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116,974 results • Page
1 of 2340
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1
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58
views
Would you bother re-mapping RNA-seq data from an old GRCh38 build to a newer version?
RNA-seq
build
genome
updated 33 minutes ago by
DGTool
▴ 10 • written 3 hours ago by
Ali
• 0
0
votes
2
replies
109
views
How to extract cells of different species after mapping with combined genome?
snrnaseq
scrnaseq
updated 1 hour ago by
Tony
• 0 • written 13 hours ago by
vk
▴ 10
0
votes
0
replies
23
views
Can I perform a correlation test with 3 biological replicates per condition?
deseq2
RNA-Seq
correlation
gene
replicate
1 hour ago by
manuelmourato25
• 0
1
vote
1
reply
158
views
finding evidence(s) of a peptide translated from an "Upstream Open Reading Frame (uORF)"
UTR
masspec
uORF
peptide
10 minutes ago by
Pierre Lindenbaum
161k
0
votes
1
reply
34
views
Details on salmon index
Salmon
updated 2 hours ago by
ATpoint
82k • written 2 hours ago by
Lorenzo
• 0
1
vote
7
replies
315
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
6 minutes ago by
egascon
• 0
0
votes
0
replies
27
views
API kegg - IndexError: list index out of range
kegg
API
Error
2 hours ago by
mirwa.zidi93
• 0
0
votes
0
replies
28
views
Blog:
The Current State and Future Prospects of Long-Read Sequencing
LRS
3 hours ago by
Novogene
▴ 420
0
votes
0
replies
34
views
qPCR gene expression data analysis
qPCR
geneexpression
anova
4 hours ago by
ebertomeup
• 0
797
votes
167
replies
143k
views
109 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 3 months ago by
Biostar
2.8k • written 7.4 years ago by
Istvan Albert
100k
0
votes
1
reply
64
views
Sam file Header problem
Sam
Header
problem
file
updated 4 hours ago by
Pierre Lindenbaum
161k • written 5 hours ago by
saifulislam99121
• 0
0
votes
4
replies
158
views
Tool:
Converting Degree Minutes (DM) to Decimal Degrees (DD) using python script
Minutes
Decimal
Degrees
python
Degree
offtopic
6 hours ago by
kuttibiotech2009
▴ 30
0
votes
1
reply
498
views
scRNAseq quality control weird double curve in nFeature vs nCount plot
scRNA-seq
QC
single
cell
BDRhapsody
analysis
updated 7 hours ago by
valdirbarth
▴ 20 • written 12 months ago by
Salomé
• 0
0
votes
0
replies
45
views
select set of intervals that cover a genomic region
GRanges
bed
7 hours ago by
ntsopoul
▴ 60
1
vote
0
replies
53
views
Tool:
Collect dispersed executable files and run them by using bingo.
bingo
7 hours ago by
dwpeng
▴ 10
0
votes
0
replies
43
views
BiomartException: Query ERROR for existing dataset in BioMart
biomart
ensembl
wheat
python
pybiomart
9 hours ago by
Luqman
• 0
1
vote
3
replies
127
views
ggrepel function: geom_text_repel()
ggrepel
ggplo2
R
3 hours ago by
sooni
▴ 20
0
votes
2
replies
111
views
how to treat the replicates while performing WGCNA
clustering
WGCNA
replicates
4 hours ago by
mavy
▴ 10
1
vote
1
reply
170
views
Calculate allelic frequency from VEP output vcf file
VEP
variant
14 hours ago by
ramiro.barrantes
• 0
1
vote
2
replies
149
views
In one PCA plot, can I calculate the percentage of different factors that contribute to the PCA?
PCA
R
VARIANCE
51 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 14 hours ago by
Ram
43k • written 3.9 years ago by
millere
• 0
0
votes
1
reply
89
views
What's next after GATK variant calling pipeline?
GATK
pipeline
figures
DNA-seq
updated 2 hours ago by
Michael
54k • written 15 hours ago by
mgranada3
▴ 30
0
votes
0
replies
65
views
Add line under stat test
stats
R
15 hours ago by
Ghada
• 0
1
vote
5
replies
754
views
Converting IGV to Figure using Illustrator (or other tools)
Illustrator
IGV
written 6 months ago by
Daniel
▴ 30
0
votes
0
replies
65
views
DOCK6 installation on MacOS M1
installation
troubleshooting
DOCK6
updated 17 hours ago by
GenoMax
142k • written 18 hours ago by
Rodolfo Adrián
• 0
1
vote
3
replies
152
views
Genotyping sites with N in reference genome
GATK
UnifiedGenotyper
updated 17 hours ago by
Zhenyu Zhang
★ 1.2k • written 18 hours ago by
shpak.max
▴ 50
0
votes
1
reply
112
views
Can 5' and 3' scRNAseq be processed with the same pipeline?
singlecell
seurat
10XGenomics
scRNAseq
updated 18 hours ago by
yura.grabovska
▴ 70 • written 19 hours ago by
ev97
▴ 20
0
votes
6
replies
235
views
Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NULL > pointer.
blast
meta
how-to
ncbi
forum
3 hours ago by
hophuquy0944
• 0
0
votes
4
replies
187
views
Sequencing Depth (Read Depth) Calculations
depth
9 hours ago by
LucisTheFather
• 0
0
votes
1
reply
99
views
Wrong ZYGOSITY by ensembl vep on DeepVariant vcf file
annotation
vcf
vep
zygosity
deepvariant
19 hours ago by
asalimih
▴ 60
0
votes
0
replies
73
views
Is it okay to assemble my 12 metatranscriptome samples with Trinity separately?
trinity
metatranscriptome
19 hours ago by
jway
• 0
2
votes
2
replies
137
views
Cannot install bwa-mem2 via conda
conda
mamba
python
code
updated 19 hours ago by
Istvan Albert
100k • written 20 hours ago by
jsmith120f
• 0
2
votes
2
replies
161
views
genome finishing
finishing
genome
updated 20 hours ago by
nd48
▴ 20 • written 1 day ago by
trezini
• 0
1
vote
5
replies
178
views
Circos Plot to Visualize Chromatin Accessibility Changes from ATAC-seq Data
circos
atacseq
updated 20 hours ago by
Pierre Lindenbaum
161k • written 21 hours ago by
biology_inform
▴ 50
1
vote
4
replies
247
views
Add stats to boxplot in R
stats
R
17 hours ago by
Ghada
• 0
0
votes
1
reply
90
views
Seurat v5 and how to correctly integrate across multiple experiments
Seurat
scRNA
R
updated 11 minutes ago by
Papyrus
★ 2.9k • written 21 hours ago by
yura.grabovska
▴ 70
0
votes
0
replies
79
views
Difference in number of reads when using duplex and simplex base calling with Dorado
base
calling
nanopore
simplex
dorado
duplex
21 hours ago by
Lélé
▴ 10
0
votes
4
replies
192
views
calculating genomic coverage/ base overlap in R
bioinoformatics
genomics
1 hour ago by
Sayantani
• 0
1
vote
4
replies
174
views
Annotating file using bcftools
annotation
plink
bcftools
updated 2 hours ago by
Pierre Lindenbaum
161k • written 1 day ago by
kl
▴ 10
0
votes
9
replies
307
views
Duplicated reads (IDs) from nanopore sequencing
bam
nanopore
sequencing
5 hours ago by
njornet
▴ 20
0
votes
3
replies
133
views
Problem with Calling Variants from RNA-Seq data
vcf
gatk
benchmark
giab
rna-seq
1 day ago by
Esraa
• 0
3
votes
3
replies
170
views
Getting differential ChIP-seq peaks between conditions after calling consensus peaks
MAnorm
ChIP-seq
consensus
peaks
updated 2 hours ago by
ATpoint
82k • written 1 day ago by
Alexandra
• 0
1
vote
1
reply
200
views
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
limma
updated 1 day ago by
dariober
14k • written 2 days ago by
Holly
▴ 10
1
vote
4
replies
247
views
Filtering VCF files based on VAF giving incorrect results
bcftools
GATK
Bioinformatics
picard
VCF
14 hours ago by
Arton
▴ 10
0
votes
0
replies
86
views
ReactomeGSA
ReactomeGSA
1 day ago by
Shaimaa Gamal
▴ 10
0
votes
0
replies
79
views
News:
New course: Manipulation of NGS Data for Genomic and Population Genetics Analyses
KeepLearning
TScourses
1 day ago by
Transmitting Science communication
▴ 70
0
votes
5
replies
262
views
bbmerge (bbmap) ~ error with insert size file output
bbtools
bbmerge
bbmap
updated 10 hours ago by
GenoMax
142k • written 1 day ago by
chrisk
• 0
0
votes
2
replies
133
views
perseus software (version 1.5.5)
preseus
mass
spectrometry
data
updated 21 minutes ago by
DGTool
▴ 10 • written 1 day ago by
iqra
• 0
0
votes
0
replies
93
views
Why the shape of RCS is contradictory to the p value for nonlinearity.
RCS
ggplot2
ggplot
R
updated 1 day ago by
GenoMax
142k • written 1 day ago by
Dude
• 0
0
votes
0
replies
88
views
NEURON, Brian2, NEST, or PyNN
NEST
NEURON
PyNN
Brian2
1 day ago by
brunofelicianodeomena
• 0
116,974 results • Page
1 of 2340
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A: How to process (seems) Agilent microarrry data?
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
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Recent Replies
Comment: Seurat v5 and how to correctly integrate across multiple experiments
by
Papyrus
★ 2.9k
In my experience integration methods are also often used for different samples/batches across the same technology. The crucial thing is to …
Comment: DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts i
by
egascon
• 0
Thank you very much! I have repeated the code adding arrayWeights() and it's works! In this case, I have a desing without intercept and c…
Comment: Is there any way to modify this pie chart ?
by
ohtang7
▴ 40
Thank you, I've tried but I see only some appear in the chart in wrong segments. Could you help me to solve this how ? ![enter image desc…
Comment: perseus software (version 1.5.5)
by
DGTool
• 0
If the tool mentioned relates to the Perseus application from the Cox lab ([here][1]), it should be free to download after accepting the li…
Answer: Would you bother re-mapping RNA-seq data from an old GRCh38 build to a newer ver
by
DGTool
• 0
At least so far to my knowledge, I don't think it would be worth re-mapping to GRCh38.p14, if it is too much trouble or with what you're lo…
Answer: How to extract cells of different species after mapping with combined genome?
by
Tony
• 0
From the marker genes of each cluster, we can determine whether the cluster belongs to human or mouse. Human genes are all capitalized, whi…
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…
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