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191 results • Page
4 of 4
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0
votes
1
reply
189
views
Microbial Signal Transduction Database
MiST
updated 5 days ago by
zx8754
11k • written 5 days ago by
Shravani
• 0
1
vote
1
reply
188
views
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
limma
updated 18 hours ago by
dariober
14k • written 1 day ago by
Holly
▴ 10
0
votes
1
reply
213
views
When should I use R-MarkDown over R-Script ?
r
rscript
rmarkdown
updated 5 days ago by
ATpoint
82k • written 5 days ago by
Amr
▴ 160
0
votes
0
replies
85
views
Empty kernel in SEACells model
single-cell
scanpy
seacells
python
anndata
2 days ago by
JACKY
▴ 140
0
votes
0
replies
180
views
How to calculate correlation coefficient for chipseq?
chipseq
bigwigsummary
deeptools
correlation
1 day ago by
Emily
▴ 20
0
votes
0
replies
97
views
Reference panel of normals for ensembl named refgenome
Mutect2
2 days ago by
gernophil
▴ 80
0
votes
0
replies
90
views
In what situations is 'outer' typically used when using anndata.concat()?
concat
anndata
scanpy
1 day ago by
Spring
• 0
0
votes
0
replies
107
views
how to downlad slices of CRAM fro ICGC ARGO
icgc
samtools
cram
6 days ago by
Javier
• 0
1
vote
0
replies
93
views
Producing sequence for splicing isoforms
isoform
rMATs
splicing
alternative
SplAdder
2 days ago by
tomas4482
▴ 400
0
votes
0
replies
104
views
lncRNA
tcga
lncrna
2 days ago by
jain72744
▴ 10
0
votes
0
replies
103
views
Is there a real ground truth for CNV data?
CNV
1 day ago by
jennyp0706
• 0
0
votes
0
replies
106
views
How can I create a eigencorplot of pca created from deseq2 object with PCAtools
eigencorplot
PCAtools
deseq2
pca
3 days ago by
BioinfGuru
★ 1.7k
1
vote
0
replies
139
views
What is Deepvariant default filtering values ?
vcf
calling
filter
variant
deepvariant
6 days ago by
Shae
▴ 10
0
votes
0
replies
124
views
News:
Online course: An Introduction to Nanopore Direct RNA Sequencing
Nanopore
RNAseq
3 days ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
162
views
Marker Features variance by cluster, sample, and treatment group
Seurat
scATAC-seq
ArchR
updated 5 days ago by
Ram
43k • written 5 days ago by
naomiboldon
• 0
0
votes
0
replies
78
views
NEURON, Brian2, NEST, or PyNN
NEST
NEURON
PyNN
Brian2
1 day ago by
brunofelicianodeomena
• 0
0
votes
0
replies
83
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
33
views
how to treat the replicates while performing WGCNA
clustering
WGCNA
replicates
4 hours ago by
mavy
▴ 10
0
votes
0
replies
168
views
How do I calculate SE or P value if I only have BETA
prscsx
beta
se
pvalue
updated 5 days ago by
zx8754
11k • written 6 days ago by
curious_butterfly
• 0
0
votes
0
replies
65
views
News:
New course: Manipulation of NGS Data for Genomic and Population Genetics Analyses
KeepLearning
TScourses
19 hours ago by
Transmitting Science communication
▴ 70
0
votes
0
replies
70
views
ReactomeGSA
ReactomeGSA
18 hours ago by
Shaimaa Gamal
▴ 10
0
votes
0
replies
154
views
Trouble converting tfam and tped to map and ped files
plink
ped
tfam
tped
map
5 days ago by
Samantha
• 0
0
votes
0
replies
63
views
Difference in number of reads when using duplex and simplex base calling with Dorado
base
calling
nanopore
simplex
dorado
duplex
13 hours ago by
Lélé
▴ 10
0
votes
0
replies
71
views
Seurat v5 and how to correctly integrate across multiple experiments
Seurat
scRNA
R
updated 12 hours ago by
ATpoint
82k • written 13 hours ago by
yura.grabovska
▴ 70
0
votes
0
replies
142
views
Allele specific expression of imprinted gens from 10x scRNA-seq data
scrna-seq
imprinted
10x
genes
5 days ago by
singcell
• 0
0
votes
0
replies
153
views
Krona Pie-chart taxanomy IDs were not found warning. Taxonomy Classification Metagenomics
Classification
Metagenomics
Krona
Kraken2
6 days ago by
Aytaç
• 0
0
votes
0
replies
158
views
supervised admixture
supervised
admixture
6 days ago by
RT
▴ 10
2
votes
0
replies
153
views
News:
course on Landscape Genomics at the EPFL in Lausanne (June 17-21)
LandscapeGenomics
SNPs
LocalAdaptation
GIS
6 days ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
60
views
Is it okay to assemble my 12 metatranscriptome samples with Trinity separately?
trinity
metatranscriptome
11 hours ago by
jway
• 0
0
votes
0
replies
180
views
Why does my Hi-C contact map show large regions making little to no contact?
BWA-MEM2
Hi-C
PretextMap
6 days ago by
Winter
• 0
0
votes
0
replies
187
views
What is workflow for de-novo assembling of nuclear and mito genomes of non-model organisms
de-novo
WGS
DNA-seq
assembling
6 days ago by
Matvii Mykhailichenko
• 0
1
vote
0
replies
176
views
phasing tumor long-reads
nanopore
ONT
haplotag
phasing
tumor
6 days ago by
eebloom
▴ 80
0
votes
0
replies
50
views
DOCK6 installation on MacOS M1
installation
troubleshooting
DOCK6
updated 8 hours ago by
GenoMax
142k • written 9 hours ago by
Rodolfo Adrián
• 0
0
votes
0
replies
47
views
Add line under stat test
stats
R
7 hours ago by
Ghada
• 0
0
votes
0
replies
49
views
What's next after GATK variant calling pipeline?
GATK
pipeline
figures
DNA-seq
7 hours ago by
mgranada3
▴ 30
0
votes
0
replies
13
views
ggrepel function: geom_text_repel()
ggrepel
ggplo2
R
1 hour ago by
sooni
▴ 20
0
votes
0
replies
9
views
BiomartException: Query ERROR for existing dataset in BioMart
biomart
ensembl
wheat
python
pybiomart
50 minutes ago by
Luqman
• 0
0
votes
0
replies
101
views
reference-free assembly error assessment tools
assembly
2 days ago by
lagartija
▴ 160
2
votes
0
replies
136
views
Herald:
The Biostar Herald for Monday, May 13, 2024
herald
2 days ago by
Biostar
2.8k
0
votes
0
replies
117
views
Comparing peptide sequences with MS/MS peptide data using MaxQuant
Transcriptomics
Mass-spectrometry
Proteins
updated 2 days ago by
Ram
43k • written 16 days ago by
atharvakarkare14
▴ 30
0
votes
0
replies
100
views
dbNSFP sift scores integration
SIFT
VEP
dbNSFP
2 days ago by
atariw
▴ 10
191 results • Page
4 of 4
Recent Votes
A: ensembl gene id
A: How to deal with the case that one gene symbol matches multiple ensembl ids?
Answer: DESeq2 error
Answer: Using ggplotly in R
Comment: How to calculate coverage of Nanopore long read data?
Answer: In one PCA plot, can I calculate the percentage of different factors that contri
Answer: Calculate allelic frequency from VEP output vcf file
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ramiro.barrantes
• 0
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AshleeThomson
▴ 80
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Recent Replies
Comment: Sequencing Depth (Read Depth) Calculations
by
LucisTheFather
• 0
Understood! Gonna try those two!
Comment: Sequencing Depth (Read Depth) Calculations
by
LucisTheFather
• 0
Thank u very much!
Comment: How to extract cells of different species after mapping with combined genome?
by
GenoMax
142k
You have used the tag `snRNAseq`. I am not familiar with singleron tech but if you have sequence data you may be able to use `xenome` or `b…
Comment: bbmerge (bbmap) ~ error with insert size file output
by
GenoMax
142k
It may be best to go back to the original data and then do `bbmerge.sh` on it to get original insert size estimates (before any operations …
Comment: bbmerge (bbmap) ~ error with insert size file output
by
chrisk
• 0
Hi Brian, Thank you and apologies for the extra future revision works. Out of curiosity we disabled neural networks 'nn=f' and the file o…
Comment: bbmerge (bbmap) ~ error with insert size file output
by
chrisk
• 0
Hi Genomax, This is the thread: https://www.biostars.org/p/9582467/ Cheers, Chris
Comment: Inquiry about deseq2 transformation
by
Chen
• 0
that's helpful, thanks :)
Comment: bbmerge (bbmap) ~ error with insert size file output
by
Brian Bushnell
20k
Ah, this is a little embarrassing; those are the vectors for the neural network. I overloaded a field that was being used for the insert s…
Comment: Annotating file using bcftools
by
kl
▴ 10
Thanks - I corrected it. It doesn't seem to annotate. I converted to binary after which is what is shown below. It is not the output I want…
Comment: Filtering VCF files based on VAF giving incorrect results
by
Arton
▴ 10
These are valid questions. Does your code address the concerns you've raised? From what I understand, FilterVcf is primarily designed for h…
Answer: Calculate allelic frequency from VEP output vcf file
by
ramiro.barrantes
• 0
Found the answer here!! https://github.com/Illumina/strelka/blob/master/docs/userGuide/README.md#somatic Although this leads to a str…
Comment: Using VEP annotation output as the input for a second VEP annotation
by
Ram
43k
That's not a valid reason to delete the post. If that information was sensitive, posting it here was a mistake in the first place. I don't …
Answer: In one PCA plot, can I calculate the percentage of different factors that contri
by
marco.barr
▴ 120
Hi, regardless of how you generated the data whether with DESeq2 or other pipeline, your differential expression matrix can be used as inpu…
Comment: Filtering VCF files based on VAF giving incorrect results
by
Pierre Lindenbaum
161k
> Do you think my commands were correct? I'm not familiar enough with this bcftools syntax. but what if there is no AD, what if both…
Answer: How can you *consistently* download BioProject IDs from NCBI's BioSample databas
by
Ash
▴ 10
I know this was asked several years ago, but finding this post helped me solve my own problem and in the process I solved this one too. …
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