats
R
16 hours ago by
Ghada
• 0
0
votes
0
replies
85
views
Seurat v5 and how to correctly integrate across multiple experiments
Seurat
scRNA
R
updated 19 hours ago by
ATpoint
82k • written 20 hours ago by
yura.grabovska
▴ 70
0
votes
0
replies
77
views
Difference in number of reads when using duplex and simplex base calling with Dorado
base
calling
nanopore
simplex
dorado
duplex
20 hours ago by
Lélé
▴ 10
0
votes
4
replies
187
views
calculating genomic coverage/ base overlap in R
bioinoformatics
genomics
26 minutes ago by
Sayantani
• 0
1
vote
4
replies
162
views
Annotating file using bcftools
annotation
plink
bcftools
updated 1 hour ago by
Pierre Lindenbaum
161k • written 23 hours ago by
kl
▴ 10
0
votes
9
replies
303
views
Duplicated reads (IDs) from nanopore sequencing
bam
nanopore
sequencing
3 hours ago by
njornet
▴ 20
0
votes
3
replies
132
views
Problem with Calling Variants from RNA-Seq data
vcf
gatk
benchmark
giab
rna-seq
23 hours ago by
Esraa
• 0
3
votes
3
replies
149
views
Getting differential ChIP-seq peaks between conditions after calling consensus peaks
MAnorm
ChIP-seq
consensus
peaks
updated 1 hour ago by
ATpoint
82k • written 1 day ago by
Alexandra
• 0
1
vote
4
replies
246
views
Filtering VCF files based on VAF giving incorrect results
bcftools
GATK
Bioinformatics
picard
VCF
12 hours ago by
Arton
▴ 10
0
votes
5
replies
260
views
bbmerge (bbmap) ~ error with insert size file output
bbtools
bbmerge
bbmap
updated 9 hours ago by
GenoMax
142k • written 1 day ago by
chrisk
• 0
0
votes
1
reply
125
views
perseus software (version 1.5.5)
preseus
mass
spectrometry
data
updated 20 hours ago by
Joe
21k • written 1 day ago by
iqra
• 0
1
vote
2
replies
204
views
Doubt about the process of annotation, detection, identification and classification of transposable elements
annotation
TransposableElements
13 hours ago by
MarcosCosta
• 0
1
vote
3
replies
265
views
Using ggplotly in R
ggplot
ggplotly
updated 18 hours ago by
jared.andrews07
★ 16k • written 1 day ago by
jen
▴ 10
0
votes
2
replies
210
views
Inquiry about deseq2 transformation
RNA-seq
deseq2
11 hours ago by
Chen
• 0
0
votes
9
replies
577
views
Applying the metacell2 algorithm using python
python
single-cell
scanpy
metacell2
updated 19 hours ago by
Wayne
★ 2.0k • written 9 days ago by
JACKY
▴ 140
0
votes
9
replies
589
views
Using VEP annotation output as the input for a second VEP annotation
Annotation
VEP
VCF
12 hours ago by
Arton
▴ 10
49 results • Page
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Recent Votes
Comment: DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts i
finding evidence(s) of a peptide translated from an "Upstream Open Reading Frame (uORF)"
A: How To Merge Two Fastq.Gz Files?
Answer: Annotating file using bcftools
Answer: Getting differential ChIP-seq peaks between conditions after calling consensus p
Answer: Getting differential ChIP-seq peaks between conditions after calling consensus p
Convert fastq.gz to fastq.bgz
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Comment: In one PCA plot, can I calculate the percentage of different factors that contri
by
diqixiaoyaoer
▴ 10
Thanks a lot. It is almost what I need but not all. From your script, I can get information that how much degree different samples contri…
Comment: finding evidence(s) of a peptide translated from an "Upstream Open Reading Frame
by
Michael
54k
sorry, this isn't a sequence search but search by id ...
Comment: calculating genomic coverage/ base overlap in R
by
Sayantani
• 0
![enter image description here][1]Hi, this is the list/ excel I am uploading ( coverage.xlsx ) ![enter image description here][1] [1…
Comment: DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts i
by
ATpoint
82k
There has been some spam bots in this thread which we cleaned up, you might still get notifications on it, just ignore.
Comment: Details on salmon index
by
ATpoint
82k
You're lucky that the senior developer @rob is often around, so you probably get your experts answer soon.
Answer: DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts i
by
ATpoint
82k
I think the issue is that there is some contamination of groups. If you plot a PCA or MDS you see that there is a clear separation between …
Comment: What's next after GATK variant calling pipeline?
by
Michael
54k
The link didn't work for me. After getting variants from HaplotypeCaller, there are a lot of different options for follow-up analyses, but …
Comment: Getting differential ChIP-seq peaks between conditions after calling consensus p
by
ATpoint
82k
That having said, linked paper and its authors developed the csaw package over at Bioconductor that uses a window approach to avoid peak ca…
Comment: Getting differential ChIP-seq peaks between conditions after calling consensus p
by
Ian
6.0k
Really interesting answer. I had missed that paper and will digest it asap. I usually use DiffBind, but recently have been looking into p…
Comment: Annotating file using bcftools
by
kl
▴ 10
It worked with this `bcftools index -t $DATADIR/cpro_imputed_hrcgrch37.R2_0.3.vcf.gz` bcftools annotate \ -a $RefGenomes/All_2018…
Comment: DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts i
by
egascon
• 0
This is true. However, there are a number of studies that have done bioinformatics analysis in whole blood to see if there is a possibility…
Comment: ggrepel function: geom_text_repel()
by
sooni
▴ 20
Thank you for help! I solved the probelm with the package.
Comment: DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts i
by
egascon
• 0
I have checked the quality of the arrays using PCA and Boxplot (images attached) and some of the samples may deviate a little but perhaps n…
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
hophuquy0944
• 0
the nt database was extracted, and this is latest version of nt database in ncbi and blastn with version 2.15. I used many query file.fast…
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
hophuquy0944
• 0
they don't have clear answer for this problem. I run all subset of this data to find out error subsets database but it seem not any error i…
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